mirror of
https://github.com/scinote-eln/scinote-web.git
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631 lines
20 KiB
Ruby
631 lines
20 KiB
Ruby
class Experiment < ApplicationRecord
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include ArchivableModel
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include SearchableModel
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include SearchableByNameModel
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belongs_to :project, inverse_of: :experiments, touch: true
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belongs_to :created_by,
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foreign_key: :created_by_id,
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class_name: 'User'
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belongs_to :last_modified_by,
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foreign_key: :last_modified_by_id,
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class_name: 'User'
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belongs_to :archived_by,
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foreign_key: :archived_by_id, class_name: 'User', optional: true
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belongs_to :restored_by,
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foreign_key: :restored_by_id,
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class_name: 'User',
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optional: true
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has_many :my_modules, inverse_of: :experiment, dependent: :destroy
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has_many :active_my_modules,
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-> { where(archived: false).order(:name) },
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class_name: 'MyModule'
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has_many :my_module_groups, inverse_of: :experiment, dependent: :destroy
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has_many :report_elements, inverse_of: :experiment, dependent: :destroy
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# Associations for old activity type
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has_many :activities, inverse_of: :experiment
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has_one_attached :workflowimg
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auto_strip_attributes :name, :description, nullify: false
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validates :name,
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length: { minimum: Constants::NAME_MIN_LENGTH,
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maximum: Constants::NAME_MAX_LENGTH },
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uniqueness: { scope: :project, case_sensitive: false }
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validates :description, length: { maximum: Constants::TEXT_MAX_LENGTH }
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validates :project, presence: true
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validates :created_by, presence: true
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validates :last_modified_by, presence: true
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validates :uuid, uniqueness: { scope: :project },
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unless: proc { |e| e.uuid.blank? }
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with_options if: :archived do |experiment|
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experiment.validates :archived_by, presence: true
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experiment.validates :archived_on, presence: true
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end
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scope :is_archived, ->(is_archived) { where("archived = ?", is_archived) }
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def self.search(
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user,
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include_archived,
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query = nil,
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page = 1,
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current_team = nil,
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options = {}
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)
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project_ids =
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Project
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.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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projects_ids =
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Project
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.search(user,
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include_archived,
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nil,
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1,
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current_team)
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.select('id')
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new_query =
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Experiment
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.where('experiments.project_id IN (?)', projects_ids)
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.where_attributes_like([:name, :description], query, options)
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return include_archived ? new_query : new_query.is_archived(false)
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elsif include_archived
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new_query =
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Experiment
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.where(project: project_ids)
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.where_attributes_like([:name, :description], query, options)
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else
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new_query =
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Experiment
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.is_archived(false)
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.where(project: project_ids)
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.where_attributes_like([:name, :description], query, options)
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end
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# Show all results if needed
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if page == Constants::SEARCH_NO_LIMIT
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new_query
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else
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new_query
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.limit(Constants::SEARCH_LIMIT)
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.offset((page - 1) * Constants::SEARCH_LIMIT)
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end
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end
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def self.viewable_by_user(user, teams)
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where(project: Project.viewable_by_user(user, teams))
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end
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def navigable?
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!project.archived?
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end
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def active_modules
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my_modules.where(archived: false)
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end
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def archived_modules
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my_modules.where(archived: true)
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end
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def assigned_samples
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Sample.joins(:my_modules).where(my_modules: { id: my_modules })
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end
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def unassigned_samples(assigned_samples)
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Sample.where(team_id: team).where.not(id: assigned_samples)
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end
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def update_canvas(
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to_archive,
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to_add,
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to_rename,
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to_move,
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to_move_groups,
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to_clone,
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connections,
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positions,
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current_user
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)
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begin
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with_lock do
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# Start with archiving to release positions for new tasks
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archive_modules(to_archive, current_user) if to_archive.any?
