scinote-web/app/models/my_module.rb

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class MyModule < ActiveRecord::Base
include ArchivableModel, SearchableModel
enum state: Extends::TASKS_STATES
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before_create :create_blank_protocol
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auto_strip_attributes :name, :description, nullify: false
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validates :name,
length: { minimum: Constants::NAME_MIN_LENGTH,
maximum: Constants::NAME_MAX_LENGTH }
validates :description, length: { maximum: Constants::TEXT_MAX_LENGTH }
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validates :x, :y, :workflow_order, presence: true
validates :experiment, presence: true
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validates :my_module_group, presence: true, if: "!my_module_group_id.nil?"
belongs_to :created_by, foreign_key: 'created_by_id', class_name: 'User'
belongs_to :last_modified_by, foreign_key: 'last_modified_by_id', class_name: 'User'
belongs_to :archived_by, foreign_key: 'archived_by_id', class_name: 'User'
belongs_to :restored_by, foreign_key: 'restored_by_id', class_name: 'User'
belongs_to :experiment, inverse_of: :my_modules
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belongs_to :my_module_group, inverse_of: :my_modules
has_many :results, inverse_of: :my_module, :dependent => :destroy
has_many :my_module_tags, inverse_of: :my_module, :dependent => :destroy
has_many :tags, through: :my_module_tags
has_many :task_comments, foreign_key: :associated_id, dependent: :destroy
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has_many :inputs, :class_name => 'Connection', :foreign_key => "input_id", inverse_of: :to, :dependent => :destroy
has_many :outputs, :class_name => 'Connection', :foreign_key => "output_id", inverse_of: :from, :dependent => :destroy
has_many :my_modules, through: :outputs, source: :to
has_many :my_module_antecessors, through: :inputs, source: :from, class_name: 'MyModule'
has_many :sample_my_modules, inverse_of: :my_module, :dependent => :destroy
has_many :samples, through: :sample_my_modules
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has_many :my_module_repository_rows,
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inverse_of: :my_module, dependent: :destroy
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has_many :repository_rows, through: :my_module_repository_rows
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has_many :user_my_modules, inverse_of: :my_module, :dependent => :destroy
has_many :users, through: :user_my_modules
has_many :activities, inverse_of: :my_module
has_many :report_elements, inverse_of: :my_module, :dependent => :destroy
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has_many :protocols, inverse_of: :my_module, dependent: :destroy
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scope :is_archived, ->(is_archived) { where('archived = ?', is_archived) }
# A module takes this much space in canvas (x, y) in database
WIDTH = 30
HEIGHT = 14
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def self.search(
user,
include_archived,
query = nil,
page = 1,
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current_team = nil,
options = {}
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)
exp_ids =
Experiment
.search(user, include_archived, nil, Constants::SEARCH_NO_LIMIT)
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.pluck(:id)
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if current_team
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experiments_ids = Experiment
.search(user,
include_archived,
nil,
1,
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current_team)
.select('id')
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new_query = MyModule
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.distinct
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.where('my_modules.experiment_id IN (?)', experiments_ids)
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.where_attributes_like([:name, :description], query, options)
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if include_archived
return new_query
else
return new_query.where('my_modules.archived = ?', false)
end
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elsif include_archived
new_query = MyModule
.distinct
.where('my_modules.experiment_id IN (?)', exp_ids)
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.where_attributes_like([:name, :description], query, options)
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else
new_query = MyModule
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.distinct
.where('my_modules.experiment_id IN (?)', exp_ids)
.where('my_modules.archived = ?', false)
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.where_attributes_like([:name, :description], query, options)
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end
# Show all results if needed
if page == Constants::SEARCH_NO_LIMIT
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new_query
else
new_query
.limit(Constants::SEARCH_LIMIT)
.offset((page - 1) * Constants::SEARCH_LIMIT)
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end
end
# Removes assigned samples from module and connections with other
# modules.
def archive (current_user)
