rbbt-util 5.28.10 → 5.28.11

checksums.yaml

@@ -1,7 +1,7 @@
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data/lib/rbbt/persist.rb

@@ -26,12 +26,17 @@ module Persist
   MAX_FILE_LENGTH = 150
 
   # Is 'file' newer than 'path'? return non-true if path is newer than file
-  def self.newer?(path, file)
+  def self.newer?(path, file, by_link = false)
     return true if not Open.exists?(file)
     path = path.find if Path === path
     file = file.find if Path === file
-    patht = Open.mtime(path)
-    filet = Open.mtime(file)
+    if by_link
+      patht = File.lstat(path).mtime
+      filet = File.lstat(file).mtime
+    else
+      patht = Open.mtime(path)
+      filet = Open.mtime(file)
+    end
     return true if patht.nil? || filet.nil?
     diff = patht - filet
     return diff if diff < 0

data/lib/rbbt/resource.rb

@@ -112,13 +112,19 @@ module Resource
               end
             when Net::HTTPRedirection, Net::HTTPFound
               location = response['location']
-              Log.debug("Feching directory from: #{location}. Into: #{final_path}")
-              FileUtils.mkdir_p final_path unless File.exist? final_path
-              TmpFile.with_file do |tmp_dir|
-                Misc.in_dir tmp_dir do
-                  CMD.cmd('tar xvfz -', :in => Open.open(location, :nocache => true))
+              if location.include? 'get_directory'
+                Log.debug("Feching directory from: #{location}. Into: #{final_path}")
+                FileUtils.mkdir_p final_path unless File.exist? final_path
+                TmpFile.with_file do |tmp_dir|
+                  Misc.in_dir tmp_dir do
+                    CMD.cmd('tar xvfz -', :in => Open.open(location, :nocache => true))
+                  end
+                  FileUtils.mv tmp_dir, final_path
+                end
+              else
+                Open.open(location, :nocache => true) do |s|
+                  Misc.sensiblewrite(final_path, s)
                 end
-                FileUtils.mv tmp_dir, final_path
               end
             when Net::HTTPInternalServerError
               @server_missing_resource_cache << url

data/lib/rbbt/util/R.rb

@@ -41,7 +41,7 @@ source('#{UTIL}');
 
     if monitor
       #io = CMD.cmd('R --no-save --quiet', options.merge(:in => cmd, :pipe => true, :log => true))
-      io = CMD.cmd('R --no-save --quiet', options.merge(:in => cmd, :pipe => true, :log => true))
+      io = CMD.cmd('R --no-save --quiet', options.merge(:in => cmd, :pipe => true, :log => true, :xvfb => true))
       while line = io.gets
         case monitor
         when Proc
@@ -52,7 +52,7 @@ source('#{UTIL}');
       end
       nil
     else
-      CMD.cmd('R --no-save --slave --quiet', options.merge(:in => cmd))
+      CMD.cmd('R --no-save --slave --quiet', options.merge(:in => cmd, :xvfb => true))
     end
   end
 

data/lib/rbbt/util/cmd.rb

@@ -100,6 +100,7 @@ module CMD
     no_fail    = options.delete(:no_fail)
     no_fail    = options.delete(:nofail) if no_fail.nil?
     no_wait    = options.delete(:no_wait)
+    xvfb       = options.delete(:xvfb)
 
     dont_close_in  = options.delete(:dont_close_in)
 
@@ -117,6 +118,14 @@ module CMD
 
     end
 
+    case xvfb
+    when TrueClass
+      cmd = "xvfb-run --server-args='-screen 0 1024x768x24' --auto-servernum #{cmd}"
+    when String
+      cmd = "xvfb-run --server-args='#{xvfb}' --auto-servernum --server-num=1 #{cmd}"
+    when String
+    end
+
     if stderr == true
       stderr = Log::HIGH
     end

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

@@ -287,15 +287,19 @@ module Misc
           when Symbol 
             obj.to_s
           when (defined?(Path) and Path)
-            if obj.exists?
-              if obj.directory?
-                files = obj.glob("**/*")
-                "directory: #{Misc.fingerprint(files)}"
+            if Step === obj.resource
+              "Step file: " + obj
+            else
+              if obj.exists?
+                if obj.directory?
+                  files = obj.glob("**/*")
+                  "directory: #{Misc.fingerprint(files)}"
+                else
+                  "file: " << Open.realpath(obj) << "--" << mtime_str(obj)
+                end
               else
-                "file: " << Open.realpath(obj) << "--" << mtime_str(obj)
+                obj + " (file missing)"
               end
-            else
-              obj + " (file missing)"
             end
           when String
             if Misc.is_filename?(obj) and ! %w(. ..).include?(obj)

data/lib/rbbt/workflow/accessor.rb

@@ -360,7 +360,7 @@ module Workflow
                      compute = options[:compute]
 
                      options = IndiferentHash.setup(options.dup)
-                     dep = dependency.call jobname, options.merge(_inputs), real_dependencies
+                     dep = dependency.call jobname, _inputs.merge(options), real_dependencies
 
