Class: Accession::Sample
- Inherits:
-
Object
- Object
- Accession::Sample
- Includes:
- Accessionable, ActiveModel::Model
- Defined in:
- lib/accession/accession/sample.rb
Overview
rubocop:todo Style/Documentation
Instance Attribute Summary collapse
-
#sample ⇒ Object
readonly
Returns the value of attribute sample.
-
#service ⇒ Object
readonly
Returns the value of attribute service.
-
#standard_tags ⇒ Object
readonly
Returns the value of attribute standard_tags.
-
#studies ⇒ Object
readonly
Returns the value of attribute studies.
-
#tags ⇒ Object
readonly
Returns the value of attribute tags.
Instance Method Summary collapse
- #accessioned? ⇒ Boolean
- #ebi_alias ⇒ Object
-
#initialize(standard_tags, sample) ⇒ Sample
constructor
A new instance of Sample.
- #name ⇒ Object
- #title ⇒ Object
- #to_xml ⇒ Object
- #update_accession_number(accession_number) ⇒ Object
Methods included from Accessionable
#date, #ebi_alias_datestamped, #filename, #schema_type, #to_file
Constructor Details
#initialize(standard_tags, sample) ⇒ Sample
Returns a new instance of Sample.
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# File 'lib/accession/accession/sample.rb', line 25 def initialize(, sample) @standard_tags = @sample = sample @studies = set_studies @tags = .extract(sample.) @service = Service.new(studies_valid? ? studies.keys.first : nil) end |
Instance Attribute Details
#sample ⇒ Object (readonly)
Returns the value of attribute sample
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# File 'lib/accession/accession/sample.rb', line 21 def sample @sample end |
#service ⇒ Object (readonly)
Returns the value of attribute service
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# File 'lib/accession/accession/sample.rb', line 21 def service @service end |
#standard_tags ⇒ Object (readonly)
Returns the value of attribute standard_tags
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# File 'lib/accession/accession/sample.rb', line 21 def @standard_tags end |
#studies ⇒ Object (readonly)
Returns the value of attribute studies
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# File 'lib/accession/accession/sample.rb', line 21 def studies @studies end |
#tags ⇒ Object (readonly)
Returns the value of attribute tags
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# File 'lib/accession/accession/sample.rb', line 21 def @tags end |
Instance Method Details
#accessioned? ⇒ Boolean
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# File 'lib/accession/accession/sample.rb', line 83 def accessioned? ebi_accession_number.present? end |
#ebi_alias ⇒ Object
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# File 'lib/accession/accession/sample.rb', line 74 def ebi_alias sample.uuid end |
#name ⇒ Object
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# File 'lib/accession/accession/sample.rb', line 33 def name @name ||= (sample..sample_public_name || sample.name).sanitize end |
#title ⇒ Object
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# File 'lib/accession/accession/sample.rb', line 37 def title @title ||= (sample..sample_public_name || sample.sanger_sample_id) end |
#to_xml ⇒ Object
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# File 'lib/accession/accession/sample.rb', line 41 def to_xml tag_groups = .by_group xml = Builder::XmlMarkup.new xml.instruct! xml.SAMPLE_SET(XML_NAMESPACE) do xml.SAMPLE(alias: ebi_alias) do xml.TITLE title if title.present? xml.SAMPLE_NAME do tag_groups[:sample_name].each do |_k, tag| xml.tag!(tag.label, tag.value) end end xml.SAMPLE_ATTRIBUTES do tag_groups[:sample_attributes].each do |_k, tag| xml.SAMPLE_ATTRIBUTE do xml.TAG tag.label xml.VALUE tag.value end end if service.ena? tag_groups[:array_express].each do |_k, tag| xml.SAMPLE_ATTRIBUTE do xml.TAG tag.array_express_label xml.VALUE tag.value end end end end end end xml.target! end |
#update_accession_number(accession_number) ⇒ Object
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# File 'lib/accession/accession/sample.rb', line 78 def update_accession_number(accession_number) sample..sample_ebi_accession_number = accession_number sample.save end |