Class: Sample

Inherits:
ActiveRecord::Base
  • Object
show all
Includes:
ActionView::Helpers::DateHelper, FieldValuer, SampleValidator
Defined in:
app/models/sample.rb

Overview

A named, biologically unique definition for an instance of a SampleType, such as a specific Primer, Fragment, Plasmid, or Yeast Strain A Sample has many Items in inventory

Class Method Summary collapse

Instance Method Summary collapse

Class Method Details

.creator(raw, user) ⇒ Object

Examples:

Create a new primer

s = Sample.creator(
  {
    sample_type_id: SampleType.find_by_name("Primer").id,
    description: "This is a test",
    name: "Yet Another Primer Test",
    project: "Auxin",
    field_values: [
      { name: "Anneal Sequence", value: "ATTCTA" },
      { name: "Overhang Sequence", value: "ATCTCGAGCT" },
      { name: "T Anneal", value: 70 }
    ]
  }, User.find(1))

  s.errors.any?


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

def self.creator(raw, user)
  sample = Sample.new
  sample.user_id = user.id
  sample.sample_type_id = raw[:sample_type_id]
  sample.updater raw

  sample
end

.for_project(project:) ⇒ Object 



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# File 'app/models/sample.rb', line 240

def self.for_project(project:)
  where(project: project)
end

.okay_to_drop?(sample, user) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'app/models/sample.rb', line 207

def self.okay_to_drop?(sample, user)

  warn('Could not find sample')                                                && (return false) unless sample
  warn("Not allowed to delete sample #{sample.id}")                            && (return false) unless sample.user_id == user.id
  warn("Could not delete sample #{sample.id} because it has associated items") && (return false) unless sample.items.empty?

  true

end

.owned_by(user:) ⇒ Object 



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# File 'app/models/sample.rb', line 244

def self.owned_by(user:)
  where(user_id: user.id)
end

.sample_from_identifier(str) ⇒ Object 



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# File 'app/models/sample.rb', line 43

def self.sample_from_identifier(str)
  return unless str

  parts = str.split(': ')
  Sample.find_by(name: parts[1..-1].join(': ')) if parts.length > 1
end

.with_sample_type(sample_type:) ⇒ Object

scopes for searching Samples



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# File 'app/models/sample.rb', line 236

def self.with_sample_type(sample_type:)
  where(sample_type_id: sample_type.id)
end

Instance Method Details

#data_hash ⇒ Object 



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# File 'app/models/sample.rb', line 217

def data_hash
  JSON.parse(data, symbolize_names: true)
end

#full_json ⇒ Object 



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# File 'app/models/sample.rb', line 221

def full_json

  sample_hash = as_json(
    include: { sample_type: { include: :object_types, methods: :field_types } },
    methods: :full_field_values
  )

  # rename field for compatibility with ng-control/sample.js
  sample_hash['field_values'] = sample_hash.delete 'full_field_values'

  sample_hash

end

#in(container) ⇒ Array<Item>

Deprecated.

use Item query

Return all items of this Sample in the provided ObjectType.

Examples:

find a 1 kb ladder for gel electrophoresis

ladder_1k = Sample.find_by_name("1 kb Ladder").in("Ladder Aliquot")

Parameters:

Returns:



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# File 'app/models/sample.rb', line 159

def in(container)

  c = ObjectType.find_by name: container
  if c
    Item.with_sample(sample: this).where(object_type: c).reject(&:deleted?)
  else
    []
  end

end

#make_item(object_type_name) ⇒ Item

Make a new Item out of this sample, with some object type.

Parameters:

  • object_type_name (String) —

    describes the object type that will be used to make a new Item

Returns:

  • (Item) —

    an item associated with this sample and in the container described by object_type_name The location of the item is determined by the location wizard



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# File 'app/models/sample.rb', line 194

def make_item(object_type_name)

  ot = ObjectType.find_by(name: object_type_name)
  raise "Could not find object type #{name}" unless ot

  Item.make({ quantity: 1, inuse: 0 }, sample: self, object_type: ot)

end

#name ⇒ String

Gets the name of Sample.

Returns:

  • (String) —

    the name of the Sample. For example, a sample whose SampleType is "Plasmid" might be named "pLAB1"



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

attr_accessible :name

#num_posts ⇒ Object 



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# File 'app/models/sample.rb', line 203

def num_posts
  post_associations.count
end

#owner ⇒ User

Get User who owns this Sample.

Returns:

  • (User) 


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# File 'app/models/sample.rb', line 177

def owner
  u = User.find_by(id: user_id)
  if u
    u.
  else
    '?'
  end
end

#parent_type ⇒ Object

interface with FieldValuer



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# File 'app/models/sample.rb', line 14

def parent_type # interface with FieldValuer
  sample_type
end

#sample_type_id ⇒ Fixnum

Gets the SampleType id of sample.

Returns:

  • (Fixnum) —

    id referring to the SampleType of which this sample is an instance of



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

attr_accessible :sample_type_id

#stringify_errors(elist) ⇒ Object 



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# File 'app/models/sample.rb', line 74

def stringify_errors(elist)
  elist.full_messages.join(',')
end

#to_s ⇒ Object 



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# File 'app/models/sample.rb', line 170

def to_s
  "<a href='/samples/#{id}' class='aquarium-item' id='#{id}'>#{id}</a>"
end

#updater(raw, user = nil) ⇒ Object 



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# File 'app/models/sample.rb', line 78

def updater(raw, user = nil)
  self.name = raw[:name]
  self.description = raw[:description]
  self.project = raw[:project]

  Sample.transaction do
    save
    raise ActiveRecord::Rollback unless errors.empty?

    sample_type = SampleType.find(raw[:sample_type_id])
    if raw[:field_values]

      raw[:field_values].each do |raw_fv|

        ft = sample_type.type(raw_fv[:name])

        if ft && raw_fv[:id] && raw_fv[:deleted]

          fv = FieldValue.find_by(id: raw_fv[:id])
          fv.destroy if fv

        elsif ft && !raw_fv[:deleted] # fv might have been made and marked deleted without ever having been saved

          if raw_fv[:id]
            begin
              fv = FieldValue.find(raw_fv[:id])
            rescue ActiveRecord::RecordNotFound => e
              errors.add :missing_field_value, "Field value #{raw_fv[:id]} not found in db."
              errors.add :missing_field_value, e.to_s
              raise ActiveRecord::Rollback
            end
          else
            fv = field_values.create(name: raw_fv[:name])
          end

          if ft.sample?
            child = if raw_fv[:new_child_sample]
                      Sample.creator(raw_fv[:new_child_sample], user || User.find(user_id))
                    else
                      Sample.sample_from_identifier raw_fv[:child_sample_name]
                    end
            fv.child_sample_id = child.id if child
            fv.child_sample_id = nil if !child && raw_fv[:child_sample_name] == ''
            if !child && ft.required && raw_fv[:child_sample_name] != ''
              errors.add :required, "Sample required for field '#{ft.name}' not found or not specified."
              raise ActiveRecord::Rollback
            end
            unless !child || child.errors.empty?
              errors.add :child_error, "#{ft.name}: " + stringify_errors(child.errors)
              raise ActiveRecord::Rollback
            end
          elsif ft.number?
            fv.value = raw_fv[:value].to_f
          else # string, url
            fv.value = raw_fv[:value]
          end

          puts "before fv saved: #{fv.inspect}"
          fv.save
          puts "fv saved. now #{fv.inspect}"

          unless fv.errors.empty?
            errors.add :field_value, "Could not save field #{raw_fv[:name]}: #{stringify_errors(fv.errors)}"
            raise ActiveRecord::Rollback
          end

        end # if

      end # each

    end # if

  end
end