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Merge pull request #32 from ZmagoD/zd_SCI_31

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Fixing modules after integrating experiment-level
This commit is contained in:
Zmago Devetak 2016-07-26 09:18:16 +02:00 • committed by GitHub
commit b13747291e
9 changed files with 563 additions and 503 deletions
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163
app/helpers/permission_helper.rb
View file

@ -122,7 +122,9 @@ module PermissionHelper
] do |proxy, *args, &block|
if args[0]
my_module = args[0]
if my_module.active? and my_module.project.active?
if my_module.active? &&
my_module.experiment.project.active? &&
my_module.experiment.active?
proxy.call(*args, &block)
else
false
@ -334,11 +336,11 @@ module PermissionHelper
end
def can_view_module(my_module)
can_view_project(my_module.project)
can_view_project(my_module.experiment.project)
end
def can_edit_module(my_module)
is_user_or_higher_of_project(my_module.project)
is_user_or_higher_of_project(my_module.experiment.project)
end
def can_archive_module(my_module)
@ -350,7 +352,7 @@ module PermissionHelper
end
def can_edit_tags_for_module(my_module)
is_user_or_higher_of_project(my_module.project)
is_user_or_higher_of_project(my_module.experiment.project)
end
def can_add_tag_to_module(my_module)
@ -362,23 +364,23 @@ module PermissionHelper
end
def can_view_module_info(my_module)
can_view_project(my_module.project)
can_view_project(my_module.experiment.project)
end
def can_view_module_users(my_module)
can_view_project(my_module.project)
can_view_project(my_module.experiment.project)
end
def can_edit_users_on_module(my_module)
is_owner_of_project(my_module.project)
is_owner_of_project(my_module.experiment.project)
end
def can_add_user_to_module(my_module)
is_owner_of_project(my_module.project)
is_owner_of_project(my_module.experiment.project)
end
def can_remove_user_from_module(my_module)
is_owner_of_project(my_module.project)
is_owner_of_project(my_module.experiment.project)
end
def can_view_module_protocols(my_module)
@ -386,84 +388,84 @@ module PermissionHelper
end
def can_view_module_activities(my_module)
is_member_of_project(my_module.project)
is_member_of_project(my_module.experiment.project)
end
def can_view_module_comments(my_module)
can_view_project(my_module.project)
can_view_project(my_module.experiment.project)
end
def can_add_comment_to_module(my_module)
is_technician_or_higher_of_project(my_module.project)
is_technician_or_higher_of_project(my_module.experiment.project)
end
def can_view_module_samples(my_module)
can_view_module(my_module) and
can_view_samples(my_module.project.organization)
can_view_samples(my_module.experiment.project.organization)
end
def can_view_module_archive(my_module)
is_user_or_higher_of_project(my_module.project)
is_user_or_higher_of_project(my_module.experiment.project)
end
# ---- RESULTS PERMISSIONS ----
def can_view_results_in_module(my_module)
can_view_project(my_module.project)
can_view_project(my_module.experiment.project)
end
def can_view_or_download_result_assets(my_module)
is_member_of_project(my_module.project) || can_view_project(my_module.project)
is_member_of_project(my_module.experiment.project) || can_view_project(my_module.experiment.project)
end
def can_view_result_comments(my_module)
can_view_project(my_module.project)
can_view_project(my_module.experiment.project)
end
def can_add_result_comment_in_module(my_module)
is_technician_or_higher_of_project(my_module.project)
is_technician_or_higher_of_project(my_module.experiment.project)
end
# ---- RESULT TEXT PERMISSIONS ----
def can_create_result_text_in_module(my_module)
is_user_or_higher_of_project(my_module.project)
is_user_or_higher_of_project(my_module.experiment.project)
end
def can_edit_result_text_in_module(my_module)
is_user_or_higher_of_project(my_module.project)
is_user_or_higher_of_project(my_module.experiment.project)
end
def can_archive_result_text_in_module(my_module)
is_owner_of_project(my_module.project)
is_owner_of_project(my_module.experiment.project)
end
# ---- RESULT TABLE PERMISSIONS ----
def can_create_result_table_in_module(my_module)
is_user_or_higher_of_project(my_module.project)
is_user_or_higher_of_project(my_module.experiment.project)
end
def can_edit_result_table_in_module(my_module)
is_user_or_higher_of_project(my_module.project)
is_user_or_higher_of_project(my_module.experiment.project)
end
def can_archive_result_table_in_module(my_module)
