sushi_fabric 0.4.3 → 0.4.6
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- data/lib/sushi_fabric/sushiApp.rb +22 -11
- data/lib/sushi_fabric/version.rb +1 -1
- metadata +45 -50
@@ -1,6 +1,6 @@
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1
1
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#!/usr/bin/env ruby
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2
2
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# encoding: utf-8
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3
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-
# Version = '
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3
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+
# Version = '20150904-134632'
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4
4
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require 'csv'
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require 'fileutils'
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@@ -125,7 +125,7 @@ class ::String
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scan(/\[(.*)\]/).flatten.join =~ /#{tag}/
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end
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end
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128
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-
def save_data_set(data_set_arr, headers, rows)
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128
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+
def save_data_set(data_set_arr, headers, rows, user=nil)
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data_set_hash = Hash[*data_set_arr]
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unless project = Project.find_by_number(data_set_hash['ProjectNumber'].to_i)
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project = Project.new
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@@ -134,7 +134,9 @@ def save_data_set(data_set_arr, headers, rows)
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end
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if project = Project.find_by_number(data_set_hash['ProjectNumber'].to_i)
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data_set = DataSet.new
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-
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if user
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data_set.user = user
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end
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data_set.name = data_set_hash['DataSetName']
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data_set.project = project
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if parent_id = data_set_hash['ParentID'] and parent_data_set = DataSet.find_by_id(parent_id.to_i)
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@@ -160,6 +162,10 @@ def save_data_set(data_set_arr, headers, rows)
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project.data_sets << data_set
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parent_data_set.data_sets << data_set if parent_data_set
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data_set.save
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if user
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user.data_sets << data_set
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user.save
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end
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end
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data_set.id
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end
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@@ -186,6 +192,7 @@ class SushiApp
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attr_accessor :dataset_name
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attr_accessor :next_dataset_comment
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attr_accessor :workflow_manager
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+
attr_accessor :current_user
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def initialize
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@gstore_dir = GSTORE_DIR
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@project = nil
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@@ -229,7 +236,8 @@ class SushiApp
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end
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end
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unless NO_ROR
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-
@
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@current_user ||= nil
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@dataset_sushi_id = save_data_set(data_set_arr.to_a.flatten, headers, rows, @current_user)
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end
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elsif @dataset_sushi_id
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@dataset_hash = []
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@@ -512,9 +520,7 @@ rm -rf #{@scratch_dir} || exit 1
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@job_scripts << @job_script
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@result_dataset << next_dataset
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end
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-
def save_data_set(data_set_arr, headers, rows)
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-
#SushiFabric.save_data_set(data_set_arr, headers, rows, user)
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-
#=begin
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+
def save_data_set(data_set_arr, headers, rows, user=nil)
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data_set_hash = Hash[*data_set_arr]
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unless project = Project.find_by_number(data_set_hash['ProjectNumber'].to_i)
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project = Project.new
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@@ -523,7 +529,9 @@ rm -rf #{@scratch_dir} || exit 1
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end
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if project = Project.find_by_number(data_set_hash['ProjectNumber'].to_i)
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data_set = DataSet.new
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-
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if user
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data_set.user = user
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end
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data_set.name = data_set_hash['DataSetName']
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data_set.project = project
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if parent_id = data_set_hash['ParentID'] and parent_data_set = DataSet.find_by_id(parent_id.to_i)
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@@ -549,10 +557,13 @@ rm -rf #{@scratch_dir} || exit 1
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project.data_sets << data_set
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parent_data_set.data_sets << data_set if parent_data_set
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data_set.save
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if user
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user.data_sets << data_set
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user.save
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end
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end
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data_set.id
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end
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-
#=end
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end
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def main
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569
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## sushi writes creates the job scripts and builds the result data set that is to be generated
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@@ -604,8 +615,8 @@ rm -rf #{@scratch_dir} || exit 1
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end
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end
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unless NO_ROR
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-
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-
@next_dataset_id = save_data_set(data_set_arr.to_a.flatten, headers, rows)
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@current_user ||= nil
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@next_dataset_id = save_data_set(data_set_arr.to_a.flatten, headers, rows, @current_user)
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# save job and dataset relation in Sushi DB
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job_ids.each do |job_id|
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data/lib/sushi_fabric/version.rb
CHANGED
metadata
CHANGED
@@ -1,57 +1,49 @@
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1
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-
--- !ruby/object:Gem::Specification
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1
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+
--- !ruby/object:Gem::Specification
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name: sushi_fabric
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3
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-
version: !ruby/object:Gem::Version
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version: 0.4.3
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version: !ruby/object:Gem::Version
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4
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prerelease:
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version: 0.4.6
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platform: ruby
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authors:
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7
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authors:
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8
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- Functional Genomics Center Zurich
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9
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autorequire:
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10
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bindir: bin
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11
11
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cert_chain: []
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12
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-
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13
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-
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14
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-
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12
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+
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13
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date: 2015-09-04 00:00:00 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: bundler
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requirement: !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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type: :development
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prerelease: false
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-
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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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requirements:
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21
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- - ~>
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- !ruby/object:Gem::Version
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version:
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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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none: false
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requirements:
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35
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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: "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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-
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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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-
- -
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-
- !ruby/object:Gem::Version
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version:
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46
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-
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47
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-
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48
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-
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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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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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49
39
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- masaomi.hatakeyama@fgcz.uzh.ch
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50
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-
executables:
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40
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executables:
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41
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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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+
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files:
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- .bzrignore
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- Gemfile
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49
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- LICENSE.txt
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@@ -67,29 +59,32 @@ files:
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- sample/sample_dataset.tsv
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- sample/sample_parameterset.tsv
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69
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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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post_install_message:
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66
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rdoc_options: []
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75
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-
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67
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+
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68
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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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required_ruby_version: !ruby/object:Gem::Requirement
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none: false
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79
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-
requirements:
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80
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-
- -
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-
- !ruby/object:Gem::Version
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version:
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83
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required_rubygems_version: !ruby/object:Gem::Requirement
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requirements:
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73
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- - ">="
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74
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- !ruby/object:Gem::Version
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75
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version: "0"
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76
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required_rubygems_version: !ruby/object:Gem::Requirement
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77
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none: false
|
85
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-
requirements:
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86
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-
- -
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87
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-
- !ruby/object:Gem::Version
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88
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-
version:
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78
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+
requirements:
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79
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+
- - ">="
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80
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+
- !ruby/object:Gem::Version
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81
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+
version: "0"
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82
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requirements: []
|
83
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+
|
90
84
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rubyforge_project:
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91
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-
rubygems_version: 1.8.23
|
85
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+
rubygems_version: 1.8.23
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86
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signing_key:
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93
87
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specification_version: 3
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94
88
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summary: workflow manager client.
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95
89
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test_files: []
|
90
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+
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