sushi_fabric 0.5.9 → 0.6.0

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Files changed (5) hide show
  1. checksums.yaml +7 -0
  2. data/README.md +19 -2
  3. data/lib/sushi_fabric/sushiApp.rb +2 -2
  4. data/lib/sushi_fabric/version.rb +1 -1
  5. metadata +51 -51
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data/README.md CHANGED
@@ -1,6 +1,6 @@
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  # SushiFabric
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- TODO: Write a gem description
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+ This library includes a core process called from [SUSHI](https://github.com/uzh/sushi). sushi_fabric command becomes available after installation. It requires [WorkflowManager](https://github.com/uzh/workflow_manager) to execute sushi_fabric command. SUSHI application must inherit the SushiFabric:SushiApp class and overwrite #next_dataset and #commands methods. Please refer to [SUSHI](https://github.com/uzh/sushi) for more details about how to make SUSHI application.
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  ## Installation
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@@ -18,7 +18,24 @@ Or install it yourself as:
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  ## Usage
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- TODO: Write usage instructions here
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+ ~~~~
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+ $ sushi_fabric -h 16-05-10 15:37
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+ Usage:
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+ sushi_fabric --class [SushiApp class] [options]
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+ (Either --dataset_id or --dataset_tsv is required)
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+ -c, --class class_name SushiApp class name (required)
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+ -i, --dataset_id dataset_id DataSet ID in Sushi DB
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+ -d, --dataset dataset_tsv DataSet file (.tsv) (This option is prior to dataset_id option)
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+ -s, --dataset_name dataset_name DataSet name in Sushi (This will be used with --dataset option, default: tsv file base name)
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+ -m parameterset_tsv, Parameterset file (.tsv)
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+ --parameterset
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+ -r, --run Real run mode. without this option, it runs with test run mode which checks only DataSet and Parameters and no submittion
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+ -p, --project project Project Number (default: 1001)
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+ -u, --user user Submit user (default: sushi_lover)
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+ -I, --load_path load_path Add path where SushiApp class is located (default: ./lib)
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+ -n next_dataset_name, Next DataSet Name (default: Analysis_Category+ID+Date )
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+ --next_dataset_name
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+ ~~~~
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  ## Contributing
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data/lib/sushi_fabric/sushiApp.rb CHANGED
@@ -1,12 +1,12 @@
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  #!/usr/bin/env ruby
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  # encoding: utf-8
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- # Version = '20160331-152819'
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+ # Version = '20160715-153019'
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  require 'csv'
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  require 'fileutils'
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  require 'yaml'
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  require 'drb/drb'
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- gem 'rails', '<=3.2.22'
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+ gem 'rails'
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  require 'rails/all'
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  module SushiFabric
data/lib/sushi_fabric/version.rb CHANGED
@@ -1,3 +1,3 @@
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  module SushiFabric
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- VERSION = "0.5.9"
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+ VERSION = "0.6.0"
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  end
metadata CHANGED
@@ -1,51 +1,54 @@
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- --- !ruby/object:Gem::Specification
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+ --- !ruby/object:Gem::Specification
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  name: sushi_fabric
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- version: !ruby/object:Gem::Version
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- prerelease:
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- version: 0.5.9
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+ version: !ruby/object:Gem::Version
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+ version: 0.6.0
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  platform: ruby
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- authors:
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+ authors:
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  - Functional Genomics Center Zurich
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  autorequire:
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  bindir: bin
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  cert_chain: []
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-
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- date: 2016-03-31 00:00:00 Z
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- dependencies:
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- - !ruby/object:Gem::Dependency
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+ date: 2016-07-15 00:00:00.000000000 Z
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+ dependencies:
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+ - !ruby/object:Gem::Dependency
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  name: bundler
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- prerelease: false
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- requirement: &id001 !ruby/object:Gem::Requirement
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- none: false
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- requirements:
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- - - ~>
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- - !ruby/object:Gem::Version
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- version: "1.3"
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+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - "~>"
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+ - !ruby/object:Gem::Version
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+ version: '1.3'
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  type: :development
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- version_requirements: *id001
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- - !ruby/object:Gem::Dependency
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- name: rake
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  prerelease: false
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- requirement: &id002 !ruby/object:Gem::Requirement
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- none: false
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- requirements:
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - "~>"
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+ - !ruby/object:Gem::Version
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+ version: '1.3'
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+ - !ruby/object:Gem::Dependency
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+ name: rake
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+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
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  - - ">="
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- - !ruby/object:Gem::Version
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- version: "0"
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+ - !ruby/object:Gem::Version
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+ version: '0'
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  type: :development
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- version_requirements: *id002
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- description: This library provides us with the methods to submit a job cooperating with workflow manager.
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- email:
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+ prerelease: false
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ description: This library provides us with the methods to submit a job cooperating
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+ with workflow manager.
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+ email:
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  - masaomi.hatakeyama@fgcz.uzh.ch
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- executables:
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+ executables:
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  - sushi_fabric
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  extensions: []
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-
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  extra_rdoc_files: []
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-
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- files:
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- - .gitignore
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- - .rspec
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+ files:
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+ - ".gitignore"
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+ - ".rspec"
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  - Gemfile
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  - LICENSE.txt
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  - README.md
@@ -62,33 +65,30 @@ files:
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  - spec/spec_helper.rb
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  - spec/sushi_app_spec.rb
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  - sushi_fabric.gemspec
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- homepage: ""
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- licenses:
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+ homepage: ''
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+ licenses:
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  - MIT
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+ metadata: {}
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  post_install_message:
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  rdoc_options: []
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-
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- require_paths:
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+ require_paths:
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  - lib
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- required_ruby_version: !ruby/object:Gem::Requirement
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- none: false
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- requirements:
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+ required_ruby_version: !ruby/object:Gem::Requirement
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+ requirements:
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  - - ">="
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- - !ruby/object:Gem::Version
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- version: "0"
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- required_rubygems_version: !ruby/object:Gem::Requirement
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- none: false
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- requirements:
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ required_rubygems_version: !ruby/object:Gem::Requirement
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+ requirements:
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  - - ">="
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- - !ruby/object:Gem::Version
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- version: "0"
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+ - !ruby/object:Gem::Version
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+ version: '0'
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  requirements: []
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-
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  rubyforge_project:
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- rubygems_version: 1.8.23
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+ rubygems_version: 2.4.5.1
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  signing_key:
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- specification_version: 3
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+ specification_version: 4
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  summary: workflow manager client.
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- test_files:
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+ test_files:
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  - spec/spec_helper.rb
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  - spec/sushi_app_spec.rb