self.x = 0
self.y = 0
# Remove association with module group.
self.my_module_group = nil
MyModule.transaction do
archived = super
# Unassociate all samples from module.
archived = SampleMyModule.destroy_all(:my_module => self) if archived
# Remove all connection between modules.
archived = Connection.delete_all(:input_id => id) if archived
archived = Connection.delete_all(:output_id => id) if archived
unless archived
raise ActiveRecord::Rollback
end
end
archived
end
# Similar as super restore, but also calculate new module position
def restore(current_user)
restored = false
# Calculate new module position
new_pos = get_new_position
self.x = new_pos[:x]
self.y = new_pos[:y]
MyModule.transaction do
restored = super
unless restored
raise ActiveRecord::Rollback
end
end
experiment.delay.generate_workflow_img
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restored
end
def unassigned_users
User.find_by_sql(
"SELECT DISTINCT users.id, users.full_name FROM users " +
"INNER JOIN user_projects ON users.id = user_projects.user_id " +
"INNER JOIN experiments ON experiments.project_id = user_projects.project_id " +
"WHERE experiments.id = #{experiment_id.to_s}" +
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" AND users.id NOT IN " +
"(SELECT DISTINCT user_id FROM user_my_modules WHERE user_my_modules.my_module_id = #{id.to_s})"
)
end
def unassigned_samples
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Sample.where(team_id: experiment.project.team).where.not(id: samples)
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end
def unassigned_tags
Tag.find_by_sql(
"SELECT DISTINCT tags.id, tags.name, tags.color FROM tags " +
"INNER JOIN experiments ON experiments.project_id = tags.project_id " +
"WHERE experiments.id = #{experiment_id.to_s} AND tags.id NOT IN " +
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"(SELECT DISTINCT tag_id FROM my_module_tags WHERE my_module_tags.my_module_id = #{id.to_s})"
)
end
def last_activities(count = Constants::ACTIVITY_AND_NOTIF_SEARCH_LIMIT)
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Activity.where(my_module_id: id).order(:created_at).last(count)
end
# Get module comments ordered by created_at time. Results are paginated
# using last comment id and per_page parameters.
def last_comments(last_id = 1, per_page = Constants::COMMENTS_SEARCH_LIMIT)
last_id = Constants::INFINITY if last_id <= 1
comments = TaskComment.joins(:my_module)
.where(my_modules: { id: id })
.where('comments.id < ?', last_id)
.order(created_at: :desc)
.limit(per_page)
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comments.reverse
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end
def last_activities(last_id = 1,
count = Constants::ACTIVITY_AND_NOTIF_SEARCH_LIMIT)
last_id = Constants::INFINITY if last_id <= 1
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Activity.joins(:my_module)
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.where(my_module_id: id)
.where('activities.id < ?', last_id)
.order(created_at: :desc)
.limit(count)
.uniq
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end
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def protocol
# Temporary function (until we fully support
# multiple protocols per module)
protocols.count > 0 ? protocols.first : nil
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end
def first_n_samples(count = Constants::SEARCH_LIMIT)
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samples.order(name: :asc).limit(count)
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end
def number_of_samples
samples.count
end
def is_overdue?(datetime = DateTime.current)
due_date.present? and datetime.utc > due_date.utc
end
def overdue_for_days(datetime = DateTime.current)
if due_date.blank? or due_date.utc > datetime.utc
return 0
else
return ((datetime.utc.to_i - due_date.utc.to_i) / (60*60*24).to_f).ceil
end
end
def is_one_day_prior?(datetime = DateTime.current)
is_due_in?(datetime, 1.day)
end
def is_due_in?(datetime, diff)
due_date.present? and datetime.utc < due_date.utc and datetime.utc > (due_date.utc - diff)
end
def space_taken
st = 0
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protocol.steps.find_each do |step|
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st += step.space_taken
end
results
.includes(:result_asset)
.find_each do |result|
st += result.space_taken
end
st
end
def archived_results
results
.select('results.*')
.select('ra.id AS result_asset_id')
.select('rt.id AS result_table_id')
.select('rx.id AS result_text_id')
.joins('LEFT JOIN result_assets AS ra ON ra.result_id = results.id')
.joins('LEFT JOIN result_tables AS rt ON rt.result_id = results.id')
.joins('LEFT JOIN result_texts AS rx ON rx.result_id = results.id')
.where(:archived => true)
end
# Treat this module as root, get all modules of that subtree
def get_downstream_modules
final = []
modules = [self]
while !modules.empty?
