Class: OperationType

Inherits:
ActiveRecord::Base
  • Object
show all
Includes:
CodeHelper, DataAssociator, FieldTyper, HasTiming, OperationTypeExport, OperationTypePlanner, OperationTypeRandom, OperationTypeWorkflow
Defined in:
app/models/operation_type.rb

Overview

Defines a type of lab procedure, with the input-types, output-types, and the instructions for converting inputs into outputs. Executable unit Operations can be instantiated from an OperationType, and specific inputs and outputs are then given.

Class Method Summary collapse

Instance Method Summary collapse

Methods included from DataAssociator

#append_notes, #associate, #associations, #data_associations, #get, #get_association, #lazy_associate, #modify, #notes, #notes=, #upload

Class Method Details

.numbers(user = nil) ⇒ Object 



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# File 'app/models/operation_type.rb', line 343

def self.numbers(user = nil)
  q = if user.nil?
        "
          SELECT   status, operation_type_id, COUNT(status)
          FROM     operations
          GROUP BY operation_type_id, status
        "
      else
        "
          SELECT   status, operation_type_id, COUNT(status)
          FROM     operations
          WHERE    user_id = #{user.id}
          GROUP BY operation_type_id, status
        "
      end

  r = ActiveRecord::Base.connection.execute(q).entries

  result = {}
  r.each do |status, ot_id, count|
    result[ot_id] ||= { planning: 0, waiting: 0, pending: 0, delayed: 0, deferred: 0, primed: 0, scheduled: 0, running: 0, error: 0, done: 0 }
    result[ot_id][status] = count
    result[ot_id][:waiting] = count if status == 'primed'
  end

  result
end

Instance Method Details

#add_cost_model(content:, user:) ⇒ Object 



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# File 'app/models/operation_type.rb', line 130

def add_cost_model(content:, user:)
  if cost_model
    cost_model.commit(content, user)
  else
    new_code('cost_model', content, user)
  end
end

#add_input(name, sample_name, container_name, opts = {}) ⇒ Object 



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

def add_input(name, sample_name, container_name, opts = {})
  add_field(name, sample_name, container_name, 'input', opts)
end

#add_io(name, sample_name, container_name, role, opts) ⇒ Object 



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# File 'app/models/operation_type.rb', line 45

def add_io(name, sample_name, container_name, role, opts)
  add_field(name, sample_name, container_name, role, opts)
end

#add_new_allowable_field_type(ft, new_type) ⇒ Object

Update Methods for Field Types from Front End Start Here



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# File 'app/models/operation_type.rb', line 182

def add_new_allowable_field_type(ft, new_type)
  st = (SampleType.find_by(name: new_type[:sample_type][:name]) if new_type[:sample_type])
  ot = (ObjectType.find_by(name: new_type[:object_type][:name]) if new_type[:object_type] && new_type[:object_type][:name] != '')

  ft.allowable_field_types.create(
    sample_type_id: st ? st.id : nil,
    object_type_id: ot ? ot.id : nil
  )
end

#add_new_field_type(new_type) ⇒ Object 



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# File 'app/models/operation_type.rb', line 210

def add_new_field_type(new_type)
  sample_type_names = []
  container_names = []
  if new_type[:allowable_field_types]

    sample_type_names = new_type[:allowable_field_types].collect do |aft|
      aft[:sample_type] ? aft[:sample_type][:name] : nil
    end

    container_names = new_type[:allowable_field_types]
                      .select { |aft| aft[:object_type] && aft[:object_type][:name] && aft[:object_type][:name] != '' }
                      .collect do |aft|
      raise "Object type '#{aft[:object_type][:name]}' not defined by browser for #{ft[:name]}." unless ObjectType.find_by(name: aft[:object_type][:name])

      aft[:object_type][:name]
    end
  else
    sample_type_names = new_type[:sample_types] if new_type[:sample_types]
    container_names = new_type[:object_types] if new_type[:object_types]
  end

  add_io(
    new_type[:name],
    sample_type_names,
    container_names,
    new_type[:role],
    array: new_type[:array],
    part: new_type[:part],
    routing: new_type[:routing],
    ftype: new_type[:ftype],
    choices: new_type[:choices]
  )

  field_types.where(name: new_type[:name], role: new_type[:role])[0]
end

#add_output(name, sample_name, container_name, opts = {}) ⇒ Object 



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# File 'app/models/operation_type.rb', line 53

def add_output(name, sample_name, container_name, opts = {})
  add_field(name, sample_name, container_name, 'output', opts)
end