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# Update only existing tasks positions to release positions for new tasks
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existing_positions = positions
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.slice(*positions.keys.map { |k| k unless k.to_s.start_with?('n') }.compact)
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update_module_positions(existing_positions) if existing_positions.any?
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# Move only existing tasks to release positions for new tasks
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existing_to_move = to_move
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.slice(*to_move.keys.map { |k| k unless k.to_s.start_with?('n') }.compact)
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move_modules(existing_to_move, current_user) if existing_to_move.any?
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# add new modules
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new_ids, cloned_pairs, originals = add_modules(
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to_add, to_clone, current_user
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)
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# Rename modules
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rename_modules(to_rename, current_user)
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# Add activities that modules were created
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originals.each do |my_module|
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log_activity(:create_module, current_user, my_module)
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end
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# Add activities that modules were cloned
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cloned_pairs.each do |mn, mo|
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Activities::CreateActivityService
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.call(activity_type: :clone_module,
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owner: current_user,
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team: project.team,
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project: mn.experiment.project,
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subject: mn,
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message_items: { my_module_original: mo.id,
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my_module_new: mn.id })
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end
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# Update connections, positions & module group variables
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# with actual IDs retrieved from the new modules creation
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updated_to_move = {}
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to_move.each do |id, value|
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updated_to_move[new_ids.fetch(id, id)] = value
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end
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updated_to_move_groups = {}
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to_move_groups.each do |ids, value|
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mapped = []
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ids.each do |id|
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mapped << new_ids.fetch(id, id)
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end
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updated_to_move_groups[mapped] = value
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end
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updated_connections = []
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connections.each do |a, b|
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updated_connections << [new_ids.fetch(a, a), new_ids.fetch(b, b)]
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end
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updated_positions = {}
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positions.each do |id, pos|
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updated_positions[new_ids.fetch(id, id)] = pos
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end
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# Update connections
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update_module_connections(updated_connections)
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# Update module positions (no validation needed here)
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update_module_positions(updated_positions)
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# Normalize module positions
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normalize_module_positions
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# Finally, update module groups
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update_module_groups(current_user)
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# Finally move any modules to another experiment
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move_modules(updated_to_move, current_user)
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# Everyhing is set, now we can move any module groups
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move_module_groups(updated_to_move_groups, current_user)
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end
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rescue ActiveRecord::ActiveRecordError,
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ArgumentError,
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ActiveRecord::RecordNotSaved => ex
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logger.error ex.message
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return false
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end
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true
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end
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def generate_workflow_img
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workflowimg.purge if workflowimg.attached?
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Experiments::GenerateWorkflowImageService.delay.call(experiment_id: id)
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end
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def workflowimg_exists?
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workflowimg.service.exist?(workflowimg.blob.key)
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end
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# Get projects where user is either owner or user in the same team
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# as this experiment
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def projects_with_role_above_user(current_user)
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team = project.team
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projects = team.projects.where(archived: false)
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current_user.user_projects
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.where(project: projects)
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.where('role < 2')
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.map(&:project)
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end
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# Projects to which this experiment can be moved (inside the same
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# team and not archived), all users assigned on experiment.project has
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# to be assigned on such project
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def moveable_projects(current_user)
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projects = projects_with_role_above_user(current_user)
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projects = projects.each_with_object([]) do |p, arr|
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arr << p if (project.users - p.users).empty?
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arr
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end
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projects - [project]
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end
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private
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# Archive all modules. Receives an array of module integer IDs.
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def archive_modules(module_ids)
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my_modules.where(id: module_ids).each(&:archive!)
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my_modules.reload
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end
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# Archive all modules. Receives an array of module integer IDs
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# and current user.
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def archive_modules(module_ids, current_user)
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my_modules.where(id: module_ids).each do |my_module|
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my_module.archive!(current_user)
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log_activity(:archive_module, current_user, my_module)
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end
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my_modules.reload
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end
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# Add modules, and returns a map of "virtual" IDs with
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# actual IDs of saved modules.