is_owner_of_project(my_module.project)
is_owner_of_project(my_module.experiment.project)
end
# ---- RESULT ASSET PERMISSIONS ----
def can_create_result_asset_in_module(my_module)
is_user_or_higher_of_project(my_module.project)
is_user_or_higher_of_project(my_module.experiment.project)
end
def can_edit_result_asset_in_module(my_module)
is_user_or_higher_of_project(my_module.project)
is_user_or_higher_of_project(my_module.experiment.project)
end
def can_archive_result_asset_in_module(my_module)
is_owner_of_project(my_module.project)
is_owner_of_project(my_module.experiment.project)
end
# ---- REPORTS PERMISSIONS ----
@ -507,11 +509,11 @@ module PermissionHelper
end
def can_add_samples_to_module(my_module)
is_technician_or_higher_of_project(my_module.project)
is_technician_or_higher_of_project(my_module.experiment.project)
end
def can_delete_samples_from_module(my_module)
is_technician_or_higher_of_project(my_module.project)
is_technician_or_higher_of_project(my_module.experiment.project)
end
# ---- SAMPLE TYPES PERMISSIONS ----
@ -562,7 +564,10 @@ module PermissionHelper
protocol.added_by == current_user
elsif protocol.in_module?
my_module = protocol.my_module
my_module.active? and my_module.project.active? and can_view_module(my_module)
my_module.active? &&
my_module.experiment.project.active? &&
can_view_module(my_module) &&
my_module.experiment.active?
else
false
end
@ -610,7 +615,10 @@ module PermissionHelper
def can_unlink_protocol(protocol)
if protocol.linked?
my_module = protocol.my_module
my_module.active? and my_module.project.active? and is_user_or_higher_of_project(my_module.project)
my_module.active? &&
my_module.project.active? &&
is_user_or_higher_of_project(my_module.project) &&
my_module.experiment.active?
else
false
end
@ -619,7 +627,10 @@ module PermissionHelper
def can_revert_protocol(protocol)
if protocol.linked?
my_module = protocol.my_module
my_module.active? and my_module.project.active? and is_user_or_higher_of_project(my_module.project)
my_module.active? &&
my_module.experiment.project.active? &&
is_user_or_higher_of_project(my_module.experiment.project) &&
my_module.experiment.active?
else
false
end
@ -628,7 +639,10 @@ module PermissionHelper
def can_update_protocol_from_parent(protocol)
if protocol.linked?
my_module = protocol.my_module
my_module.active? and my_module.project.active? and is_user_or_higher_of_project(my_module.project)
my_module.active? &&
my_module.experiment.project.active? &&
is_user_or_higher_of_project(my_module.experiment.project) &&
my_module.experiment.active?
else
false
end
@ -637,7 +651,10 @@ module PermissionHelper
def can_load_protocol_from_repository(protocol, source)
if can_view_protocol(source)
my_module = protocol.my_module
my_module.active? and my_module.project.active? and is_user_or_higher_of_project(my_module.project)
my_module.active? &&
my_module.experiment.project.active? &&
is_user_or_higher_of_project(my_module.experiment.project) &&
my_module.experiment.active?
else
false
end
@ -648,11 +665,12 @@ module PermissionHelper
my_module = protocol.my_module
parent = protocol.parent
my_module.active? and
my_module.project.active? and
is_normal_user_or_admin_of_organization(parent.organization) and
is_user_or_higher_of_project(my_module.project) and
(parent.in_repository_public? or parent.in_repository_private?) and
my_module.active? &&
my_module.experiment.project.active? &&
my_module.experiment.active? &&
is_normal_user_or_admin_of_organization(parent.organization) &&
is_user_or_higher_of_project(my_module.experiment.project) &&
(parent.in_repository_public? or parent.in_repository_private?) &&
parent.added_by == current_user
else
false
@ -662,7 +680,7 @@ module PermissionHelper
# ---- STEPS PERMISSIONS ----
def can_load_protocol_into_module(my_module)
is_user_or_higher_of_project(my_module.project)
is_user_or_higher_of_project(my_module.experiment.project)
end
def can_export_protocol_from_module(my_module)
@ -670,18 +688,21 @@ module PermissionHelper
end
def can_copy_protocol_to_repository(my_module)
is_normal_user_or_admin_of_organization(my_module.project.organization)
is_normal_user_or_admin_of_organization(my_module.experiment.project.organization)
end
def can_link_copied_protocol_in_repository(protocol)
can_copy_protocol_to_repository(protocol.my_module) and
is_user_or_higher_of_project(protocol.my_module.project)
is_user_or_higher_of_project(protocol.my_module.experiment.project)
end
def can_view_steps_in_protocol(protocol)
if protocol.in_module?