#add_parameter(name:, type:, choices:) ⇒ Object 



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# File 'app/models/operation_type.rb', line 57

def add_parameter(name:, type:, choices:)
  add_field(name, nil, nil, 'input', ftype: type, choices: choices)
end

#add_precondition(content:, user:) ⇒ Object 



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# File 'app/models/operation_type.rb', line 146

def add_precondition(content:, user:)
  if precondition
    precondition.commit(content, user)
  else
    new_code('precondition', content, user)
  end
end

#add_protocol(content:, user:) ⇒ Object 



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# File 'app/models/operation_type.rb', line 108

def add_protocol(content:, user:)
  if protocol
    protocol.commit(content, user)
  else
    new_code('protocol', content, user)
  end
end

#add_test(content:, user:) ⇒ Object 



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# File 'app/models/operation_type.rb', line 166

def add_test(content:, user:)
  if test
    test.commit(content, user)
  else
    new_code('test', content, user)
  end
end

#category ⇒ String

Gets category of OperationType.

Returns:

  • (String) —

    the category of the OperationType, as in "Cloning"



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# File 'app/models/operation_type.rb', line 31

attr_accessible :category

#cost_model ⇒ Object 



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# File 'app/models/operation_type.rb', line 126

def cost_model
  code('cost_model')
end

#cost_model? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'app/models/operation_type.rb', line 138

def cost_model?
  !cost_model.nil? && cost_model.defined_methods.include?('cost')
end

#create_operation(status:, user_id:, x: -1,, y: -1,, parent_id: -1)) ⇒ Object 



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# File 'app/models/operation_type.rb', line 41

def create_operation(status:, user_id:, x: -1, y: -1, parent_id: -1)
  operations.create(status: status, user_id: user_id, x: x, y: y, parent_id: parent_id)
end

#documentation ⇒ Object 



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# File 'app/models/operation_type.rb', line 158

def documentation
  code('documentation')
end

#done ⇒ Object 



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# File 'app/models/operation_type.rb', line 100

def done
  operations.where(status: 'done')
end

#error_out_obsolete_operations ⇒ Object 



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# File 'app/models/operation_type.rb', line 310

def error_out_obsolete_operations
  Operation.where(operation_type_id: id, status: %w[pending scheduled]).each do |op|
    op.field_values.each do |fv|
      if !fv.field_type || !fv.allowable_field_type
        puts("ERRORING OUT OP #{op.id}")
        op.error(:obsolete, 'The operation type definition for this operation has changed too much since it was created.')
      end
    end
  end
end

#input(name) ⇒ Object

Returns the input of this OperationType with the given name.

Parameters:

  • name (String) —

    the name of the input



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# File 'app/models/operation_type.rb', line 72

def input(name)
  inputs.select { |field_type| field_type[:name] == name }.first
end

#inputs ⇒ Array<FieldType>

The input types of this OperationType.

Returns:

  • (Array<FieldType>) —

    meta definitions of the inputs that would be required to instantiate an operation of this type.



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# File 'app/models/operation_type.rb', line 65

def inputs
  field_types.select { |ft| ft.role == 'input' }
end

#name ⇒ String

Gets name of OperationType.

Returns:

  • (String) —

    the name of the OperationType, as in "Rehydrate Primer"



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# File 'app/models/operation_type.rb', line 26

attr_accessible :name

#output(name) ⇒ FieldType

Returns the output of this OperationType with the given name.

Parameters:

  • name (String) —

    the name of the input

Returns:



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# File 'app/models/operation_type.rb', line 88

def output(name)
  outputs.select { |field_type| field_type[:name] == name }.first
end

#outputs ⇒ Array<FieldType>

The output types of this OperationType.

Returns:

  • (Array<FieldType>) —

    meta definitions of the outputs that could be produced by a successful operation of this type



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# File 'app/models/operation_type.rb', line 80

def outputs
  field_types.select { |ft| ft.role == 'output' }
end

#pending ⇒ Object 



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# File 'app/models/operation_type.rb', line 96

def pending
  operations.where(status: 'pending')
end

#precondition ⇒ Object 



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# File 'app/models/operation_type.rb', line 142

def precondition
  code('precondition')
end

#precondition? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'app/models/operation_type.rb', line 154

def precondition?
  !precondition.nil? && precondition.defined_methods.include?('precondition')
end

#protocol ⇒ Object 



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# File 'app/models/operation_type.rb', line 104

def protocol
  code('protocol')
end

#protocol? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'app/models/operation_type.rb', line 116

def protocol?
  !protocol.nil? && protocol.defined_classes.include?('Protocol')
end

#stats ⇒ Object 



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# File 'app/models/operation_type.rb', line 321

def stats
  r = { 'done' => 0, 'error' => 0 }

  operations.each do |op|
    r[op.status] ||= 0
    r[op.status] = r[op.status] + 1
  end

  r['success'] = if r['done'] + r['error'] != 0
                   r['done'].to_f / (r['done'] + r['error'])
                 else
                   0.0
                 end

  unless operations.empty?
    r['first_run'] = operations[0].updated_at
    r['last_run'] = operations.last.updated_at
  end

  r
end

#test ⇒ Object 



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# File 'app/models/operation_type.rb', line 162

def test
  code('test')
end

#test? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'app/models/operation_type.rb', line 174

def test?
  !test.nil? && test.defined_classes.include?('ProtocolTest')
end

#update_allowable_field_type(old_aft, new_aft) ⇒ Object 



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# File 'app/models/operation_type.rb', line 192

def update_allowable_field_type(old_aft, new_aft)
  if new_aft[:sample_type]
    st = SampleType.find_by(name: new_aft[:sample_type][:name])
    old_aft.sample_type_id = st.id if st
  else
    old_aft.sample_type_id = nil
  end

  if new_aft[:object_type] && new_aft[:object_type][:name] != ''
    ot = ObjectType.find_by(name: new_aft[:object_type][:name])
    old_aft.object_type_id = ot.id if ot
  else
    old_aft.sample_type_id = nil
  end

  old_aft.save
end

#update_field_type(old_type:, new_type:) ⇒ Object 



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# File 'app/models/operation_type.rb', line 246

def update_field_type(old_type:, new_type:)
  keepers = []
  old_type.name = new_type[:name]

  if old_type.sample?
    old_type.routing = new_type[:routing]
    old_type.array = new_type[:array]
    old_type.part = new_type[:part]
    old_type.preferred_operation_type_id = new_type[:preferred_operation_type_id]
    old_type.preferred_field_type_id = new_type[:preferred_field_type_id]

    puts "PREF(#{old_type.name}): #{new_type[:preferred_field_type_id]}"

    if new_type[:allowable_field_types]
      new_type[:allowable_field_types].each do |newaft|
        matching_types = old_type.allowable_field_types.select { |aft| aft.id == newaft[:id] }
        if matching_types.length == 1
          oldaft = matching_types[0]
          keepers << oldaft
          update_allowable_field_type oldaft, newaft
        elsif matching_types.empty?
          keepers << add_new_allowable_field_type(old_type, newaft)
        else
          raise 'More than one allowable field type matched.'
        end
      end
    end

  else
    old_type.ftype = new_type[:ftype]
    old_type.choices = new_type[:choices]
  end

  old_type.save

  old_type.allowable_field_types.reject { |aft| keepers.include? aft }.each(&:destroy) unless keepers.empty?
end

#update_field_types(fts) ⇒ Object 



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# File 'app/models/operation_type.rb', line 284

def update_field_types(fts)
  keepers = []

  if fts
    fts.each do |new_ft|
      matching_fts = field_types.select { |field_type| field_type.id == new_ft[:id] && field_type.role == new_ft[:role] }
      if matching_fts.length == 1
        old_ft = matching_fts[0]
        keepers << old_ft
        update_field_type(old_type: old_ft, new_type: new_ft)
      elsif matching_fts.empty?
        keepers << add_new_field_type(new_ft)
      else
        raise "Multiple inputs (or outputs) named #{new_ft[:name]}"
      end
    end
  end

  field_types.reject { |ft| keepers.include? ft }.each do |ft|
    puts "DELETING FT #{ft.name}/#{ft.role}"
    ft.destroy
  end

  error_out_obsolete_operations
end

#waiting ⇒ Object 



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# File 'app/models/operation_type.rb', line 92

def waiting
  operations.where(status: 'waiting')
end