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

sge 0.0.1 → 0.0.2

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

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
+ru_ixrss     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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+mem          0.025
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+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;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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+failed       0
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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
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+qsub_time    Mon Feb 28 00:05:05 2011
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+==============================================================
+qname        bdd-calcul-x.q
+hostname     compute-4.cloud.weborama.fr
+group        prodsoft
+owner        prodsoft
+project      WOUSDAT
+department   defaultdepartment
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+jobnumber    598011
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+account      other
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+qsub_time    Mon Feb 28 00:05:05 2011
+start_time   Mon Feb 28 00:05:06 2011
+end_time     Mon Feb 28 00:09:07 2011
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+==============================================================
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+group        prodsoft
+owner        prodsoft
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+start_time   Mon Feb 28 00:09:07 2011
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+==============================================================
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+==============================================================
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+==============================================================
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+==============================================================
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+owner        prodsoft
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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
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+priority     0
+qsub_time    Mon Feb 28 00:05:05 2011
+start_time   Mon Feb 28 00:09:09 2011
+end_time     Mon Feb 28 00:11:32 2011
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+arid         undefined
+==============================================================
+qname        bdd-calcul-x.q
+hostname     compute-9.cloud.weborama.fr
+group        prodsoft
+owner        prodsoft
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