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# to_add is an array of hashes, each containing 'name',
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# 'x', 'y' and 'id'.
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# to_clone is a hash, storing new cloned modules as keys,
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# and original modules as values.
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def add_modules(to_add, to_clone, current_user)
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originals = []
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cloned_pairs = {}
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ids_map = {}
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to_add.each do |m|
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original = MyModule.find_by_id(to_clone.fetch(m[:id], nil)) if to_clone.present?
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if original.present?
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my_module = original.deep_clone(current_user)
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cloned_pairs[my_module] = original
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else
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my_module = MyModule.new(experiment: self)
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originals << my_module
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end
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my_module.name = m[:name]
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my_module.x = m[:x]
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my_module.y = m[:y]
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my_module.created_by = current_user
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my_module.last_modified_by = current_user
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my_module.save!
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my_module.assign_user(current_user)
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ids_map[m[:id]] = my_module.id.to_s
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end
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my_modules.reload
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return ids_map, cloned_pairs, originals
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end
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# Rename modules; this method accepts a map where keys
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# represent IDs of modules, and values new names for
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# such modules. If a module with given ID doesn't exist,
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# it's obviously not updated.
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def rename_modules(to_rename, current_user)
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to_rename.each do |id, new_name|
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my_module = MyModule.find_by_id(id)
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if my_module.present?
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my_module.name = new_name
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my_module.save!
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log_activity(:rename_task, current_user, my_module)
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end
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end
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end
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# Move modules; this method accepts a map where keys
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# represent IDs of modules, and values represent experiment
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# IDs of new names to which the given modules should be moved.
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# If a module with given ID doesn't exist (or experiment ID)
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# it's obviously not updated. Any connection on module is destroyed.
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def move_modules(to_move, current_user)
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to_move.each do |id, experiment_id|
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my_module = my_modules.find_by_id(id)
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experiment = project.experiments.find_by_id(experiment_id)
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next unless my_module.present? && experiment.present?
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experiment_original = my_module.experiment
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my_module.experiment = experiment
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# Calculate new module position
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new_pos = my_module.get_new_position
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my_module.x = new_pos[:x]
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my_module.y = new_pos[:y]
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unless my_module.outputs.destroy_all && my_module.inputs.destroy_all
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raise ActiveRecord::ActiveRecordError
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end
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next unless my_module.save
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Activities::CreateActivityService.call(activity_type: :move_task,
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owner: current_user,
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subject: my_module,
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project: project,
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team: project.team,
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message_items: {
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my_module: my_module.id,
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experiment_original:
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experiment_original.id,
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experiment_new: experiment.id
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})
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end
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# Generate workflow image for the experiment in which we moved the task
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generate_workflow_img_for_moved_modules(to_move)
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end
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# Move module groups; this method accepts a map where keys
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# represent IDs of modules which are in module group,
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# and values represent experiment
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# IDs of new names to which the given module group should be moved.
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# If a module with given ID doesn't exist (or experiment ID)
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# it's obviously not updated. Position for entire module group is updated
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# to bottom left corner.
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def move_module_groups(to_move, current_user)
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to_move.each do |ids, experiment_id|
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modules = my_modules.find(ids)
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groups = Set.new(modules.map(&:my_module_group))
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experiment = project.experiments.find_by_id(experiment_id)
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groups.each do |group|
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next unless group && experiment.present?
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# Find the lowest point for current modules(max_y) and the leftmost
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# module(min_x)
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if experiment.active_modules.empty?
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max_y = 0
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min_x = 0
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else
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max_y = experiment.active_modules.maximum(:y) + MyModule::HEIGHT
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min_x = experiment.active_modules.minimum(:x)
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end
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# Set new positions
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curr_min_x = modules.min_by(&:x).x
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curr_min_y = modules.min_by(&:y).y
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modules.each { |m| m.x += -curr_min_x + min_x }
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modules.each { |m| m.y += -curr_min_y + max_y }
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modules.each do |m|
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experiment_org = m.experiment
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m.experiment = experiment
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m.save!