my_module = protocol.my_module
my_module.active? and my_module.project.active? and can_view_module(my_module)
my_module.active? &&
my_module.experiment.project.active? &&
my_module.experiment.active? &&
can_view_module(my_module)
elsif protocol.in_repository?
protocol.in_repository_active? and can_view_protocol(protocol)
else
@ -692,7 +713,10 @@ module PermissionHelper
def can_create_step_in_protocol(protocol)
if protocol.in_module?
my_module = protocol.my_module
my_module.active? and my_module.project.active? and is_user_or_higher_of_project(my_module.project)
my_module.active? &&
my_module.experiment.project.active? &&
my_module.experiment.active? &&
is_user_or_higher_of_project(my_module.experiment.project)
elsif protocol.in_repository?
protocol.in_repository_active? and can_edit_protocol(protocol)
else
@ -703,7 +727,10 @@ module PermissionHelper
def can_reorder_step_in_protocol(protocol)
if protocol.in_module?
my_module = protocol.my_module
my_module.active? and my_module.project.active? and is_user_or_higher_of_project(my_module.project)
my_module.active? &&
my_module.experiment.project.active? &&
my_module.experiment.active? &&
is_user_or_higher_of_project(my_module.experiment.project)
elsif protocol.in_repository?
protocol.in_repository_active? and can_edit_protocol(protocol)
else
@ -720,7 +747,10 @@ module PermissionHelper
def can_edit_step_in_protocol(protocol)
if protocol.in_module?
my_module = protocol.my_module
my_module.active? and my_module.project.active? and is_user_or_higher_of_project(my_module.project)
my_module.active? &&
my_module.experiment.project.active? &&
my_module.experiment.active? &&
is_user_or_higher_of_project(my_module.experiment.project)
elsif protocol.in_repository?
protocol.in_repository_active? and can_edit_protocol(protocol)
else
@ -731,7 +761,10 @@ module PermissionHelper
def can_delete_step_in_protocol(protocol)
if protocol.in_module?
my_module = protocol.my_module
my_module.active? and my_module.project.active? and is_owner_of_project(my_module.project)
my_module.active? &&
my_module.experiment.project.active? &&
my_module.experiment.active? &&
is_owner_of_project(my_module.experiment.project)
elsif protocol.in_repository?
protocol.in_repository_active? and can_edit_protocol(protocol)
else
@ -742,7 +775,10 @@ module PermissionHelper
def can_view_step_comments(protocol)
if protocol.in_module?
my_module = protocol.my_module
my_module.active? and my_module.project.active? and can_view_project(my_module.project)
my_module.active? &&
my_module.experiment.project.active? &&
my_module.experiment.active? &&
can_view_project(my_module.experiment.project)
else
# In repository, comments are disabled
false
@ -752,7 +788,10 @@ module PermissionHelper
def can_add_step_comment_in_protocol(protocol)
if protocol.in_module?
my_module = protocol.my_module
my_module.active? and my_module.project.active? and is_technician_or_higher_of_project(my_module.project)
my_module.active? &&
my_module.experiment.project.active? &&
my_module.experiment.active? &&
is_technician_or_higher_of_project(my_module.experiment.project)
else
# In repository, user cannot complete steps
false
@ -762,8 +801,10 @@ module PermissionHelper
def can_view_or_download_step_assets(protocol)
if protocol.in_module?
my_module = protocol.my_module
my_module.active? and my_module.project.active? and
(is_member_of_project(my_module.project) || can_view_project(my_module.project))
my_module.active? &&
my_module.experiment.project.active? &&
my_module.experiment.active? &&
(is_member_of_project(my_module.experiment.project) || can_view_project(my_module.experiment.project))
elsif protocol.in_repository?
