rbbt-rest 1.3.31 → 1.3.32
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/lib/rbbt/rest/client.rb +13 -6
- data/lib/rbbt/rest/common/misc.rb +11 -2
- data/lib/rbbt/rest/entity/rest.rb +2 -2
- data/lib/rbbt/rest/knowledge_base/helpers.rb +92 -58
- data/lib/rbbt/rest/knowledge_base.rb +1 -1
- data/lib/rbbt/rest/workflow.rb +1 -1
- data/share/views/compass/rbbt/table.sass +2 -0
- data/share/views/compass/style.sass +1 -0
- metadata +2 -2
checksums.yaml
CHANGED
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@@ -1,7 +1,7 @@
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---
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SHA1:
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metadata.gz:
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data.tar.gz:
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metadata.gz: baafff671bbb97e58be46dfcaaee6a3c64b103b4
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4
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data.tar.gz: d7106534d2b1b70944e2bc875b7cbeadef8c26a6
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 098f9a74ed00d545f866e0d397a131191c2d14c8078ba09156a7694d253320ebae52268a80808969410cd05b694725af8a08e45bc665b3569876ea19806d5a0a
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7
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data.tar.gz: d36a5bc597de18f4214be7d0179030e3354080c6b6834132cecd0ed2e2314c4701c8f4650082da8c0ac30a5ca7a3f8157e4ccfc157db9c60d8652c639d6dfb5d
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data/lib/rbbt/rest/client.rb
CHANGED
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@@ -26,13 +26,20 @@ class WorkflowRESTClient
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def job(task, name, inputs)
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task_info = task_info(task)
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fixed_inputs = {}
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input_types = task_info[:input_types]
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inputs.each do |k,v|
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k = k.to_sym
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if TSV === v
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fixed_inputs[k] = v.to_s
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else
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case input_types[k].to_sym
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when :tsv, :array, :file, :text
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fixed_inputs[k] = (String === v and Open.exists?(v)) ? Open.open(v) : v
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else
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fixed_inputs[k] = v
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end
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end
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end
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RemoteStep.new(url, task, name, fixed_inputs, task_info[:result_type], task_info[:result_description], @exec_exports.include?(task))
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@@ -118,11 +118,20 @@ module RbbtRESTHelpers
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when :boolean
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param2boolean(value)
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when :text
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when :text, :file
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if param_file and (value.nil? or (String === value and value.empty?))
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param_file[:tempfile].read
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else
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value
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case value
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when String
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value.gsub(/\r\n/, "\n")
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when File, IO
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value
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when Hash
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value[:tempfile]
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else
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raise "Missing class for #{ type }: #{ Misc.fingerprint value }"
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end
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end
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when :array
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@@ -75,11 +75,11 @@ module Entity
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if entity.respond_to? :entity_link_params
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params = entity.entity_link_params
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else
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params = {}
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params = entity.respond_to?(:info) ? entity.info : {}
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end
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end
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url = File.join('/', 'entity', Entity::REST.clean_element(type.to_s), entity)
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url << "?" << Misc.hash2GET_params(params) if params.any?
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url
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@@ -3,10 +3,19 @@ require 'rbbt/knowledge_base'
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module KnowledgeBaseRESTHelpers
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class << self
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attr_accessor :knowledge_base_dir, :
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attr_accessor :knowledge_base_dir, :syndications
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def add_syndication(name, kb)
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@syndications ||= {}
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@syndications[name] = kb
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end
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def syndications
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@syndications ||= {}
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end
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end
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self.knowledge_base_dir = "var/
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self.knowledge_base_dir = Path.setup("var/sinatra/knowledge_bases")
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def prepare_entities_for_json(entities)
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case entities
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@@ -25,65 +34,90 @@ module KnowledgeBaseRESTHelpers
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end
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end
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def get_kb(name)
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end
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#def get_kb(name)
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# @@knowledge_bases ||= IndiferentHash.setup({})
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# case name
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# when :genomics, "genomics"
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# @@knowledge_bases[name] ||= Genomics.knowledge_base
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# else
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# @@knowledge_bases[name] ||= KnowledgeBase.new File.join(KnowledgeBaseRESTHelpers.knowledge_base_dir, name)
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# end
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#end
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#def user_kb(user)
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# user = "guest" if user.nil?
