Class: Xanthus::Dataverse

Inherits:
Repository show all
Defined in:
lib/xanthus/dataverse.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods inherited from Repository

#prepare_readme_file, #prepare_xanthus_file

Constructor Details

#initialize ⇒ Dataverse

Returns a new instance of Dataverse.



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# File 'lib/xanthus/dataverse.rb', line 17

def initialize
  super
  @server = 'default_server'
  @repo = 'default_repo'
  @token = 'default_token'
  @dataset_name = 'default_name'
  @author = 'default_author'
  @affiliation = 'default_affiliation'
  @email = 'default_email'
  @description = 'default_description'
  @subject = 'default_subject'
  @doi = 'not_set'
end

Instance Attribute Details

#affiliation ⇒ Object

Returns the value of attribute affiliation.



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# File 'lib/xanthus/dataverse.rb', line 11

def affiliation
  @affiliation
end

#author ⇒ Object

Returns the value of attribute author.



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# File 'lib/xanthus/dataverse.rb', line 10

def author
  @author
end

#dataset_name ⇒ Object

Returns the value of attribute dataset_name.



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# File 'lib/xanthus/dataverse.rb', line 9

def dataset_name
  @dataset_name
end

#description ⇒ Object

Returns the value of attribute description.



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# File 'lib/xanthus/dataverse.rb', line 13

def description
  @description
end

#doi ⇒ Object

Returns the value of attribute doi.



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# File 'lib/xanthus/dataverse.rb', line 15

def doi
  @doi
end

#email ⇒ Object

Returns the value of attribute email.



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# File 'lib/xanthus/dataverse.rb', line 12

def email
  @email
end

#repo ⇒ Object

Returns the value of attribute repo.



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# File 'lib/xanthus/dataverse.rb', line 7

def repo
  @repo
end

#server ⇒ Object

Returns the value of attribute server.



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# File 'lib/xanthus/dataverse.rb', line 6

def server
  @server
end

#subject ⇒ Object

Returns the value of attribute subject.



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# File 'lib/xanthus/dataverse.rb', line 14

def subject
  @subject
end

#token ⇒ Object

Returns the value of attribute token.



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# File 'lib/xanthus/dataverse.rb', line 8

def token
  @token
end

Instance Method Details

#add(content) ⇒ Object 



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# File 'lib/xanthus/dataverse.rb', line 174

def add content
  self.add_file_to_dataverse content, "#{content} is a Xanthus generated file (check metadata for description)", 'data'
end

#add_file_to_dataverse(name, description, folder) ⇒ Object 



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# File 'lib/xanthus/dataverse.rb', line 148

def add_file_to_dataverse name, description, folder
  output = `curl --speed-time 15 --speed-limit 1000 --retry 50 --retry-max-time 0 -H X-Dataverse-key:#{@token} -X POST -F "file=@#{name}" -F 'jsonData={"description":"#{description}","directoryLabel":"#{folder}","categories":["Data"], "restrict":"false"}' "#{@server}/api/datasets/:persistentId/add?persistentId=#{@doi}"`
  puts output
end

#create_dataset ⇒ Object 



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# File 'lib/xanthus/dataverse.rb', line 114

def create_dataset
  Dir.chdir 'dataverse_dataset' do
    File.open('dataset.json', 'w+') do |f|
      f.write(self.dataset_json)
    end
    puts "Creating dataverse #{@dataset_name} in #{@repo} at #{@server}..."
    output = `curl --speed-time 15 --speed-limit 1000 --retry 50 --retry-max-time 0 -H X-Dataverse-key:#{@token} -X POST #{@server}/api/dataverses/#{@repo}/datasets --upload-file dataset.json`
    puts output # needed to escape curl output
    parsed = JSON.parse(output)
    @doi = parsed['data']['persistentId']
    puts "Dataverse #{@doi} created."
  end
end

#dataset_json ⇒ Object 



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# File 'lib/xanthus/dataverse.rb', line 31

def dataset_json
json = %Q{
  {
"datasetVersion": {
  "metadataBlocks": {
    "citation": {
      "fields": [
        {
          "value": "#{@dataset_name}",
          "typeClass": "primitive",
          "multiple": false,
          "typeName": "title"
        },
        {
          "value": [
            {
              "authorName": {
                "value": "#{@author}",
                "typeClass": "primitive",
                "multiple": false,
                "typeName": "authorName"
              },
              "authorAffiliation": {
                "value": "#{@affiliation}",
                "typeClass": "primitive",
                "multiple": false,
                "typeName": "authorAffiliation"
              }
            }
          ],
          "typeClass": "compound",
          "multiple": true,
          "typeName": "author"
        },
        {
          "value": [
              { "datasetContactEmail" : {
                  "typeClass": "primitive",
                  "multiple": false,
                  "typeName": "datasetContactEmail",
                  "value" : "#{@email}"
              },
              "datasetContactName" : {
                  "typeClass": "primitive",
                  "multiple": false,
                  "typeName": "datasetContactName",
                  "value": "#{@author}"
              }
          }],
          "typeClass": "compound",
          "multiple": true,
          "typeName": "datasetContact"
        },
        {
          "value": [ {
             "dsDescriptionValue":{
              "value": "#{@description.gsub(/\r/," ").gsub(/\n/," ")}",
              "multiple":false,
             "typeClass": "primitive",
             "typeName": "dsDescriptionValue"
          }}],
          "typeClass": "compound",
          "multiple": true,
          "typeName": "dsDescription"
        },
        {
          "value": [
            "#{@subject}"
          ],
          "typeClass": "controlledVocabulary",
          "multiple": true,
          "typeName": "subject"
        }
      ],
      "displayName": "Citation Metadata"
    }
  }
}
  }
}
  return json
end

#init(config) ⇒ Object 



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# File 'lib/xanthus/dataverse.rb', line 128

def init config
  # initialize with config information
  @author = config.authors
  @affiliation = config.affiliation
  @email = config.email
  @description = config.description
  @dataset_name = config.name+'-'+Time.now.strftime("%Y-%m-%d_%H-%M")

  FileUtils.mkdir_p 'dataverse_dataset'
  self.create_dataset
  Dir.chdir 'dataverse_dataset' do
    FileUtils.mkdir_p 'repo'
    Dir.chdir 'repo' do
      self.xanthus_file
      self.readme_file config
      self.inputs_file config
    end
  end
end

#inputs_file(config) ⇒ Object 



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# File 'lib/xanthus/dataverse.rb', line 163

def inputs_file config
  config.jobs.each do |name,job|
    job.inputs.each do |k, files|
      files.each do |file|
        system('cp', '-f', "../../#{file}", "#{file}")
        self.add_file_to_dataverse file, 'Job input file.', 'metadata'
      end
    end
  end
end

#readme_file(config) ⇒ Object 



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# File 'lib/xanthus/dataverse.rb', line 158

def readme_file config
  self.prepare_readme_file config
  self.add_file_to_dataverse 'README.md', 'readme describing the dataset.', 'metadata'
end

#xanthus_file ⇒ Object 



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# File 'lib/xanthus/dataverse.rb', line 153

def xanthus_file
  self.prepare_xanthus_file
  self.add_file_to_dataverse '.xanthus', 'xanthus file used to generate the data.', 'metadata'
end