protocol.in_repository_active? and can_view_protocol(protocol)
else
@ -774,7 +815,10 @@ module PermissionHelper
def can_complete_step_in_protocol(protocol)
if protocol.in_module?
my_module = protocol.my_module
my_module.active? and my_module.project.active? and is_technician_or_higher_of_project(my_module.project)
my_module.active? &&
my_module.experiment.project.active? &&
my_module.experiment.active? &&
is_technician_or_higher_of_project(my_module.experiment.project)
else
# In repository, user cannot complete steps
false
@ -784,7 +828,10 @@ module PermissionHelper
def can_uncomplete_step_in_protocol(protocol)
if protocol.in_module?
my_module = protocol.my_module
my_module.active? and my_module.project.active? and is_user_or_higher_of_project(my_module.project)
my_module.active? &&
my_module.experiment.project.active? &&
my_module.experiment.active? &&
is_user_or_higher_of_project(my_module.experiment.project)
else
# In repository, user cannot complete steps
false
@ -794,7 +841,10 @@ module PermissionHelper
def can_check_checkbox(protocol)
if protocol.in_module?
my_module = protocol.my_module
my_module.active? and my_module.project.active? and is_technician_or_higher_of_project(my_module.project)
my_module.active? &&
my_module.experiment.project.active? &&
my_module.experiment.active? &&
is_technician_or_higher_of_project(my_module.experiment.project)
else
# In repository, user cannot check checkboxes
false
@ -804,7 +854,10 @@ module PermissionHelper
def can_uncheck_checkbox(protocol)
if protocol.in_module?
my_module = protocol.my_module
my_module.active? and my_module.project.active? and is_user_or_higher_of_project(my_module.project)
my_module.active? &&
my_module.experiment.project.active? &&
my_module.experiment.active? &&
is_user_or_higher_of_project(my_module.experiment.project)
else
# In repository, user cannot check checkboxes
false

436
app/models/experiment.rb
View file

@ -22,4 +22,440 @@ class Experiment < ActiveRecord::Base
experiment.validates :archived_by, presence: true
experiment.validates :archived_on, presence: true
end
def modules_without_group
MyModule.where(experiment_id: id).where(my_module_group: nil)
.where(archived: false)
end
def active_module_groups
self.my_module_groups.joins(:my_modules)
.where('my_modules.archived = ?', false)
.distinct
end
def assigned_modules(user)
role = self.project.user_role(user)
if role.blank?
return MyModule.none
elsif role == "owner"
return self.active_modules
else
return self.active_modules
.joins(:user_my_modules)
.where("user_my_modules.user_id IN (?)", user.id)
.distinct
end
end
def active_modules
my_modules.where(:archived => false)
end
def archived_modules
my_modules.where(:archived => true)
end
def assigned_samples
Sample.joins(:my_modules).where(my_modules: {id: my_modules} )
end
def unassigned_samples(assigned_samples)
Sample.where(organization_id: organization).where.not(id: assigned_samples)
end
def update_canvas(
to_archive,
to_add,
to_rename,
to_clone,
connections,
positions,
current_user,
module_groups
)
cloned_modules = []
begin
Experiment.transaction do
# First, add new modules
new_ids, cloned_pairs, originals = add_modules(
to_add, to_clone, current_user)
cloned_modules = cloned_pairs.collect { |mn, _| mn }
# Rename modules
rename_modules(to_rename)
# Add activities that modules were created
originals.each do |m|
Activity.create(
type_of: :create_module,
user: current_user,
project: selfproject,
my_module: m,
message: I18n.t(
"activities.create_module",
user: current_user.full_name,
module: m.name
)
)
end
# Add activities that modules were cloned
cloned_pairs.each do |mn, mo|
Activity.create(
type_of: :clone_module,
project: mn.experiment.project,
my_module: mn,
user: current_user,
message: I18n.t(
"activities.clone_module",
user: current_user.full_name,
module_new: mn.name,
module_original: mo.name
)
)
end
# Then, archive modules that need to be archived
archive_modules(to_archive, current_user)
# Update connections, positions & module group variables
# with actual IDs retrieved from the new modules creation
updated_connections = []
connections.each do |a,b|
updated_connections << [new_ids.fetch(a, a), new_ids.fetch(b, b)]
end
updated_positions = Hash.new
positions.each do |id, pos|
updated_positions[new_ids.fetch(id, id)] = pos
end
updated_module_groups = {}
module_groups.each do |id, name|
updated_module_groups[new_ids.fetch(id, id)] = name
end
# Update connections
update_module_connections(updated_connections)
# Update module positions (no validation needed here)
update_module_positions(updated_positions)
# Normalize module positions
normalize_module_positions
# Finally, update module groups
update_module_groups(updated_module_groups, current_user)
end
rescue ActiveRecord::ActiveRecordError, ArgumentError, ActiveRecord::RecordNotSaved
