RubyGems - sge - Versions diffs - 0.0.1 → 0.0.2 - Mend

sge 0.0.1 → 0.0.2

Files changed (21) hide show

data/Gemfile +22 -0
data/Guardfile +17 -0
data/README.markdown +22 -0
data/lib/sge.rb +4 -4
data/lib/sge/qacct.rb +2 -0
data/lib/sge/qacct/job.rb +54 -0
data/lib/sge/qacct/transformer.rb +31 -0
data/lib/sge/qstat.rb +2 -0
data/lib/sge/utils.rb +12 -0
data/lib/sge/version.rb +1 -1
data/spec/data/qacct.sge +1592 -0
data/spec/data/qacct.yml +1592 -0
data/spec/qacct/job_spec.rb +53 -0
data/spec/qacct/transformer_spec.rb +47 -0
data/spec/{qstat_job_spec.rb → qstat/job_spec.rb} +1 -1
data/spec/{qstat_parser_spec.rb → qstat/parser_spec.rb} +0 -0
data/spec/utils_spec.rb +17 -0
data/utils/transform_to_yaml.sh +3 -0
metadata +33 -18
data/lib/sge/job.rb +0 -18
data/spec/job_spec.rb +0 -53

data/Gemfile CHANGED

@@ -2,3 +2,25 @@ source "http://rubygems.org"
 # Specify your gem's dependencies in sge.gemspec
 gemspec
+require 'rbconfig'
+HOST_OS = RbConfig::CONFIG['host_os']
+gem "guard", ">= 0.6.2"
+gem "guard-bundler", ">= 0.1.3"
+gem "guard-rspec", ">= 0.4.3"
+case HOST_OS
+  when /darwin/i
+    gem 'rb-fsevent'
+    gem 'growl'
+    gem "ruby_gntp"
+  when /linux/i
+    gem 'libnotify'
+    gem 'rb-inotify'
+  when /mswin|windows/i
+    gem 'rb-fchange'
+    gem 'win32console'
+    gem 'rb-notifu'
+end

data/Guardfile ADDED

@@ -0,0 +1,17 @@
+# A sample Guardfile
+# More info at https://github.com/guard/guard#readme
+guard 'rspec', :version => 2 do
+  watch(%r{^spec/.+_spec\.rb$})
+  watch(%r{^lib/sge/(.+)\.rb$}) { |m| puts m[1] ;"spec/#{m[1]}_spec.rb" }
+  watch('spec/spec_helper.rb')  { "spec" }
+  watch(%r{^spec/support/(.+)\.rb$}){ "spec" }
+end
+guard 'bundler' do
+  watch('Gemfile')
+  # Uncomment next line if Gemfile contain `gemspec' command
+  watch(/^.+\.gemspec/)
+end

data/README.markdown ADDED

@@ -0,0 +1,22 @@
+# SGE library for ruby
+This is used to parse SGE output from qacct and qstat -xml and load them into ruby objects
+# Note on Patches/Pull Requests
+* Fork the project.
+* Make your feature addition or bug fix.
+* Add tests for it. This is important so I don’t break it in a future version unintentionally.
+* Commit, do not mess with rakefile, version, or history. (if you want to have your own version, that is fine but bump version in a commit by itself I can ignore when I pull)
+* Send me a pull request. Bonus points for topic branches.
+# Copyright
+Copyright &copy; 2012 Ramihajamalala Hery. See LICENSE for details

data/lib/sge.rb CHANGED

@@ -1,6 +1,6 @@
 require "sge/version"
-require 'sge/command_runner'
 require 'sge/job_helpers'
-require 'sge/qstat/parser'
-require 'sge/job'
-require 'sge/qstat/job'
+require 'sge/utils'
+require 'sge/command_runner'
+require 'sge/qstat'
+require 'sge/qacct'

data/lib/sge/qacct.rb ADDED

	@@ -0,0 +1,2 @@
1	+ require 'sge/qacct/transformer'
2	+ require 'sge/qacct/job'

