sushi_fabric 1.0.9 → 1.1.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 35b2e022d1f18333d99515a5032500f8c9737cdeb924bf8af1fc23167a85847a
-  data.tar.gz: 7610de543b92274995a7e5ef0cfaa17cc12686106003da9e9e095d58727757de
+  metadata.gz: 07c091813e683833c643c422de04c2a225ad3475ce46cf864003836c6b1056f9
+  data.tar.gz: 03fa7b3efd213571886969d39e40cdb88e6af13e3b37a0ab195fafcc94a061da
 SHA512:
-  metadata.gz: 57c7a0d1834299762b01d2e192aa855d07fbb04c3a304c24968a637f3ebab3e64ad0775ad465b9002156303c91551b28b0126a5412f1f2dbf9871ad71ea4a3aa
-  data.tar.gz: 003d07dbbbe71b0a02535b17d7e3f7cb2166141708575cde12d66aa9bdb50df19c977459e63a0ba0fbff73a2fa251c8929852cd38f7c6acf4c5d1190c24df802
+  metadata.gz: 49dc7c8c246fb31206cf949c0f2279ed6bced0d3c947a6c843cc0017899ede527650b6b862ff9846f8504be70e2a8360742ec68c40638878db647f3707d3f796
+  data.tar.gz: 23ceb3abf7b4928ccdc92b1fc04fe745d9924374a7767d583f5a64e8947464463aa4577ba548ef1648cf4ce13c0a5f39aae93ba5468bce0d8d809c4aada436e2

data/lib/sushi_fabric/sushiApp.rb

@@ -1,6 +1,6 @@
 #!/usr/bin/env ruby
 # encoding: utf-8
-# Version = '20210410-141359'
+# Version = '20211104-160141'
 
 require 'csv'
 require 'fileutils'
@@ -20,6 +20,7 @@ module SushiFabric
     config.scratch_dir = '/tmp/scratch'
     config.module_source = nil
     config.course_mode = nil
+    config.rails_host = nil
   end
 
   # load custmized parameters if there is
@@ -41,6 +42,7 @@ module SushiFabric
     config.scratch_dir = '/tmp/scratch'
     config.module_source = nil
     config.course_mode = nil
+    config.rails_host = nil
   end
 end
       EOF
@@ -53,7 +55,7 @@ end
   SUSHI_APP_DIR = config.sushi_app_dir
   SCRATCH_DIR = config.scratch_dir
   MODULE_SOURCE = config.module_source
-  
+  RAILS_HOST = config.rails_host 
   unless File.exist?(GSTORE_DIR)
     FileUtils.mkdir_p GSTORE_DIR
   end
@@ -238,8 +240,6 @@ class SushiApp
     @params['cores'] = nil
     @params['ram'] = nil
     @params['scratch'] = nil
-    @params['node'] = ''
-    @params['queue'] = ''
     @params['partition'] = ''
     @params['process_mode'] = 'SAMPLE'
     @params['samples'] = ''
@@ -515,6 +515,7 @@ rm -rf #{@scratch_dir} || exit 1
     gsub_options << "-p #{@params['partition']}" unless @params['partition'].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 << "-i #{@params['nice']}" unless @params['nice'].to_s.empty?
     command = "wfm_monitoring --server #{WORKFLOW_MANAGER} --user #{@user} --project #{@project.gsub(/p/,'')} --logdir #{@gstore_script_dir} #{job_script} #{gsub_options.join(' ')}"
     puts "submit: #{command}"
 
@@ -523,8 +524,8 @@ rm -rf #{@scratch_dir} || exit 1
     script_content = File.read(job_script)
     job_id = 0
     begin
-      job_id = @workflow_manager.start_monitoring(job_script, @user, 0, script_content, project_number, gsub_options.join(' '), @gstore_script_dir)
-      #job_id = @workflow_manager.start_monitoring2(job_script, script_content, @user, project_number, gsub_options.join(' '), @gstore_script_dir)
+      #job_id = @workflow_manager.start_monitoring(job_script, @user, 0, script_content, project_number, gsub_options.join(' '), @gstore_script_dir)
+      job_id = @workflow_manager.start_monitoring3(job_script, script_content, @user, project_number, gsub_options.join(' '), @gstore_script_dir, @next_dataset_id, RAILS_HOST)
     rescue => e
       time = Time.now.strftime("[%Y.%m.%d %H:%M:%S]")
       @logger.error("*"*50)

data/lib/sushi_fabric/version.rb

@@ -1,3 +1,3 @@
 module SushiFabric
-  VERSION = "1.0.9"
+  VERSION = "1.1.3"
 end

data/sushi_fabric.gemspec

@@ -19,6 +19,6 @@ Gem::Specification.new do |spec|
   spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
   spec.require_paths = ["lib"]
 
-  spec.add_development_dependency "bundler", "~> 1.3"
+  spec.add_development_dependency "bundler", "~> 2.2.10"
   spec.add_development_dependency "rake"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: sushi_fabric
 version: !ruby/object:Gem::Version
-  version: 1.0.9
+  version: 1.1.3
 platform: ruby
 authors:
 - Functional Genomics Center Zurich
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-04-10 00:00:00.000000000 Z
+date: 2021-11-04 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -16,14 +16,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.3'
+        version: 2.2.10
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.3'
+        version: 2.2.10
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement
@@ -84,7 +84,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.0.3
+rubygems_version: 3.0.3.1
 signing_key: 
 specification_version: 4
 summary: workflow manager client.