return false
end
return true
end
private
# Archive all modules. Receives an array of module integer IDs.
def archive_modules(module_ids)
module_ids.each do |m_id|
my_module = self.my_modules.find_by_id(m_id)
unless my_module.blank?
my_module.archive!
end
end
modules.reload
end
# Archive all modules. Receives an array of module integer IDs and current user.
def archive_modules(module_ids, current_user)
module_ids.each do |m_id|
my_module = self.my_modules.find_by_id(m_id)
unless my_module.blank?
my_module.archive!(current_user)
end
end
my_modules.reload
end
# Add modules, and returns a map of "virtual" IDs with
# actual IDs of saved modules.
# to_add is an array of hashes, each containing 'name',
# 'x', 'y' and 'id'.
# to_clone is a hash, storing new cloned modules as keys,
# and original modules as values.
def add_modules(to_add, to_clone, current_user)
originals = []
cloned_pairs = {}
ids_map = Hash.new
to_add.each do |m|
original = MyModule.find_by_id(to_clone.fetch(m[:id], nil))
if original.present? then
my_module = original.deep_clone(current_user)
cloned_pairs[my_module] = original
else
my_module = MyModule.new(
experiment: self)
originals << my_module
end
my_module.name = m[:name]
my_module.x = m[:x]
my_module.y = m[:y]
my_module.created_by = current_user
my_module.last_modified_by = current_user
my_module.save!
ids_map[m[:id]] = my_module.id.to_s
end
my_modules.reload
return ids_map, cloned_pairs, originals
end
# Rename modules; this method accepts a map where keys
# represent IDs of modules, and values new names for
# such modules. If a module with given ID doesn't exist,
# it's obviously not updated.
def rename_modules(to_rename)
to_rename.each do |id, new_name|
my_module = MyModule.find_by_id(id)
if my_module.present?
my_module.name = new_name
my_module.save!
end
end
end
# Update connections for all modules in this project.
# Input is an array of arrays, where first element represents
# source node, and second element represents target node.
# Example input: [ [1, 2], [2, 3], [4, 5], [2, 5] ]
def update_module_connections(connections)
require 'rgl/base'
require 'rgl/adjacency'
require 'rgl/topsort'
dg = RGL::DirectedAdjacencyGraph.new
connections.each do |a,b|
# Check if both vertices exist
if (my_modules.find_all {|m| [a.to_i, b.to_i].include? m.id }).count == 2
dg.add_edge(a, b)
end
end
# Check if cycles exist!
topsort = dg.topsort_iterator.to_a
if topsort.length == 0 and dg.edges.size > 1
raise ArgumentError, "Cycles exist."
end
# First, delete existing connections
# but keep a copy of previous state
previous_sources = {}
previous_sources.default = []
my_modules.each do |m|
previous_sources[m.id] = []
m.inputs.each do |c|
previous_sources[m.id] << c.from
end
end
self.my_modules.each do |m|
unless m.outputs.destroy_all
raise ActiveRecord::ActiveRecordError
end
end
# Add new connections
filtered_edges = dg.edges.collect { |e| [e.source, e.target] }
filtered_edges.each do |a, b|
Connection.create!(:input_id => b, :output_id => a)
end
# Unassign samples from former downstream modules
# for all destroyed connections
unassign_samples_from_old_downstream_modules(previous_sources)
visited = []
# Assign samples to all new downstream modules
filtered_edges.each do |a, b|
source = self.my_modules.find(a.to_i)
target = self.my_modules.find(b.to_i)
# Do this only for new edges
if previous_sources[target.id].exclude?(source)
# Go as high upstream as new edges take us
# and then assign samples to all downsteam samples
assign_samples_to_new_downstream_modules(previous_sources, visited, source)
end
end
# Save topological order of modules (for modules without workflow,
# leave them unordered)
self.my_modules.each do |m|
if topsort.include? m.id.to_s
m.workflow_order = topsort.find_index(m.id.to_s)
else
m.workflow_order = -1
end
m.save!
