sushi_fabric 0.3.9 → 0.4.3

data/lib/sushi_fabric/sushiApp.rb

@@ -1,6 +1,6 @@
 #!/usr/bin/env ruby
 # encoding: utf-8
-# Version = '20150604-164027'
+# Version = '20150716-161756'
 
 require 'csv'
 require 'fileutils'
@@ -185,6 +185,7 @@ class SushiApp
   attr_accessor :next_dataset_name
   attr_accessor :dataset_name
   attr_accessor :next_dataset_comment
+  attr_accessor :workflow_manager
   def initialize
     @gstore_dir = GSTORE_DIR
     @project = nil
@@ -197,7 +198,7 @@ class SushiApp
     @params['process_mode'] = 'SAMPLE'
     @job_ids = []
     @required_columns = []
-    @workflow_manager = DRbObject.new_with_uri(WORKFLOW_MANAGER)
+    #@workflow_manager = workflow_manager_instance||DRbObject.new_with_uri(WORKFLOW_MANAGER)
   end
   def set_input_dataset
     if @dataset_tsv_file
@@ -384,13 +385,16 @@ rm -rf #{@scratch_dir} || exit 1
     gsub_options << "-n #{@params['node']}" unless @params['node'].to_s.empty?
     gsub_options << "-r #{@params['ram']}" unless @params['ram'].to_s.empty?
     gsub_options << "-s #{@params['scratch']}" unless @params['scratch'].to_s.empty?
-    gsub_options << "-u #{@user}" if @user
     command = "wfm_monitoring --server #{WORKFLOW_MANAGER} --project #{@project.gsub(/p/,'')} --logdir #{@gstore_script_dir} #{job_script} #{gsub_options.join(' ')}"
+    puts "submit: #{command}"
+
+    project_number = @project.gsub(/p/, '')
+    @workflow_manager||=DRbObject.new_with_uri(WORKFLOW_MANAGER)
+    script_content = File.read(job_script)
+    @workflow_manager.start_monitoring(job_script, @user, 0, script_content, project_number, gsub_options.join(' '), @gstore_script_dir)
   end
   def submit(job_script)
-    command = submit_command(job_script)
-    puts "submit: #{command}"
-    job_id = `#{command}`
+    job_id = submit_command(job_script)
     job_id = job_id.to_i
     unless job_id.to_i > 1
       raise 'failed in job submitting'
@@ -440,6 +444,7 @@ rm -rf #{@scratch_dir} || exit 1
     file_path
   end
   def copy_commands(org_dir, dest_parent_dir, now=nil)
+    @workflow_manager||=DRbObject.new_with_uri(WORKFLOW_MANAGER)
     @workflow_manager.copy_commands(org_dir, dest_parent_dir, now)
   end
   def copy_inputdataset_parameter_jobscripts
@@ -466,6 +471,14 @@ rm -rf #{@scratch_dir} || exit 1
     command = "rm -rf #{@scratch_result_dir}"
     `#{command}`
   end
+  def cluster_nodes
+    @workflow_manager||=DRbObject.new_with_uri(WORKFLOW_MANAGER)
+    @workflow_manager.cluster_nodes
+  end
+  def default_node
+    @workflow_manager||=DRbObject.new_with_uri(WORKFLOW_MANAGER)
+    @workflow_manager.default_node
+  end
 
   def make_job_script
     @out = open(@job_script, 'w')

data/lib/sushi_fabric/version.rb

@@ -1,3 +1,3 @@
 module SushiFabric
-  VERSION = "0.3.9"
+  VERSION = "0.4.3"
 end

metadata

@@ -1,41 +1,46 @@
 --- !ruby/object:Gem::Specification
 name: sushi_fabric
 version: !ruby/object:Gem::Version
-  version: 0.3.9
+  version: 0.4.3
+  prerelease: 
 platform: ruby
 authors:
 - Functional Genomics Center Zurich
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-06-04 00:00:00.000000000 Z
+date: 2015-07-16 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
   requirement: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '1.3'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '1.3'
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
 description: This library provides us with the methods to submit a job cooperating
@@ -47,17 +52,17 @@ executables:
 extensions: []
 extra_rdoc_files: []
 files:
-- ".bzrignore"
+- .bzrignore
 - Gemfile
 - LICENSE.txt
 - README.md
 - Rakefile
 - bin/sushi_fabric
 - config/environments/development.rb
-- lib/sushi_fabric.rb
 - lib/sushi_fabric/optparse_ex.rb
 - lib/sushi_fabric/sushiApp.rb
 - lib/sushi_fabric/version.rb
+- lib/sushi_fabric.rb
 - sample/WordCountApp.rb
 - sample/sample_dataset.tsv
 - sample/sample_parameterset.tsv
@@ -65,25 +70,26 @@ files:
 homepage: ''
 licenses:
 - MIT
-metadata: {}
 post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
   requirements:
-  - - ">="
+  - - ! '>='
     - !ruby/object:Gem::Version
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
   requirements:
-  - - ">="
+  - - ! '>='
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.4.5
+rubygems_version: 1.8.23.2
 signing_key: 
-specification_version: 4
+specification_version: 3
 summary: workflow manager client.
 test_files: []

checksums.yaml

@@ -1,7 +0,0 @@
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-  data.tar.gz: 20e0b60dba4ccb53b8859eb35026f2394b2639b9
-SHA512:
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