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# Add activity
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Activities::CreateActivityService.call(
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activity_type: :move_task,
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owner: current_user,
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subject: m,
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project: experiment.project,
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team: experiment.project.team,
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message_items: {
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my_module: m.id,
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experiment_original: experiment_org.id,
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experiment_new: experiment.id
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}
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)
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end
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group.experiment = experiment
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group.save!
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end
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end
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# Generate workflow image for the experiment in which we moved the workflow
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generate_workflow_img_for_moved_modules(to_move)
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end
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# Generates workflow img when the workflow or module is moved
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# to other experiment
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def generate_workflow_img_for_moved_modules(to_move)
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Experiment.where(id: to_move.values.uniq).each do |exp|
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exp.generate_workflow_img
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end
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end
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# Update connections for all modules in this project.
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# Input is an array of arrays, where first element represents
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# source node, and second element represents target node.
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# Example input: [ [1, 2], [2, 3], [4, 5], [2, 5] ]
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def update_module_connections(connections)
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require 'rgl/base'
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require 'rgl/adjacency'
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require 'rgl/topsort'
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dg = RGL::DirectedAdjacencyGraph.new
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connections.each do |a, b|
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# Check if both vertices exist
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if (my_modules.find_all { |m| [a.to_i, b.to_i].include? m.id }).count == 2
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dg.add_edge(a, b)
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end
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end
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# Check if cycles exist!
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topsort = dg.topsort_iterator.to_a
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if topsort.length.zero? && dg.edges.size > 1
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raise ArgumentError, 'Cycles exist.'
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end
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# First, delete existing connections
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# but keep a copy of previous state
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previous_sources = {}
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previous_sources.default = []
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my_modules.includes(inputs: { from: [:inputs, outputs: :to] }).each do |m|
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previous_sources[m.id] = []
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m.inputs.each do |c|
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previous_sources[m.id] << c.from
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end
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end
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# There are no callbacks in Connection, so delete_all should be safe
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Connection.where(output_id: my_modules).delete_all
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# Add new connections
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filtered_edges = dg.edges.collect { |e| [e.source, e.target] }
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filtered_edges.each do |a, b|
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Connection.create!(input_id: b, output_id: a)
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end
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# Unassign samples from former downstream modules
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# for all destroyed connections
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unassign_samples_from_old_downstream_modules(previous_sources)
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visited = []
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# Assign samples to all new downstream modules
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filtered_edges.each do |a, b|
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source = my_modules.includes({ inputs: :from }, :samples).find(a.to_i)
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target = my_modules.find(b.to_i)
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# Do this only for new edges
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next unless previous_sources[target.id].exclude?(source)
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# Go as high upstream as new edges take us
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# and then assign samples to all downsteam samples
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assign_samples_to_new_downstream_modules(previous_sources,
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visited,
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source)
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end
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# Save topological order of modules (for modules without workflow,
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# leave them unordered)
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my_modules.includes(:my_module_group).each do |m|
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m.workflow_order =
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if topsort.include? m.id.to_s
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topsort.find_index(m.id.to_s)
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else
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-1
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end
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m.save!
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end
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# Make sure to reload my modules, which now have updated connections
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# and samples
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my_modules.reload
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true
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end
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|
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# When connections are deleted, unassign samples that
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# are not inherited anymore
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def unassign_samples_from_old_downstream_modules(sources)
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my_modules.each do |my_module|
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sources[my_module.id].each do |src|
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# Only do this for newly deleted connections
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next unless src.outputs.map(&:to).exclude? my_module
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|
my_module.downstream_modules.each do |dm|
|
|
# Get unique samples for all upstream modules
|
|
um = dm.upstream_modules
|
|
um.shift # remove current module
|
|
ums = um.map(&:samples).flatten.uniq
|
|
src.samples.find_each do |sample|
|
|
dm.samples.destroy(sample) if ums.exclude? sample
|
|
end
|
|
end
|
|
end
|
|
end
|
|
end
|
|
|
|
# Assign samples to new connections recursively
|
|
def assign_samples_to_new_downstream_modules(sources, visited, my_module)
|
|
# If samples are already assigned for this module, stop going upstream
|
|
return if visited.include?(my_module)
|
|
visited << my_module
|
|
# Edge case, when module is source or it doesn't have any new input
|
|
# connections
|
|
if my_module.inputs.blank? ||
|
|
(my_module.inputs.map(&:from) - sources[my_module.id]).empty?