end
# Make sure to reload my modules, which now have updated connections and samples
self.my_modules.reload
true
end
# When connections are deleted, unassign samples that
# are not inherited anymore
def unassign_samples_from_old_downstream_modules(sources)
self.my_modules.each do |my_module|
sources[my_module.id].each do |s|
# Only do this for newly deleted connections
if s.outputs.map{|i| i.to}.exclude? my_module
my_module.get_downstream_modules.each do |dm|
# Get unique samples for all upstream modules
um = dm.get_upstream_modules
um.shift # remove current module
ums = um.map{|m| m.samples}.flatten.uniq
s.samples.each do |sample|
dm.samples.delete(sample) if ums.exclude? sample
end
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
if visited.include? (my_module)
return
end
visited << my_module
# Edge case, when module is source or it doesn't have any new input connections
if my_module.inputs.blank? or (
my_module.inputs.map{|c| c.from} -
sources[my_module.id]
).empty?
my_module.get_downstream_modules.each do |dm|
new_samples = my_module.samples.select { |el| dm.samples.exclude?(el) }
dm.samples.push(*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(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)
positions.each do |id, pos|
unless MyModule.update(id, x: pos[:x], y: pos[:y])
raise ActiveRecord::ActiveRecordError
end
end
self.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 = (self.my_modules.collect { |m| m.x }).min
y_diff = (self.my_modules.collect { |m| m.y }).min
self.my_modules.each do |m|
unless
m.update_attribute(:x, m.x - x_diff) and
m.update_attribute(:y, m.y - y_diff)
raise ActiveRecord::ActiveRecordError
end
end
end
# Recalculate module groups in this project. Input is
# a hash of module ids and their corresponding module names.
def update_module_groups(module_groups, current_user)
require 'rgl/base'
require 'rgl/adjacency'
require 'rgl/connected_components'
dg = RGL::DirectedAdjacencyGraph[]
group_ids = Set.new
active_modules.each do |m|
unless m.my_module_group.blank?
group_ids << m.my_module_group.id
end
unless dg.has_vertex? m.id
dg.add_vertex m.id
end
m.outputs.each do |o|
dg.add_edge m.id, o.to.id
end
end
workflows = []
dg.to_undirected.each_connected_component { |w| workflows << w }
# Retrieve maximum allowed module group name
max_length = (MyModuleGroup.validators_on(:name).select { |v| v.class == ActiveModel::Validations::LengthValidator }).first.options[:maximum]
# For each workflow, generate new names
new_index = 1
wf_names = []
suffix = I18n.t("my_module_groups.new.suffix")
cut_index = -(suffix.length + 1)
workflows.each do |w|
modules = MyModule.find(w)
# Get an array of module names
names = []
modules.each do |m|
names << module_groups.fetch(m.id.to_s, "")
end
names = names.uniq
name = (names.select { |v| v != "" }).join(", ")
if w.length <= 1
name = nil
elsif name.blank?
name = I18n.t("my_module_groups.new.name", index: new_index)
new_index += 1
while MyModuleGroup.find_by(name: name).present?
name = I18n.t("my_module_groups.new.name", index: new_index)
new_index += 1
end
elsif name.length > max_length
# If length is too long, shorten it
name = name[0..(max_length + cut_index)] + suffix
end
wf_names << name
end
# Remove any existing module groups from modules
unless MyModuleGroup.destroy_all(:id => group_ids.to_a)
raise ActiveRecord::ActiveRecordError
end
# Second, create new groups
workflows.each_with_index do |w, i|
# Single modules are not considered part of any workflow
if w.length > 1
group = MyModuleGroup.new(
name: wf_names[i],
project: self,
my_modules: MyModule.find(w))
group.created_by = current_user
group.save!