                      dep = [dep] unless Array === dep
 

data/lib/rbbt/workflow/step.rb

@@ -156,7 +156,7 @@ class Step
 
   def dependencies=(dependencies)
     @dependencies = dependencies
-    set_info :dependencies, dependencies.collect{|dep| [dep.task_name, dep.name, dep.path]}
+    set_info :dependencies, dependencies.collect{|dep| [dep.task_name, dep.name, dep.path]} if dependencies
   end
 
   def recursive_inputs

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

@@ -188,7 +188,7 @@ class Step
                 info_lock.lock if check_lock and false
                 begin
                   Open.open(info_file, :mode => 'rb') do |file|
-                    INFO_SERIALIZER.load(file) #|| {}
+                    IndiferentHash.setup(INFO_SERIALIZER.load(file)) #|| {}
                   end
                 ensure
                   info_lock.unlock if check_lock and false
@@ -227,7 +227,7 @@ class Step
     Open.lock(info_file, :lock => info_lock) do
       i = info(false).dup
       i[key] = value 
-      @info_cache = i
+      @info_cache = IndiferentHash.setup(i)
       dump = INFO_SERIALIZER.dump(i)
       Misc.sensiblewrite(info_file, dump, :force => true, :lock => false)
       @info_cache_time = Time.now
@@ -242,7 +242,7 @@ class Step
     Open.lock(info_file, :lock => info_lock) do
       i = info(false)
       i.merge! hash
-      @info_cache = i
+      @info_cache = IndiferentHash.setup(i)
       dump = INFO_SERIALIZER.dump(i)
       Misc.sensiblewrite(info_file, dump, :force => true, :lock => false)
       @info_cache_time = Time.now
@@ -537,7 +537,7 @@ class Step
   end
 
   def file(name)
-    Path.setup(File.join(files_dir, name.to_s))
+    Path.setup(File.join(files_dir, name.to_s), workflow, self)
   end
 
   def save_file(name, content)

data/lib/rbbt/workflow/util/provenance.rb

@@ -66,7 +66,7 @@ class Step
     str << "\n"
   end
 
-  def self.prov_report(step, offset = 0, task = nil, seen = [])
+  def self.prov_report(step, offset = 0, task = nil, seen = [], expand_repeats = false)
     info = step.info  || {}
     info[:task_name] = task
     path  = step.path
@@ -82,9 +82,13 @@ class Step
       new = ! seen.include?(path)
       if new
         seen << path
-        str << prov_report(dep, offset + 1, task, seen)
+        str << prov_report(dep, offset + 1, task, seen, expand_repeats)
       else
-        str << Log.color(:green, Log.uncolor(prov_report(dep, offset+1, task)))
+        if expand_repeats
+          str << Log.color(:green, Log.uncolor(prov_report(dep, offset+1, task)))
+        else
+          str << Log.color(:green, " " * (offset + 1) + Log.uncolor(prov_report_msg(status, name, path, info)))
+        end
       end
     end if step.dependencies
     str

data/share/rbbt_commands/system/status

@@ -49,27 +49,27 @@ def pid_msg(pid)
 end
 
 
-def status_msg(status)
-  color = case status.to_sym
-          when :error, :aborted, :missing, :dead, :broken
-            :red
-          when :streaming, :started
-            :cyan
-          when :done
-            :green
-          when :noinfo
-            :blue
-          when :dependencies, :waiting, :setup
-            :yellow
-          else
-            if status.to_s.index ">"
-              :cyan
-            else
-              :cyan
-            end
-          end
-  Log.color(color, status.to_s)
-end
+#def status_msg(status)
+#  color = case status.to_sym
+#          when :error, :aborted, :missing, :dead, :broken
+#            :red
+#          when :streaming, :started
+#            :cyan
+#          when :done
+#            :green
+#          when :noinfo, :notfound
+#            :blue
+#          when :dependencies, :waiting, :setup
+#            :yellow
+#          else
+#            if status.to_s.index ">"
+#              :cyan
+#            else
+#              :cyan
+#            end
+#          end
+#  Log.color(color, status.to_s)
+#end
 
 def input_msg(file, inputs)
 
@@ -218,7 +218,7 @@ workflows.sort.each do |workflow,tasks|
             status << Log.color(:red, " (dead)") 
           end
         end
-        str << " #{ status_msg status }"
+        str << " #{ Step.prov_status_msg status }"
         str << " (dirty)" if status == 'done' && Workflow.load_step(file).dirty?
 
         if inputs and inputs.any? 

data/share/rbbt_commands/workflow/prov

@@ -24,6 +24,7 @@ $ rbbt workflow prov <job-result>
 -i--inputs* List of inputs to print
 -if--info_fields* List of info fields to print
 -t--touch Update modification times to be consistent
+-e--expand_repeats Show all the dependency tree even if reapeated dependencies have already been seen before
 EOF
 
 SOPT.usage if options[:help]
@@ -130,6 +131,6 @@ if options[:plot]
   end
 
 else
-  puts Step.prov_report(step).strip
+  puts Step.prov_report(step, 0, nil, [], options[:expand_repeats]).strip
 end
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.28.10
+  version: 5.28.11
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2020-11-17 00:00:00.000000000 Z
+date: 2020-11-25 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake