rbbt-util 5.21.123 → 5.21.125

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 7d9b73ef742e367384eeec735b980ad4ef809bf3
-  data.tar.gz: 3a2d1e5c49ccbb386c4bbe42b57cc031c6271010
+  metadata.gz: 3f4308847ea6b93d07967434826c0e6653085329
+  data.tar.gz: 7612101d90cc312ae800df4cc6959d5dbe7fd126
 SHA512:
-  metadata.gz: 0460b59b327c793efaddfe14f3109a4b34ff5346b48c0284ec9d55e5f66cdaf3e508472ac5e554ab13aff8af9716230c05f10dbac81b93a3aaaa977832ce08c7
-  data.tar.gz: 01606ac902c2c9da0ee2bc24c46ca83483ce1b67d55af4ab0bc84d111d551a4ff3d2daf3907970feb6510c5f3040061a5951ba842449f8f25c5f5c6b9e9d4a0f
+  metadata.gz: be5ce8fc22674fee613268e576f051f4fc30bd1de0943fd4ae655442e234936da7d5a7dd7691904c8ad36ccaf3b87edbd087262946f142869a2f8cc213bddabf
+  data.tar.gz: 7b21c5b128e898ee61f08a89ee9d45ad9eea8f0da549682adb70e27ac9c688e3e319f81bafeef206b53940240bf4e29d7788cd1bc5a4ea5c5de652a736301e9b

data/bin/rbbt

@@ -176,7 +176,7 @@ def print_error(error, backtrace = nil)
   if backtrace
     puts Log.color :red, "Backtrace: "
     puts
-    puts backtrace.reverse * "\n"
+    puts Log.color_stack(backtrace.reverse) * "\n"
     puts
   end
   puts Log.color :red, error

data/lib/rbbt/hpc.rb

@@ -0,0 +1,122 @@
+require 'rbbt-util'
+require 'rbbt/util/cmd'
+
+module Marenostrum
+  SERVER='mn1'
+  module SLURM
+    TEMPLATE=<<-EOF
+
+
+    EOF
+    def self.issue(cmd, name = nil, time = nil, options = {})
+      name = "rbbt-job-" << rand(10000).to_s if name.nil?
+      time = "00:00:10" if time.nil?
+      workdir = "rbbt-workdir/" << name
+
+      new_options = Misc.add_defaults options, "job-name" => name, "workdir" => workdir,
+        "output" => "log", 
+        "error" => "log.err", 
+        "ntasks" => "1", 
+        "time" => time.to_s,
+        "user" => ENV["USER"],
+        "key_file" => File.join(ENV['HOME'], '.ssh/id_rsa.pub')
+
+      options.merge!(new_options)
+      IndiferentHash.setup(options)
+
+      key_file, user = options.values_at :key_file, :user
+
+      template = <<-EOF
+#!/bin/bash
+#{options.collect do |name,value|
+      next if name == 'user'
+      next if name == 'key_file'
+name = "--" << name.to_s.sub(/^--/,'')
+[name, '"' << value << '"'] * "="
+  end.compact.collect{|str| "#SBATCH #{str}"} * "\n"
+}
+#{ cmd }
+      EOF
+
+      TmpFile.with_file do |slurm|
+        res = nil
+        begin
+          Open.write(slurm, template)
+          Log.medium("Issuing job:\n" + template)
+
+          cmd = "ssh -i #{key_file} #{ user }@#{ SERVER } mkdir -p '#{ workdir }'; scp -i #{key_file} #{ slurm } #{ user }@#{ SERVER }:'#{ workdir }/#{ name }.slurm'; ssh -i #{key_file} #{ user }@#{ SERVER } sbatch #{ workdir }/#{ name }.slurm"
+          Log.debug cmd
+          res = CMD.cmd(cmd).read
+        rescue
+          raise "Could not issue job"
+        end
+
+        res.scan(/\d+/).first
+      end
+    end
+
+    def self.query(id, options = {})
+      key_file, user = options.values_at :key_file, :user
+
+      res = nil
+      begin
+        cmd = "ssh -i #{key_file} #{ user }@#{ SERVER } squeue |grep '#{id}\\|JOBID'"
+        Log.debug cmd
+        res = CMD.cmd(cmd).read
+      rescue
+        raise "Could not query job: #{ id }" << $!.message
+      end
+
+      res
+    end
+
+    def self.done?(id, options = {})
+      ! query(id, options).include? id
+    end
+
+    def self.gather(id, file = nil, options = {})
+      key_file, user, workdir, output = options.values_at :key_file, :user, :workdir, :output
+
+      TmpFile.with_file do |result|
+
+        begin
+          cmd = "scp -i #{key_file} #{ user }@#{ SERVER }:'#{workdir}/#{output}' '#{ result }' " 
+          Log.debug cmd
+          CMD.cmd(cmd)
+          if file.nil?
+            Open.read(result)
+          else
+            Misc.sensiblewrite(result, file)
+          end
+        rescue
+          raise "Could not gather job: #{ id }: " << $!.message
+        end
+      end
+    end
+
+    def self.run(cmd, name = nil, time = nil, options = {})
+      sleep_time = Misc.process_options options, :sleep
+
+      id = issue(cmd, name, time, options)
+
+      if sleep_time.nil?
+        times = [1,2,3,5,10,30]
+      else
+        times = Array ===  sleep_time ? sleep_time.dup : [sleep_time]
+      end
+
+      while not done?(id, options)
+        Log.debug "Waiting on #{ id }"
+        sleep_time = times.shift || sleep_time
+        sleep sleep_time
+      end
+
+      gather(id, nil, options)
+    end
+  end
+end
+
+Log.severity = 0 if __FILE__ == $0
+iii Marenostrum::SLURM.run('ls', nil, nil, :qos => "debug", :user => 'bsc26892') if __FILE__ == $0
+
+

data/lib/rbbt/util/R/plot.rb

@@ -1,7 +1,7 @@
 module R
   module SVG
 
-    def self.ggplotPNG(*args)
+    def self.ggplotSVG(*args)
       ggplot(*args)
     end
 

data/lib/rbbt/workflow/accessor.rb

@@ -809,6 +809,7 @@ module Workflow
 
                      new_=[]
                      dep.each{|d| 
+                       next if d.nil?
                        if Hash === d
                          d[:workflow] ||= wf 
                          d[:task] = task_name

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.21.123
+  version: 5.21.125
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-02-16 00:00:00.000000000 Z
+date: 2018-02-27 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -209,6 +209,7 @@ files:
 - lib/rbbt/entity.rb
 - lib/rbbt/entity/identifiers.rb
 - lib/rbbt/fix_width_table.rb
+- lib/rbbt/hpc.rb
 - lib/rbbt/knowledge_base.rb
 - lib/rbbt/knowledge_base/enrichment.rb
 - lib/rbbt/knowledge_base/entity.rb