data/lib/sge/qacct/job.rb ADDED

@@ -0,0 +1,54 @@
+module SGE
+  module QAcct
+    # This class is used for loading jobs from a YAML file generated by transform_qacct_to_yaml
+    class Job
+      FIELDS = [:qname, :hostname, :group, :owner, :project, :department, :jobname, :jobnumber, :taskid, :account, :priority, :qsub_time, :start_time, :end_time, :granted_pe, :slots, :failed, :exit_status, :ru_wallclock, :ru_utime, :ru_stime, :ru_maxrss, :ru_ixrss, :ru_ismrss, :ru_idrss, :ru_isrss, :ru_minflt, :ru_majflt, :ru_nswap, :ru_inblock, :ru_oublock, :ru_msgsnd, :ru_msgrcv, :ru_nsignals, :ru_nvcsw, :ru_nivcsw, :cpu, :mem, :io, :iow, :maxvmem, :arid]
+      attr_accessor *FIELDS
+      def initialize(opts = {})
+        FIELDS.each do |a|
+          instance_variable_set("#{a}", opts[a]) if opts.key?(a)
+        end
+      end
+      def self.load_documents(opts,&block)
+        documents = []
+        transformer = SGE::QAcct::Transformer.new
+        # Compute command
+        cmd = command(opts)
+        # Make a fifo to dump
+        fifo = opts[:file] || SGE::Utils.mkfifo(opts[:tmp_dir])
+        # Add transformer to yaml command
+        cmd = transformer.command(opts.merge(:cmd => cmd, :file => fifo))
+        # Execute this command
+        execute(cmd)
+        # Load documents
+        if block_given?
+          transformer.load_from_yaml_file(fifo, opts[:remove_tmp_file], &block)
+        else
+          transformer.load_from_yaml_file(fifo, opts[:remove_tmp_file]) do |doc|
+            documents << doc
+          end
+          documents
+        end
+      end
+      def self.command(opts)
+       return opts[:cmd] if opts[:cmd]
+       raise "Not Implemented Yet"
+      end
+      def self.execute(cmd)
+        # The same as `#{cmd}`
+        Kernel.system(cmd)
+      end
+    end
+  end
+end

data/lib/sge/qacct/transformer.rb ADDED

@@ -0,0 +1,31 @@
+require 'yaml'
+module SGE
+  module QAcct
+    class Transformer
+      def load_from_yaml_file(yaml_file, remove_file = false,&block)
+        raise "A block must be given" unless block_given?
+        File.open(yaml_file,"r") do |file|
+          YAML.load_documents(file,&block)
+        end
+        File.unlink(yaml_file) if remove_file
+      end
+      def transformer_file
+        File.expand_path('../../../../utils/transform_to_yaml.sh',__FILE__)
+      end
+      def command(opts = {})
+        file = opts[:file].to_s.strip
+        if file.empty?
+          raise "We need a file to dump the yaml"
+        end
+        cmd = opts[:cmd] || "echo"
+        cmd << " | #{transformer_file} > #{file}"
+        cmd << " &" unless opts[:blocking]
+        cmd
+      end
+    end
+  end
+end

data/lib/sge/qstat.rb ADDED

	@@ -0,0 +1,2 @@
1	+ require 'sge/qstat/parser'
2	+ require 'sge/qstat/job'

data/lib/sge/utils.rb ADDED

@@ -0,0 +1,12 @@
+module SGE
+  module Utils
+    extend self
+    def mkfifo(tmp_dir)
+      tmp_pipe = `mktemp -u #{File.join(tmp_dir || "/tmp","fifo.XXXX")}`.strip
+      `mkfifo #{tmp_pipe}`
+      tmp_pipe
+    end
+  end
+end