|
|
my_module.downstream_modules.each do |dm|
|
|
new_samples = my_module.samples.where.not(id: dm.samples)
|
|
dm.samples << new_samples
|
|
end
|
|
else
|
|
my_module.inputs.each do |input|
|
|
# Go upstream for new in connections
|
|
if sources[my_module.id].exclude?(input.from)
|
|
assign_samples_to_new_downstream_modules(sources, visited, input.from)
|
|
end
|
|
end
|
|
end
|
|
end
|
|
|
|
# Updates positions of modules.
|
|
# Input is a map where keys are module IDs, and values are
|
|
# hashes like { x: <x>, y: <y> }.
|
|
def update_module_positions(positions)
|
|
modules = my_modules.where(id: positions.keys)
|
|
modules.each do |m|
|
|
m.update_columns(x: positions[m.id.to_s][:x], y: positions[m.id.to_s][:y])
|
|
end
|
|
my_modules.reload
|
|
end
|
|
|
|
# Normalize module positions in this project.
|
|
def normalize_module_positions
|
|
# This method normalizes module positions so x-s and y-s
|
|
# are all positive
|
|
x_diff = my_modules.pluck(:x).min
|
|
y_diff = my_modules.pluck(:y).min
|
|
|
|
my_modules.each do |m|
|
|
m.update_columns(x: m.x - x_diff, y: m.y - y_diff)
|
|
end
|
|
end
|
|
|
|
# Recalculate module groups in this project. Input is
|
|
# a hash of module ids and their corresponding module names.
|
|
def update_module_groups(current_user)
|
|
require 'rgl/base'
|
|
require 'rgl/adjacency'
|
|
require 'rgl/connected_components'
|
|
|
|
dg = RGL::DirectedAdjacencyGraph[]
|
|
group_ids = Set.new
|
|
active_modules.includes(:my_module_group, outputs: :to).each do |m|
|
|
group_ids << m.my_module_group.id unless m.my_module_group.blank?
|
|
dg.add_vertex m.id unless dg.has_vertex? m.id
|
|
m.outputs.each do |o|
|
|
dg.add_edge m.id, o.to.id
|
|
end
|
|
end
|
|
workflows = []
|
|
dg.to_undirected.each_connected_component do |w|
|
|
workflows << my_modules.find(w)
|
|
end
|
|
|
|
# Remove any existing module groups from modules
|
|
unless MyModuleGroup.where(id: group_ids.to_a).destroy_all
|
|
raise ActiveRecord::ActiveRecordError
|
|
end
|
|
|
|
# Second, create new groups
|
|
workflows.each do |modules|
|
|
# Single modules are not considered part of any workflow
|
|
next unless modules.length > 1
|
|
MyModuleGroup.create!(experiment: self,
|
|
my_modules: modules,
|
|
created_by: current_user)
|
|
end
|
|
|
|
my_module_groups.reload
|
|
true
|
|
end
|
|
|
|
def log_activity(type_of, current_user, my_module)
|
|
Activities::CreateActivityService
|
|
.call(activity_type: type_of,
|
|
owner: current_user,
|
|
team: my_module.experiment.project.team,
|
|
project: my_module.experiment.project,
|
|
subject: my_module,
|
|
message_items: { my_module: my_module.id })
|
|
end
|
|
end
|