torque_rm 0.2.2 → 0.2.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: d347dabb8547f7e0910cbff2b85597b0bb8b41c7
+  metadata.gz: 0a3c575e33e3109de2fad9850237a9655c66da8c
+  data.tar.gz: 96083ade5954f07f18683df48a0ed09734253a7a
 SHA512:
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-  data.tar.gz: 6b05080ffd4438fd55b18fd10d9e68ac335b454149f7df4374348d7433cbb9f9cc4d4a3c70084a1681d3a1125efaa02eefcbda578b3b875e643bded0505e0176
+  metadata.gz: 1da18e68261fb612d5d7fb60ccf34f61ebe0f2ddaf104902a30964e7de58084fe5a4eadfa971220e1ab8cf6f59fd1aa6d71f4a5f359c0b7336108c171cbe1062
+  data.tar.gz: a042cf22ed24af4dfdc403fef6216a2aaaaa8cadb7dfb0a75b9c2883773c6100586ac0042c928e31b04959afd401e99f3e0e59618a0b55ea91f850daf53cd7f1

data/VERSION

@@ -1 +1 @@
-0.2.2
+0.2.3

data/bin/torque_rm_rest

@@ -52,22 +52,17 @@ end
 
 ### JOBS
 
-get '/qstat/:job_id', :provides => [:json] do |job_id|
+get '/qstat/:job_id', :provides => [:json, :html] do |job_id|
+  job = TORQUE::Qstat.new.query job_id: job_id
   respond_to do |format|
     format.json do
-    	job = TORQUE::Qstat.new.query job_id: job_id
-      # q = TORQUE::Qstat.new
-      # p = TORQUE::Qstat::Parser.new
-      # t = TORQUE::Qstat::Trans.new
-
-      # s= "Job Id: 2770.deep.space.nine\n    Job_Name = STDIN\n    Job_Owner = johndoe@deep.space.nine\n    resources_used.cput = 00:00:00\n    resources_used.mem = 3148kb\n    resources_used.vmem = 32528kb\n    resources_used.walltime = 00:28:05\n    job_state = R\n    queue = bio\n    server = deep.space.nine\n    Checkpoint = u\n    ctime = Mon Sep  2 18:43:10 2013\n    Error_Path = deep.space.nine:/mnt/bio/ngs/data/home/johndoe/STDIN.e2770\n    exec_host = scrapper/0\n    exec_port = 15003\n    Hold_Types = n\n    Join_Path = n\n    Keep_Files = n\n    Mail_Points = a\n    mtime = Mon Sep  2 18:43:11 2013\n    Output_Path = deep.space.nine:/mnt/bio/ngs/data/home/johndoe/STDIN.o2770\n\t\n    Priority = 0\n    qtime = Mon Sep  2 18:43:10 2013\n    Rerunable = True\n    Resource_List.ncpus = 2\n    Resource_List.nice = 0\n    session_id = 16963\n    Variable_List = PBS_O_QUEUE=bio,PBS_O_HOST=deep.space.nine,\n\tPBS_O_HOME=/mnt/bio/ngs/data/home/johndoe,PBS_O_LANG=it_IT.UTF-8,\n\tPBS_O_LOGNAME=johndoe,\n\tPBS_O_PATH=/mnt/bio/ngs/data/opt/fastx_toolkit/bin:/mnt/bio/ngs/data/\n\topt/bedtools/bin:/mnt/bio/ngs/data/opt/fuseki:/mnt/bio/ngs/data/opt/je\n\tna/bin:/mnt/bio/ngs/data/opt/CASAVA/bin:/mnt/bio/ngs/data/bin/cloaked-\n\thipster/utils:/mnt/bio/ngs/data/bin/cloaked-hipster/utils/ngs/pipeline\n\ts:/mnt/bio/ngs/data/bin/cloaked-hipster/utils/db:/mnt/bio/ngs/data/opt\n\t/trimmomatic:/mnt/bio/ngs/data/opt/PHYLOCSF/hmmer-3.0-linux-intel-x86_\n\t64/binaries:/mnt/bio/ngs/data/opt/PHYLOCSF/mlin-PhyloCSF-983a652/:/mnt\n\t/bio/ngs/data/bin/cloaked-hipster/ncrnapp/PBS_pipeline/:/mnt/bio/ngs/d\n\tata/opt/bowtie-0.12.9:/mnt/bio/ngs/data/opt/bowtie_current:/mnt/bio/ng\n\ts/data/opt/STAR_current:/mnt/bio/ngs/data/opt/RSeQC-2.3.5/RQC/usr/loca\n\tl/bin:/mnt/bio/ngs/data/opt/tophat_current:/mnt/bio/ngs/data/opt/PASA/\n\tscripts:/mnt/bio/ngs/data/opt/PASA/bin:/mnt/bio/ngs/data/opt/fasta/bin\n\t:/mnt/bio/ngs/data/opt/cufflinks:/mnt/bio/ngs/data/opt/samtools:/mnt/b\n\tio/ngs/data/opt/samtools/bcftools:/mnt/bio/ngs/data/opt/samtools/misc:\n\t/mnt/bio/ngs/data/opt/STAR_current/bin:/mnt/bio/ngs/data/opt/gmap/bin:\n\t/mnt/bio/ngs/data/opt/velvet:/mnt/bio/ngs/data/opt/velvet/contrib/colu\n\tmbus_scripts:/opt/blat:/mnt/bio/ngs/data/opt/oases/:/mnt/bio/ngs/data/\n\topt/oases/scripts:/mnt/bio/ngs/data/opt/trinityrnaseq:/mnt/bio/ngs/dat\n\ta/opt/trinityrnaseq/util:/usr/local/bin/:/mnt/bio/ngs/data/home/bonnal\n\traoul/.rbenv/bin:/mnt/bio/ngs/data/home/johndoe/.rbenv/shims:/mnt/\n\tbio/ngs/data/home/johndoe/.rbenv/bin:/usr/local/sbin:/usr/local/bi\n\tn:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games,\n\tPBS_O_MAIL=/var/mail/johndoe,PBS_O_SHELL=/bin/bash,\n\tPBS_SERVER=spark,PBS_O_WORKDIR=/mnt/bio/ngs/data/home/johndoe\n    etime = Mon Sep  2 18:43:10 2013\n    submit_args = -l ncpus=2 -l nice=0\n    start_time = Mon Sep  2 18:43:11 2013\n    start_count = 1\n    fault_tolerant = False\n    submit_host = deep.space.nine"
-      # job = job_id == "2770" ? q.mock(t.apply(p.parse(s.gsub(/\n\t/,'')))) : []
       if job.empty?
         return status 404
       else
         json :job => job.first
       end
     end
+    format.html { haml :qstat_job, :format => :html5, :locals => {:job => job.first}}
   end
 	# if job.empty?
  #    "There is no job running with id #{job_id}"
@@ -115,6 +110,19 @@ post '/qstat/:job_id/del', :provides => [:json] do |job_id|
 end
 
 
+get '/qsub' do
+  haml :qsub
+end
+
+post '/submit' do
+  job = TORQUE::Qsub.new
+  job.script =  params[:script]
+  job_id = job.submit
+  haml :qsub_submit, :locals => {:job => job, :job_id => job_id}
+end
+
+
+
 
 __END__
 

data/lib/torque_rm.rb

@@ -7,6 +7,8 @@ require 'torque_rm/qsub'
 require 'torque_rm/qstat'
 require 'torque_rm/qdel'
 require 'active_support/core_ext/hash/conversions'
+require 'securerandom'
+
 
 # Try to laod the default configuration
 TORQUE.load_config

data/lib/torque_rm/common.rb

@@ -20,6 +20,15 @@ module TORQUE
 		@@username = username
 	end
 
+  def self.username
+    @@username
+  end
+
+  def self.user
+    @@username
+  end
+
+
 
   def self.qcommands_path=(path)
   	@@qcommands_path = path
@@ -71,4 +80,5 @@ module TORQUE
   def self.hostname
   	self.server.hostname
   end
+
 end

data/lib/torque_rm/qstat.rb

@@ -31,7 +31,7 @@ module TORQUE
 
       # Cast generic types from string to most near type selected by pattern matching
       def casting
-        each_pair do |k,v| #converting
+        @table.each_pair do |k,v| #converting
           if v =~ (/[0-9][0-9]:[0-9][0-9]:[0-9][0-9]/)
             send "#{k}=", Time.parse(v)
           elsif k.to_s =~ /time/ && v.is_a?(String) && v =~ (/^[0-9]+$/)
@@ -49,7 +49,7 @@ module TORQUE
       end #casting
 
       def alias_case_insensitive_methods
-        each_pair do |k,v| #adding methods
+        @table.each_pair do |k,v| #adding methods
           unless k == k.downcase
             original=k.to_sym
             newer=k.downcase.to_sym
@@ -285,13 +285,13 @@ module TORQUE
               end # do
               if hash.key? :job_id
                 # if hash[:job_id]..is_a? String
-                  jobs.select! {|job| (hash[:job_id].to_s == job.job_id || hash[:job_id].to_s == job.job_id.split(".").first)}
+                  jobs.select {|job| (hash[:job_id].to_s == job.job_id || hash[:job_id].to_s == job.job_id.split(".").first)}
                 # else
                   # warn "You gave me #{hash[:job_id].class}, only String is supported."
                 # end
               elsif hash.key? :job_ids
                 if hash[:job_ids].is_a? Array
-                  jobs.select! {|job| (hash[:job_ids].include?(job.job_id) || hash[:job_ids].include?(job.job_id.split(".").first))}
+                  jobs.select {|job| (hash[:job_ids].include?(job.job_id) || hash[:job_ids].include?(job.job_id.split(".").first))}
                 elsif hash[:job_ids].is_a? String
                   warn "To be implemented for String object."
                 else

data/lib/torque_rm/qsub.rb

@@ -16,10 +16,10 @@ module TORQUE
   
   class Qsub
   	attr_accessor :a, :A,:b,:c,:C,:d,:D,:e,:f,:h,:I,:j,:k,:l
-  	attr_accessor :m,:M,:N,:o,:p,:P,:q,:r,:S,:t,:u,:v,:V,:W,:X,:z, :script
+  	attr_accessor :m,:M,:o,:p,:P,:q,:r,:S,:t,:u,:v,:V,:W,:X,:z, :script
   	attr_accessor :walltime,:gres,:ppn, :procs
     attr_accessor :id
-  	attr_writer :nodes
+  	attr_writer :nodes, :N
 
     # def script(*args)
     #   if args.size == 1
@@ -29,6 +29,14 @@ module TORQUE
     #   end
     # end
 
+    def N
+      if @N.nil?
+        @N = SecureRandom.urlsafe_base64(20)
+      else
+        @N
+      end
+    end
+
 
     alias :cpus :ppn
     alias :cpus= :ppn=
@@ -221,9 +229,10 @@ module TORQUE
     # if root or working directories are not defined the user home directory is
     # the default directory
     def script_dir
-      root_directory || working_directory || '~'
+      root_directory || working_directory || user_directory
     end
 
+    # in case name of the job has not been specified, it will be generated randomly
     def script_filename
       "#{name}.pbs"
     end
@@ -232,6 +241,14 @@ module TORQUE
       File.join(script_dir,script_filename)
     end
 
+    def user_directory
+      if run_as_user
+        File.join("/home",run_as_user)
+      elsif TORQUE.username
+        File.join("/home",TORQUE.username)
+      end
+    end
+
 
 	# Defines the options that will apply to the job. If the job executes upon a host which does not support checkpoint, these options will be ignored.
 	# Valid checkpoint options are:

data/torque_rm.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "torque_rm"
-  s.version = "0.2.2"
+  s.version = "0.2.3"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Raoul Jean Pierre Bonnal"]
-  s.date = "2013-09-17"
+  s.date = "2013-09-18"
   s.description = "TORQUE Resource Manager for Ruby. Submit, check and control your job directly from Ruby."
   s.email = "ilpuccio.febo@gmail.com"
   s.executables = ["torque_rm_rest"]
@@ -44,7 +44,9 @@ Gem::Specification.new do |s|
     "torque_rm.gemspec",
     "web/helpers/qstat.rb",
     "web/views/qstat.haml",
-    "web/views/qstat_job.haml"
+    "web/views/qstat_job.haml",
+    "web/views/qsub.haml",
+    "web/views/qsub_submit.haml"
   ]
   s.homepage = "http://github.com/helios/torque_rm"
   s.licenses = ["MIT"]

data/web/views/qstat.haml

@@ -5,7 +5,9 @@
   %tbody
     - jobs.each do |job|
       %tr{job_line_color(job)}
-        %td= job.job_id.split(".").first
+        %td
+          %a{:href=>"qstat/#{job.job_id.split(".").first}"}
+            = job.job_id.split(".").first
         %td= job.job_name
         %td= job.node
         %td= "#{job.memory} mb"

data/web/views/qsub.haml

@@ -0,0 +1,3 @@
+%form{:method=> "post", :action=>"submit"}
+  %input{:type=>"textarea", :rows=>"80", :cols=>"40", :name => "script"}
+  %input{:type => "submit", :value => "Place in queue!"}

data/web/views/qsub_submit.haml

@@ -0,0 +1,4 @@
+%p
+  Your job has been submitted with id 
+  %a{:href=>"qstat/#{job_id.split(".").first}"}
+    = job_id.split(".").first

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: torque_rm
 version: !ruby/object:Gem::Version
-  version: 0.2.2
+  version: 0.2.3
 platform: ruby
 authors:
 - Raoul Jean Pierre Bonnal
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-09-17 00:00:00.000000000 Z
+date: 2013-09-18 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rye
@@ -257,6 +257,8 @@ files:
 - web/helpers/qstat.rb
 - web/views/qstat.haml
 - web/views/qstat_job.haml
+- web/views/qsub.haml
+- web/views/qsub_submit.haml
 - README.html
 homepage: http://github.com/helios/torque_rm
 licenses: