Class: Etna::Clients::Magma::FileLinkingWorkflow

Inherits:
Struct
  • Object
show all
Defined in:
lib/etna/clients/magma/workflows/file_linking_workflow.rb

Constant Summary collapse

PATIENT_TIMEPOINT_REGEX = 
/([^-]+-[^-]+)-(DN?[0-9]+).*/

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(opts) ⇒ FileLinkingWorkflow

Returns a new instance of FileLinkingWorkflow.



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# File 'lib/etna/clients/magma/workflows/file_linking_workflow.rb', line 10

def initialize(opts)
  super(**{attribute_options: {}, matching_expressions: []}.update(opts))
end

Instance Attribute Details

#attribute_options ⇒ Object

Returns the value of attribute attribute_options

Returns:

  • (Object) —

    the current value of attribute_options



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# File 'lib/etna/clients/magma/workflows/file_linking_workflow.rb', line 7

def attribute_options
  @attribute_options
end

#bucket_name ⇒ Object

Returns the value of attribute bucket_name

Returns:

  • (Object) —

    the current value of bucket_name



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# File 'lib/etna/clients/magma/workflows/file_linking_workflow.rb', line 7

def bucket_name
  @bucket_name
end

#magma_crud ⇒ Object

Returns the value of attribute magma_crud

Returns:

  • (Object) —

    the current value of magma_crud



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# File 'lib/etna/clients/magma/workflows/file_linking_workflow.rb', line 7

def magma_crud
  @magma_crud
end

#matching_expressions ⇒ Object

Returns the value of attribute matching_expressions

Returns:

  • (Object) —

    the current value of matching_expressions



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# File 'lib/etna/clients/magma/workflows/file_linking_workflow.rb', line 7

def matching_expressions
  @matching_expressions
end

#metis_client ⇒ Object

Returns the value of attribute metis_client

Returns:

  • (Object) —

    the current value of metis_client



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# File 'lib/etna/clients/magma/workflows/file_linking_workflow.rb', line 7

def metis_client
  @metis_client
end

#model_name ⇒ Object

Returns the value of attribute model_name

Returns:

  • (Object) —

    the current value of model_name



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# File 'lib/etna/clients/magma/workflows/file_linking_workflow.rb', line 7

def model_name
  @model_name
end

#project_name ⇒ Object

Returns the value of attribute project_name

Returns:

  • (Object) —

    the current value of project_name



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# File 'lib/etna/clients/magma/workflows/file_linking_workflow.rb', line 7

def project_name
  @project_name
end

Instance Method Details

#containing_record_workflow ⇒ Object 



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# File 'lib/etna/clients/magma/workflows/file_linking_workflow.rb', line 104

def containing_record_workflow
  @containing_record_workflow ||= EnsureContainingRecordWorkflow.new(magma_crud: magma_crud, models: models)
end

#each_revision ⇒ Object 



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# File 'lib/etna/clients/magma/workflows/file_linking_workflow.rb', line 74

def each_revision
  find_matches.each do |key, file_paths|
    match_map, attribute_name = key
    record_identifiers = matches_to_record_identifiers(match_map)
    id = containing_record_workflow.ensure_record(model_name, record_identifiers)
    file_paths.each do |file_path|
      yield [id, revision_for(id, attribute_name, file_path, match_map, record_identifiers)]
    end
  end
end

#find_matches ⇒ Object 



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# File 'lib/etna/clients/magma/workflows/file_linking_workflow.rb', line 18

def find_matches
  {}.tap do |all_matches|
    metis_client.folders(
        project_name: project_name,
        bucket_name: bucket_name
    ).each do |folder|
      metis_client.list_folder(
          Etna::Clients::Metis::ListFolderRequest.new(
              project_name: project_name,
              bucket_name: bucket_name,
              folder_path: folder.folder_path,
          ),
      ).files.all.each do |file|
        matches = matching_expressions
                  .map { |regex, attribute_name| [regex.match(file.file_path), regex, attribute_name] }
                  .select { |match, regex, attribute_name| !match.nil? }

        if matches.length > 1
          raise "File path #{file.file_path} matches multiple regex, #{matches.map(&:second)}.  Please modify the matching expressions to disambiguate"
        end

        if matches.length == 1
          match, _, attribute_name = matches.first
          match_map = match.names.zip(match.captures).to_h
          key = [match_map, attribute_name]

          if attribute_options.dig(attribute_name, :file_collection)
            (all_matches[key] ||= []).push(file.file_path)
          else
            if all_matches.include?(key)
              raise "Field #{attribute_name} for #{match_map} identified for two files, #{file.file_path} and #{all_matches[key]}.  Please modify the existing matching expressionts to disambiguate"
            end

            all_matches[key] = [file.file_path]
          end
        end
      end
    end
  end
end

#link_files ⇒ Object 



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# File 'lib/etna/clients/magma/workflows/file_linking_workflow.rb', line 85

def link_files
  magma_crud.update_records do |update_request|
    each_revision do |id, revision|
      update_request.update_revision(model_name, id, revision)
    end
  end
end

#magma_client ⇒ Object 



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# File 'lib/etna/clients/magma/workflows/file_linking_workflow.rb', line 14

def magma_client
  magma_crud.magma_client
end

#matches_to_record_identifiers(match_data) ⇒ Object

Subclasses should override this to implement custom logic for how regex matches should match to linking.



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# File 'lib/etna/clients/magma/workflows/file_linking_workflow.rb', line 60

def matches_to_record_identifiers(match_data)
  {"project" => project_name}
end

#models ⇒ Object 



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# File 'lib/etna/clients/magma/workflows/file_linking_workflow.rb', line 108

def models
  @models ||= begin
    magma_client.retrieve(RetrievalRequest.new(project_name: self.project_name, model_name: 'all')).models
  end
end

#patient_timepoint_from(word) ⇒ Object 



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# File 'lib/etna/clients/magma/workflows/file_linking_workflow.rb', line 64

def patient_timepoint_from(word)
  match = PATIENT_TIMEPOINT_REGEX.match(word)
  return {} unless match

  return {
      'patient' => match[1],
      'timepoint' => "#{match[1]}-#{match[2]}",
  }
end

#revision_for(id, attribute_name, file_path, match_map, record_identifiers) ⇒ Object 



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# File 'lib/etna/clients/magma/workflows/file_linking_workflow.rb', line 93

def revision_for(id, attribute_name, file_path, match_map, record_identifiers)
  if attribute_options.dig(attribute_name, :file_collection)
    file_path = ::File.dirname(file_path)
    {attribute_name => "https://metis.ucsf.edu/#{project_name}/browse/#{bucket_name}/#{file_path}"}
  else
    {attribute_name => {
      path: "metis://#{project_name}/#{bucket_name}/#{file_path}",
      original_filename: File.basename(file_path)}}
  end
end