data/lib/sge/version.rb CHANGED

@@ -1,3 +1,3 @@
 module SGE
-  VERSION = "0.0.1"
+  VERSION = "0.0.2"
 end

data/spec/data/qacct.sge ADDED

@@ -0,0 +1,1592 @@
+==============================================================
+qname        bdd-calcul-x.q
+hostname     compute-5.cloud.weborama.fr
+group        prodsoft
+owner        prodsoft
+project      WOUSDAT
+department   defaultdepartment
+jobname      s20110227_23;init_jour;17
+jobnumber    598013
+taskid       undefined
+account      other
+priority     0
+qsub_time    Mon Feb 28 00:05:05 2011
+start_time   Mon Feb 28 00:05:06 2011
+end_time     Mon Feb 28 00:09:05 2011
+granted_pe   NONE
+slots        1
+failed       0
+exit_status  0
+ru_wallclock 239
+ru_utime     0.712
+ru_stime     0.312
+ru_maxrss    0
+ru_ixrss     0
+ru_ismrss    0
+ru_idrss     0
+ru_isrss     0
+ru_minflt    117733
+ru_majflt    0
+ru_nswap     0
+ru_inblock   0
+ru_oublock   0
+ru_msgsnd    0
+ru_msgrcv    0
+ru_nsignals  0
+ru_nvcsw     2643
+ru_nivcsw    457
+cpu          1.024
+mem          0.029
+io           0.007
+iow          0.000
+maxvmem      344.859M
+arid         undefined
+==============================================================
+qname        bdd-calcul-x.q
+hostname     compute-4.cloud.weborama.fr
+group        prodsoft
+owner        prodsoft
+project      WOUSDAT
+department   defaultdepartment
+jobname      s20110227_23;init_jour;11
+jobnumber    598007
+taskid       undefined
+account      other
+priority     0
+qsub_time    Mon Feb 28 00:05:05 2011
+start_time   Mon Feb 28 00:05:06 2011
+end_time     Mon Feb 28 00:09:05 2011
+granted_pe   NONE
+slots        1
+failed       0
+exit_status  0
+ru_wallclock 239
+ru_utime     0.735
+ru_stime     0.299
+ru_maxrss    0
+ru_ixrss     0
+ru_ismrss    0
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+ru_nivcsw    522
+cpu          1.034
+mem          0.026
+io           0.007
+iow          0.000
+maxvmem      344.750M
+arid         undefined
+==============================================================
+qname        bdd-calcul-x.q
+hostname     compute-4.cloud.weborama.fr
+group        prodsoft
+owner        prodsoft
+project      WOUSDAT
+department   defaultdepartment
+jobname      s20110227_23;init_jour;13
+jobnumber    598009
+taskid       undefined
+account      other
+priority     0
+qsub_time    Mon Feb 28 00:05:05 2011
+start_time   Mon Feb 28 00:05:06 2011
+end_time     Mon Feb 28 00:09:05 2011
+granted_pe   NONE
+slots        1
+failed       0
+exit_status  0
+ru_wallclock 239
+ru_utime     0.711
+ru_stime     0.315
+ru_maxrss    0
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+ru_nivcsw    576
+cpu          1.026
+mem          0.025
+io           0.007
+iow          0.000
+maxvmem      282.406M
+arid         undefined
+==============================================================
+qname        bdd-calcul-x.q
+hostname     compute-4.cloud.weborama.fr
+group        prodsoft
+owner        prodsoft
+project      WOUSDAT
+department   defaultdepartment
+jobname      s20110227_23;init_jour;16
+jobnumber    598012
+taskid       undefined
+account      other
+priority     0
+qsub_time    Mon Feb 28 00:05:05 2011
+start_time   Mon Feb 28 00:05:06 2011
+end_time     Mon Feb 28 00:09:05 2011
+granted_pe   NONE
+slots        1
+failed       0
+exit_status  0
+ru_wallclock 239
+ru_utime     0.716
+ru_stime     0.311
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+arid         undefined
+==============================================================
+qname        bdd-calcul-x.q
+hostname     compute-4.cloud.weborama.fr
+group        prodsoft
+owner        prodsoft
+project      WOUSDAT
+department   defaultdepartment
+jobname      s20110227_23;init_jour;12
+jobnumber    598008
+taskid       undefined
+account      other
+priority     0
+qsub_time    Mon Feb 28 00:05:05 2011
+start_time   Mon Feb 28 00:05:06 2011
+end_time     Mon Feb 28 00:09:06 2011
+granted_pe   NONE
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+arid         undefined
+==============================================================
+qname        bdd-calcul-x.q
+hostname     compute-4.cloud.weborama.fr
+group        prodsoft
+owner        prodsoft
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+==============================================================
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+hostname     compute-4.cloud.weborama.fr
+group        prodsoft
+owner        prodsoft
+project      WOUSDAT
+department   defaultdepartment
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+jobnumber    598011
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+qsub_time    Mon Feb 28 00:05:05 2011
+start_time   Mon Feb 28 00:05:06 2011
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+==============================================================
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+owner        prodsoft
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+==============================================================
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+==============================================================
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+==============================================================
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+==============================================================
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+==============================================================
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+qsub_time    Mon Feb 28 00:05:05 2011
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+==============================================================
+qname        bdd-calcul-x.q
+hostname     compute-9.cloud.weborama.fr
+group        prodsoft
+owner        prodsoft
+project      WOUSDAT
+department   defaultdepartment
+jobname      s20110227_23;recuperation_data_weboscope_pro;269207
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