rbbt-util 5.21.8 → 5.21.9

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: a22977fcc3e07a9eac6f544d77a61be31caddc9c
+  metadata.gz: b865dd691227ababbe46a03ea0ed6960754aea22
+  data.tar.gz: 7d68152324663bf6e220f3f66faa9e585815f30f
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+  data.tar.gz: f1cc66e3892f332b0dca011c06a3b952f0517f18aba6b3e3dda8550b4d3503d77702a90abad1aa65b06256ebea5e566f3f14fc46b2d1994814c7e9ac623970a0

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

@@ -659,4 +659,9 @@ module Misc
     end
   end
 
+  def self.sort_mutations(stream)
+    CMD.cmd('grep ":" | sort -u | sed "s/^M:/MT:/" | env LC_ALL=C sort -k1,1 -k2,2n -t:', :in => stream, :pipe => true, :no_fail => true)
+  end
+
+
 end

data/lib/rbbt/workflow/accessor.rb

@@ -374,7 +374,7 @@ class Step
   end
 
   def stalled?
-    ! (done? || error? || aborted?) && ! running?
+    started? && ! (done? || error? || aborted?) && ! running?
   end
 
   def error?

data/share/rbbt_commands/workflow/info

@@ -16,6 +16,7 @@ $ rbbt workflow info <job-result>
 -h--help Help
 -a--all Print all info entries
 -r--recursive Print recursive input values
+-o--original Print original object
 EOF
 
 SOPT.usage if options[:help]
@@ -59,6 +60,12 @@ end
 step = get_step file
 
 info = step.info
+
+if options[:original]
+  puts info.inspect
+  exit 0
+end
+
 dependencies = info[:dependencies]
 inputs = info[:inputs]
 status = info[:status]

data/share/rbbt_commands/workflow/prov

@@ -19,6 +19,7 @@ Examine the provenance of a job result
 $ rbbt workflow prov <job-result>
 
 -h--help Help
+-p--plot* draw the dependency plot into <file.png>
 EOF
 
 SOPT.usage if options[:help]
@@ -82,4 +83,78 @@ end
 step = get_step file
 $main_mtime = File.exist?(step.path) ? File.mtime(step.path) : nil
 
-puts report(step).strip
+def adjacency(step)
+
+  info = step.info || {}
+  path  = step.path
+  status = info[:status] || :missing
+  status = "remote" if Open.remote?(path)
+  if status == 'remote'
+    workflow, task, name = path.sub(/\{.*/,'').split("/")[-3..-1]
+  else
+    workflow, task, name = path.split("/")[-3..-1]
+  end
+  name = name.split(":").last
+  status = :unsync if status == :done and not File.exist? path
+  edge_info = {:status =>  status, :workflow => workflow, :task => task, :name => name, :label => task, :shape => shapes[workflow], :color => status == 'remote' ? 'blue' : 'green'}
+  id = Misc.digest(path)
+  edges = []
+  node_info = {}
+  node_info[id] = edge_info
+  if info[:dependencies]
+    info[:dependencies].each do |task,name,path|
+      dep = get_step path
+      _id, _edges, _node_info = adjacency(dep)
+      edges << [id, _id] 
+      edges.concat _edges
+      node_info.merge!(_node_info)
+    end 
+  end
+
+  [id, edges, node_info]
+end
+
+if options[:plot]
+  id, edges, node_info = adjacency(step)
+  node_info[id][:color] = 'red'
+  TmpFile.with_file do |edge_file|
+    Open.write(edge_file) do |f|
+      f.puts "from,to"
+      edges.each do |from,to|
+        f.puts [from,to]*","
+      end
+    end
+    TmpFile.with_file do |node_info_file|
+      Open.write(node_info_file) do |f|
+        fields = node_info.first.last.keys
+        f.puts "id," + fields * ","
+        node_info.each do |id,info|
+          f.puts ([id] + info.values_at(*fields)) * ","
+        end
+      end
+
+      require 'rbbt/util/R'
+
+      ppp Open.read edge_file
+      ppp Open.read node_info_file
+
+      R.run <<-EOF
+      nodes <- read.csv("#{node_info_file}", header=T, as.is=T)
+      links <- read.csv("#{edge_file}", header=T, as.is=T)
+
+      library(igraph)
+
+      net <- graph.data.frame(links, nodes, directed=T)
+      net <- simplify(net, remove.multiple = F, remove.loops = T)
+
+      png("#{options[:plot]}")
+      plot(net, edge.arrow.size=0.4, vertex.label=net$label, vertex.color=net$color)
+      dev.off()
+      EOF
+    end
+  end
+
+else
+  puts report(step).strip
+end
+

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.21.8
+  version: 5.21.9
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-08-28 00:00:00.000000000 Z
+date: 2016-09-06 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake