pbs_job 0.0.1 → 0.0.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: d3d52813019b0a936c1cbb679f93db234ffb087a
+  metadata.gz: f0ed432454ec7d005367c6dbc36829f87e02bd6c
+  data.tar.gz: 30d243a63104ea3e728855e75f5c28d853cdbee9
 SHA512:
-  metadata.gz: b57061cfd8bc858dce808277bbfe3353b663fd72f4a29f572ce8a01fa7aaa1ae4b99a47713a3b6090d03106aa48d39699b652bd1d10ebbd73649d734a893c8e9
-  data.tar.gz: d3ba18b5ae94087a58b85210d55923e7467c89814a7378e098ffad66f39f237c69a6c27f3f9581675afc6cfbfc20f8e2ba5f511366321006996e0194831772ec
+  metadata.gz: 423426faac483f807ff4bad364efbdcf833d93e678b1f1e648fc6a54cfc1a3ca8ece52abdbbfd36f61840ff690cf8f3aa7d6907d1d12a5d233fdbe7cc8961e56
+  data.tar.gz: 01a8abd84949a154d85311ccacc91bf620693aeaec7bbb3915093bfec39ded37071266ee57315c12b12eed23fa9bc65d015cf9c9a3616a6a94884e4b0efa45bc

data/bin/pbs_job

@@ -7,6 +7,9 @@ module PbsJob
   class New < Thor::Group
     include Thor::Actions
 
+    STREAMS_DIR_NAME = 'streams'
+    EXECUTABLE_PERMISSIONS = 0775
+
     argument :name, :desc => 'Name of the new job.'
     argument :email_address, :desc => 'Email to which to send PBS alerts.'
 
@@ -22,10 +25,18 @@ module PbsJob
       :script,
       {
         :desc => 'Type of script to make the task script',
-        :default => '<script type>',
+        :default => 'bash',
         :aliases => 's'
       }
     )
+    class_option(
+      :task_working_dir,
+      {
+        :desc => 'Working directory in which to run task',
+        :default => File.expand_path('~'),
+        :aliases => 'w'
+      }
+    )
 
     def self.source_root
       File.expand_path('../../', __FILE__)
@@ -36,15 +47,15 @@ module PbsJob
     end
 
     def qsub_script
-      create_file_from_template 'job.qsub'
+      create_script_from_template 'job.qsub'
     end
 
     def pbs_script
-      create_file_from_template 'job.pbs'
+      create_script_from_template 'job.pbs'
     end
 
     def task
-      create_file_from_template 'task'
+      create_script_from_template 'task'
     end
 
     def results
@@ -62,13 +73,22 @@ module PbsJob
 
     private
 
+    def file_path(script_name)
+      File.join full_name, script_name
+    end
+
     def create_file_from_template(file_name)
       template(
         "templates/#{file_name}.tt",
-        "#{full_name}/#{file_name}"
+        file_path(file_name)
       )
     end
 
+    def create_script_from_template(script_name)
+      create_file_from_template script_name
+      chmod file_path(script_name), EXECUTABLE_PERMISSIONS
+    end
+
     # @returns [String] Name with date appended
     def full_name
       @full_name ||= -> do
@@ -83,11 +103,11 @@ module PbsJob
     end
 
     def streams_path
-      @streams_path ||= File.join full_name, 'streams'
+      @streams_path ||= File.join full_name, STREAMS_DIR_NAME
     end
 
     def abs_stream_prefix
-      @abs_stream_prefix ||= File.join abs_job_root, streams_path, full_name
+      @abs_stream_prefix ||= File.join abs_job_root, STREAMS_DIR_NAME, full_name
     end
   end
 

data/lib/pbs_job/version.rb

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

data/spec/pbs_job_spec.rb

@@ -21,6 +21,17 @@ HELP
   TASK = "#{JOB_ROOT}/task"
   RESULTS = "#{JOB_ROOT}/results"
   STREAMS = "#{JOB_ROOT}/streams"
+  SUCCESSFUL_OUTPUT = <<-OUT
+\e[1m\e[32m      create\e[0m  #{JOB_ROOT}
+\e[1m\e[32m      create\e[0m  #{QSUB_SCRIPT}
+\e[1m\e[32m       chmod\e[0m  #{QSUB_SCRIPT}
+\e[1m\e[32m      create\e[0m  #{PBS_SCRIPT}
+\e[1m\e[32m       chmod\e[0m  #{PBS_SCRIPT}
+\e[1m\e[32m      create\e[0m  #{TASK}
+\e[1m\e[32m       chmod\e[0m  #{TASK}
+\e[1m\e[32m      create\e[0m  #{RESULTS}
+\e[1m\e[32m      create\e[0m  #{STREAMS}
+OUT
 
   it 'prints usage and options without arguments' do
     pbs_job
@@ -39,9 +50,11 @@ Usage:
   pbs_job new NAME EMAIL_ADDRESS [OPTIONS]
 
 Options:
-  r, [--link-results=LINK_RESULTS]  # Directory to which to redirect results
-  s, [--script=SCRIPT]              # Type of script to make the task script
-                                    # Default: <script type>
+  r, [--link-results=LINK_RESULTS]          # Directory to which to redirect results
+  s, [--script=SCRIPT]                      # Type of script to make the task script
+                                            # Default: bash
+  w, [--task-working-dir=TASK_WORKING_DIR]  # Working directory in which to run task
+                                            # Default: /home/vagrant
 
 Creates a new PBS job with the name NAME and arranges for PBS alerts to be sent to EMAIL_ADDRESS, customized by OPTIONS
 GEN_HELP
@@ -57,18 +70,12 @@ GEN_HELP
     it 'creates a file structure for job components' do
       in_tmp_dir do
         pbs_job "new #{NAME} #{EMAIL_ADDRESS}"
-        stdout.must_equal <<-DIR
-\e[1m\e[32m      create\e[0m  #{JOB_ROOT}
-\e[1m\e[32m      create\e[0m  #{QSUB_SCRIPT}
-\e[1m\e[32m      create\e[0m  #{PBS_SCRIPT}
-\e[1m\e[32m      create\e[0m  #{TASK}
-\e[1m\e[32m      create\e[0m  #{RESULTS}
-\e[1m\e[32m      create\e[0m  #{STREAMS}
-DIR
+
+        stdout.must_equal SUCCESSFUL_OUTPUT
         File.directory?(JOB_ROOT).must_equal true
-        File.file?(QSUB_SCRIPT).must_equal true
-        File.file?(PBS_SCRIPT).must_equal true
-        File.file?(TASK).must_equal true
+        check_script QSUB_SCRIPT
+        check_script PBS_SCRIPT
+        check_script TASK
         File.directory?(RESULTS).must_equal true
         File.directory?(STREAMS).must_equal true
       end
@@ -78,18 +85,12 @@ DIR
     it '--script allows specification of the script type of task' do
       in_tmp_dir do
         pbs_job "new #{NAME} #{EMAIL_ADDRESS} --script=bash"
-        stdout.must_equal <<-DIR
-\e[1m\e[32m      create\e[0m  #{JOB_ROOT}
-\e[1m\e[32m      create\e[0m  #{QSUB_SCRIPT}
-\e[1m\e[32m      create\e[0m  #{PBS_SCRIPT}
-\e[1m\e[32m      create\e[0m  #{TASK}
-\e[1m\e[32m      create\e[0m  #{RESULTS}
-\e[1m\e[32m      create\e[0m  #{STREAMS}
-DIR
+
+        stdout.must_equal SUCCESSFUL_OUTPUT
         File.directory?(JOB_ROOT).must_equal true
-        File.file?(QSUB_SCRIPT).must_equal true
-        File.file?(PBS_SCRIPT).must_equal true
-        File.file?(TASK).must_equal true
+        check_script QSUB_SCRIPT
+        check_script PBS_SCRIPT
+        check_script TASK
         File.directory?(RESULTS).must_equal true
         File.directory?(STREAMS).must_equal true
       end
@@ -100,18 +101,12 @@ DIR
       linked_results = '/scratch/results'
       in_tmp_dir do
         pbs_job "new #{NAME} #{EMAIL_ADDRESS} --link-results=#{linked_results}"
-        stdout.must_equal <<-DIR
-\e[1m\e[32m      create\e[0m  #{JOB_ROOT}
-\e[1m\e[32m      create\e[0m  #{QSUB_SCRIPT}
-\e[1m\e[32m      create\e[0m  #{PBS_SCRIPT}
-\e[1m\e[32m      create\e[0m  #{TASK}
-\e[1m\e[32m      create\e[0m  #{RESULTS}
-\e[1m\e[32m      create\e[0m  #{STREAMS}
-DIR
+
+        stdout.must_equal SUCCESSFUL_OUTPUT
         File.directory?(JOB_ROOT).must_equal true
-        File.file?(QSUB_SCRIPT).must_equal true
-        File.file?(PBS_SCRIPT).must_equal true
-        File.file?(TASK).must_equal true
+        check_script QSUB_SCRIPT
+        check_script PBS_SCRIPT
+        check_script TASK
         File.symlink?(RESULTS).must_equal true
         File.readlink(RESULTS).must_equal linked_results
         File.directory?(STREAMS).must_equal true
@@ -125,4 +120,9 @@ DIR
       yield dir if block_given?
     end
   end
+
+  def check_script(script_path)
+    File.file?(script_path).must_equal true
+    File.executable?(script_path).must_equal true
+  end
 end

data/templates/job.pbs.tt

@@ -1,4 +1,4 @@
 #!/usr/bin/env bash
 #PBS -m abe -M <%= email_address %>
-cd <%= abs_job_root %>
-./task > "<%= abs_stream_prefix %>.out" 2> "<%= abs_stream_prefix %>.err"
+cd <%= options[:task_working_dir] %>
+"<%= abs_job_root %>/task" > "<%= abs_stream_prefix %>.out" 2> "<%= abs_stream_prefix %>.err"

data/templates/job.qsub.tt

@@ -1,3 +1,3 @@
 #!/usr/bin/env bash
 # This script runs job.pbs with qsub. Customize as necessary
-qsub job.pbs -N "<%= full_name %>" -e "<%= abs_stream_prefix %>.e" -o "<%= abs_stream_prefix %>.o"
+qsub "<%= abs_job_root %>/job.pbs" -N "<%= full_name %>" -e "<%= abs_stream_prefix %>.e" -o "<%= abs_stream_prefix %>.o"

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: pbs_job
 version: !ruby/object:Gem::Version
-  version: 0.0.1
+  version: 0.0.2
 platform: ruby
 authors:
 - Dustin Morrill