my_module = modules.shift
if !final.include?(my_module)
final << my_module
end
modules.push(*my_module.my_modules.flatten)
end
final
end
# Treat this module as inversed root, get all modules of that inversed subtree
def get_upstream_modules
final = []
modules = [self]
while !modules.empty?
my_module = modules.shift
if !final.include?(my_module)
final << my_module
end
modules.push(*my_module.my_module_antecessors.flatten)
end
final
end
# Generate the samples belonging to this module
# in JSON form, suitable for display in handsontable.js
def samples_json_hot(order)
data = []
samples.order(created_at: order).each do |sample|
sample_json = []
sample_json << sample.name
if sample.sample_type.present?
sample_json << sample.sample_type.name
else
sample_json << I18n.t("samples.table.no_type")
end
if sample.sample_group.present?
sample_json << sample.sample_group.name
else
sample_json << I18n.t("samples.table.no_group")
end
sample_json << I18n.l(sample.created_at, format: :full)
sample_json << sample.user.full_name
data << sample_json
end
# Prepare column headers
headers = [
I18n.t("samples.table.sample_name"),
I18n.t("samples.table.sample_type"),
I18n.t("samples.table.sample_group"),
I18n.t("samples.table.added_on"),
I18n.t("samples.table.added_by")
]
{ data: data, headers: headers }
end
# Generate the repository rows belonging to this module
# in JSON form, suitable for display in handsontable.js
def repository_json_hot(repository_id, order)
data = []
repository_rows
.where(repository_id: repository_id)
.order(created_at: order).find_each do |row|
row_json = []
row_json << row.name
row_json << I18n.l(row.created_at, format: :full)
row_json << row.created_by.full_name
data << row_json
end
# Prepare column headers
headers = [
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I18n.t('repositories.table.row_name'),
I18n.t('repositories.table.added_on'),
I18n.t('repositories.table.added_by')
]
{ data: data, headers: headers }
end
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def deep_clone(current_user)
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deep_clone_to_experiment(current_user, experiment)
end
def deep_clone_to_experiment(current_user, experiment)
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# Copy the module
clone = MyModule.new(
name: self.name,
experiment: experiment,
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description: self.description,
x: self.x,
y: self.y)
clone.save
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# Remove the automatically generated protocol,
# & clone the protocol instead
clone.protocol.destroy
clone.reload
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# Update the cloned protocol if neccesary
clone.protocols << self.protocol.deep_clone_my_module(self, current_user)
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clone.reload
# fixes linked protocols
clone.protocols.each do |protocol|
next unless protocol.linked?
protocol.updated_at = protocol.parent_updated_at
protocol.save
end
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return clone
end
# Find an empty position for the restored module. It's
# basically a first empty row with empty space inside x=[0, 32).
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def get_new_position
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return { x: 0, y: 0 } if experiment.blank?
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# Get all modules position that overlap with first column, [0, WIDTH) and
# sort them by y coordinate.
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positions = experiment.active_modules.collect { |m| [m.x, m.y] }
.select { |x, _| x >= 0 && x < WIDTH }
.sort_by { |_, y| y }
return { x: 0, y: 0 } if positions.empty? || positions.first[1] >= HEIGHT
# It looks we'll have to find a gap between the modules if it exists (at
# least 2*HEIGHT wide
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ind = positions.each_cons(2).map { |f, s| s[1] - f[1] }
.index { |y| y >= 2 * HEIGHT }
return { x: 0, y: positions[ind][1] + HEIGHT } if ind
# We lucked out, no gaps, therefore we need to add it after the last element
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{ x: 0, y: positions.last[1] + HEIGHT }
end
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def completed?
state == 'completed'
end
# Check if my_module is ready to become completed
def check_completness_status
if protocol && protocol.steps.count > 0
completed = true
protocol.steps.find_each do |step|
completed = false unless step.completed
end
return true if completed
end
false
end
def complete
self.state = 'completed'
self.completed_on = DateTime.now
end
def uncomplete
self.state = 'uncompleted'
self.completed_on = nil
end
private
def create_blank_protocol
protocols << Protocol.new_blank_for_module(self)
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end
end