Class: SampleType

Inherits:
ActiveRecord::Base
  • Object
show all
Includes:
FieldTyper
Defined in:
app/models/sample_type.rb

Overview

Meta-type of Sample. Many Samples may exist of this Type.

Class Method Summary collapse

Instance Method Summary collapse

Class Method Details

.clean_up_allowable_field_types(raw_sample_types) ⇒ Object 



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# File 'app/models/sample_type.rb', line 187

def self.clean_up_allowable_field_types(raw_sample_types)

  raw_sample_types.each do |rst|
    next unless rst

    st = SampleType.find_by(name: rst[:name])

    st.field_types.each do |ft|
      next unless rst[:field_types]

      rst[:field_types].each do |rft|
        next unless rft
        next unless rft[:sample_types]
        next unless ft.name == rft[:name] && ft.role == rft[:role] && ft.sample?

        names = rft[:sample_types]
        ft.allowable_field_types.each do |aft|
          names.delete(aft.sample_type.name) if names.member?(aft.sample_type.name)
        end
        names.each do |name|
          empty_afts = ft.allowable_field_types.select { |aft| aft.sample_type_id.nil? }
          if empty_afts.any?
            st = SampleType.find_by(name: name)
            empty_afts[0].sample_type_id = st ? st.name : nil
          end
        end
      end
    end

  end

end

.compare_and_upgrade(raw_sample_types) ⇒ Object 



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# File 'app/models/sample_type.rb', line 75

def self.compare_and_upgrade(raw_sample_types)

  notes = []
  inconsistencies = []
  make = []

  raw_sample_types.each do |rst|

    st = find_by(name: rst[:name])

    if st
      note = "Found sample type '#{rst[:name]}'"
      sample_type_inconsistencies = st.inconsistencies rst
      inconsistencies += sample_type_inconsistencies
      if sample_type_inconsistencies.none?
        note += ' with same definition as imported type.'
        notes << note
      else
        note += ' which not consistent with the imported sample type of the same name.'
        inconsistencies << note
      end
    else
      notes << "Sample type named '#{rst[:name]}' not found. It will be eventually have to be created from the imported definition."
      make << rst
    end

  end

  unless inconsistencies.any?

    # make sample types
    make.each do |rst|
      st = SampleType.create_from_raw rst
      if st.errors.any?
        inconsistencies << "Error: Could not create sample type #{rst[:name]}: #{st.errors.full_messages.join(', ')}"
      else
        notes << "Created new sample type #{st.name} with id #{st.id}"
      end
    end

    # make allowable field types (assumes sample types have been made)
    make.each do |rst|
      st = SampleType.find_by name: rst[:name]
      next unless st

      st.create_afts_from_raw rst
      if st.errors.any?
        inconsistencies << "Could not create sample type #{rst[:name]}: #{st.errors.full_messages.join(', ')}"
        st.destroy
      end
    end

  end

  { notes: notes, inconsistencies: inconsistencies }

end

.create_from_raw(raw_sample_type) ⇒ Object 



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# File 'app/models/sample_type.rb', line 133

def self.create_from_raw(raw_sample_type)

  st = SampleType.new name: raw_sample_type[:name], description: raw_sample_type[:description]
  st.save

  if raw_sample_type[:field_types]
    raw_sample_type[:field_types].each do |rft|

      ft = FieldType.new(
        name: rft[:name],
        parent_id: st.id,
        parent_class: 'SampleType',
        array: rft[:array],
        choices: rft[:choices],
        required: rft[:required],
        ftype: rft[:ftype],
        role: rft[:role],
        routing: rft[:routing]
      )

      ft.save

      st.errors.add :field_type_creation, "Could not create field type named #{rft[:name]}: #{ft.errors.full_messages.join(', ')}" if ft.errors.any?

    end

  end

  st

end

Instance Method Details

#create_afts_from_raw(raw_sample_type) ⇒ Object 



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# File 'app/models/sample_type.rb', line 165

def create_afts_from_raw(raw_sample_type)

  field_types.each do |ft|
    raw_sample_type[:field_types].each do |rft|
      next unless ft.name == rft[:name]

      l = rft[:sample_types] ? rft[:sample_types].length : 0
      (0..l - 1).each do |i|
        st = SampleType.find_by(name: rft[:sample_types][i])
        ot = ObjectType.find_by(name: rft[:sample_types][i])
        aft = AllowableFieldType.new(
          field_type_id: ft.id,
          sample_type_id: st ? st.id : nil,
          object_type_id: ot ? ot.id : nil
        )
        aft.save
      end
    end
  end

end

#export ⇒ Object 



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# File 'app/models/sample_type.rb', line 25

def export
  attributes
end

#inconsistencies(raw_sample_type) ⇒ Object 



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# File 'app/models/sample_type.rb', line 49

def inconsistencies(raw_sample_type)

  results = []

  results << "names #{name} and #{raw_sample_type[:name]} do not agree." unless name == raw_sample_type[:name]

  unless description == raw_sample_type[:description]
    results << "#{name} descriptions do not agree"
    return results
  end

  if raw_sample_type[:field_types]
    raw_sample_type[:field_types].each do |rft|
      fts = field_types.select { |ft| ft.name == rft[:name] }
      if fts.length == 1
        results += fts[0].inconsistencies(rft, name)
      else
        results << "#{name} does not have a field named #{rft[:name]}, although the imported version of this sample type does."
      end
    end
  end

  results

end

#name ⇒ String

Gets name of SampleType.

Returns:

  • (String) —

    the name of the SampleType, as in "Primer"



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# File 'app/models/sample_type.rb', line 17

attr_accessible :name

#required_sample_types(st_list = []) ⇒ Object

used in operation_type_export



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# File 'app/models/sample_type.rb', line 30

def required_sample_types(st_list = [])

  field_types.select(&:sample?).each do |ft|

    ft.allowable_field_types.each do |aft|

      if aft.sample_type && !st_list.member?(aft.sample_type)
        st_list << aft.sample_type
        st_list = aft.sample_type.required_sample_types(st_list)
      end

    end

  end

  st_list

end