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# @@user_knowledge_bases ||= IndiferentHash.setup({})
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# @@user_knowledge_bases[user] ||= begin
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# kb = KnowledgeBase.new File.join(KnowledgeBaseRESTHelpers.knowledge_base_dir, File.join('user', user)), Organism.default_code("Hsa")
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# kb.format["Gene"] = "Ensembl Gene ID"
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# kb.syndicate Genomics.knowledge_base, :genomics
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# if defined? user_studies
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# TSV.traverse user_studies[user], :cpus => 10 do |study|
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# Study.setup(study)
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# study.sample_genes if study.has_genotypes?
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# end
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# user_studies[user].each do |study|
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# Study.setup(study)
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# kb.syndicate study.knowledge_base, study
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# end
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# end
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# kb
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# end
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#end
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#def get_knowledge_base(name, namespace = nil)
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# @@knowledge_bases ||= IndiferentHash.setup({})
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# @@knowledge_bases[name] ||= begin
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# begin
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# mod = Kernel.const_get name
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# return mod.knowledge_base if mod.respond_to? :knowledge_base
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# rescue Exception
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# end
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# kb = case
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# when [:genomics, "genomics"].include?(name)
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# Genomics.knowledge_base
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# when (Misc.path_relative_to(settings.cache_dir, name) and File.exists?(name))
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# KnowledgeBase.new name
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# when KnowledgeBase.registry.include?(name)
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# KnowledgeBase.registry[name]
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# when (defined? Study and Study.studies.include?(name))
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# Study.setup(name).knowledge_base
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# when name.to_s == "user"
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# user_kb(user)
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# else
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# KnowledgeBase.new File.join(KnowledgeBaseRESTHelpers.knowledge_base_dir, name)
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# end
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# namespace ? kb.version(namespace) : kb
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# end
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#end
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def user_kb(user)
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study.sample_genes if study.has_genotypes?
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end
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user_studies[user].each do |study|
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Study.setup(study)
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kb.syndicate study.knowledge_base, study
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end
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end
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kb
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end
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@@user_kbs ||= {}
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@@user_kbs[user] ||= begin
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kb = KnowledgeBase.new(KnowledgeBaseRESTHelpers.knowledge_base_dir.users[user], Organism.default_code("Hsa"))
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KnowledgeBaseRESTHelpers.syndications.each do |name, new|
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Log.low "Syndicating database #{ name } for user #{user}"
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kb.syndicate name, new
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end if KnowledgeBaseRESTHelpers.syndications.any?
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kb
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end
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end
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def get_knowledge_base(name, namespace = nil)
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when [:genomics, "genomics"].include?(name)
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Genomics.knowledge_base
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when (Misc.path_relative_to(settings.cache_dir, name) and File.exists?(name))
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KnowledgeBase.new name
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when KnowledgeBase.registry.include?(name)
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KnowledgeBase.registry[name]
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when (defined? Study and Study.studies.include?(name))
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Study.setup(name).knowledge_base
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when name.to_s == "user"
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user_kb(user)
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else
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KnowledgeBase.new File.join(KnowledgeBaseRESTHelpers.knowledge_base_dir, name)
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end
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namespace ? kb.version(namespace) : kb
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end
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def get_knowledge_base(name=:user, namespace = nil)
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kb = case name.to_s
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when "user"
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user_kb(user)
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else
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Genomics.knowledge_base
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end
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(namespace and namespace != kb.namespace) ? kb.version(namespace) : kb
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end
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end
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data/lib/rbbt/rest/workflow.rb
CHANGED
metadata
CHANGED
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@@ -1,14 +1,14 @@
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1
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--- !ruby/object:Gem::Specification
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name: rbbt-rest
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version: !ruby/object:Gem::Version
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version: 1.3.
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version: 1.3.32
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platform: ruby
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authors:
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- Miguel Vazquez
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autorequire:
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bindir: bin
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cert_chain: []
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date: 2014-08-
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date: 2014-08-30 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: rake
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