end
end
my_module_groups.reload
true
end
end

16
app/models/my_module.rb
View file

@ -117,20 +117,22 @@ class MyModule < ActiveRecord::Base
User.find_by_sql(
"SELECT DISTINCT users.id, users.full_name FROM users " +
"INNER JOIN user_projects ON users.id = user_projects.user_id " +
"WHERE user_projects.project_id = #{project_id.to_s}" +
"INNER JOIN experiments ON experiments.project_id = user_projects.project_id " +
"WHERE experiments.id = #{experiment_id.to_s}" +
" 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
Sample.where(organization_id: project.organization).where.not(id: samples)
Sample.where(organization_id: experiment.project.organization).where.not(id: samples)
end
def unassigned_tags
Tag.find_by_sql(
"SELECT DISTINCT tags.id, tags.name, tags.color FROM tags " +
"WHERE tags.project_id = #{project_id.to_s} AND tags.id NOT IN " +
"INNER JOIN experiments ON experiments.project_id = tags.project_id " +
"WHERE experiments.id = #{experiment_id.to_s} AND tags.id NOT IN " +
"(SELECT DISTINCT tag_id FROM my_module_tags WHERE my_module_tags.my_module_id = #{id.to_s})"
)
end
@ -285,7 +287,7 @@ class MyModule < ActiveRecord::Base
# Copy the module
clone = MyModule.new(
name: self.name,
project: self.project,
experiment: self.experiment,
description: self.description,
x: self.x,
y: self.y)
@ -306,7 +308,7 @@ class MyModule < ActiveRecord::Base
# Writes to user log.
def log(message)
final = "[%s] %s" % [name, message]
project.log(final)
experiment.project.log(final)
end
private
@ -318,12 +320,12 @@ class MyModule < ActiveRecord::Base
# Find an empty position for the restored module. It's
# basically a first empty row with x=0.
def get_new_position
if project.blank?
if experiment.blank?
return { x: 0, y: 0 }
end
new_y = 0
positions = project.active_modules.collect{ |m| [m.x, m.y] }
positions = experiment.active_modules.collect{ |m| [m.x, m.y] }
(0..10000).each do |n|
unless positions.include? [0, n]
new_y = n

3
app/models/my_module_group.rb
View file

@ -29,7 +29,8 @@ class MyModuleGroup < ActiveRecord::Base
new_query = MyModuleGroup
.distinct
.where("my_module_groups.project_id IN (?)", project_ids)
.joins(:experiment)
.where("experiment.project_id IN (?)", project_ids)
.where_attributes_like(:name, a_query)
# Show all results if needed

2
app/models/organization.rb
View file

@ -257,7 +257,7 @@ class Organization < ActiveRecord::Base
projects.includes(
my_modules: { protocols: { steps: :assets }, results: { result_asset: :asset } }
).find_each do |project|
project.my_modules.find_each do |my_module|
project.project_my_modules.find_each do |my_module|
my_module.protocol.steps.find_each do |step|
step.assets.find_each { |asset| st += asset.estimated_size }
end

438
app/models/project.rb
View file

@ -27,7 +27,6 @@ class Project < ActiveRecord::Base
def self.search(user, include_archived, query = nil, page = 1)
if query
a_query = query.strip
.gsub("_","\\_")
@ -89,14 +88,6 @@ class Project < ActiveRecord::Base
.limit(per_page)
end
def active_modules
self.my_modules.where(:archived => false)
end
def archived_modules
self.my_modules.where(:archived => true)
end
def unassigned_users
User
.joins("INNER JOIN user_organizations ON users.id = user_organizations.user_id ")
@ -105,20 +96,6 @@ class Project < ActiveRecord::Base
.where("users.id NOT IN (?)", UserProject.where(project: self).select(:id).distinct)
end
def assigned_modules(user)
role = self.user_role(user)
if role.blank?
return MyModule.none
elsif role == "owner"
return self.my_modules.where(archived: false)
else
return self.my_modules.where(archived: false)
.joins(:user_my_modules)
.where("user_my_modules.user_id IN (?)", user.id)
.distinct
end
end
def user_role(user)
unless self.users.include? user
return nil
@ -127,431 +104,22 @@ class Project < ActiveRecord::Base
return (self.user_projects.select { |up| up.user == user }).first.role
end
def modules_without_group
MyModule.where(project_id: id).where(my_module_group: nil)
.where(archived: false)
end
def active_module_groups
self.my_module_groups.joins(:my_modules)
.where('my_modules.archived = ?', false)
.distinct
end
def assigned_samples
Sample.joins(:my_modules).where(my_modules: {id: my_modules} )
end
def unassigned_samples(assigned_samples)
Sample.where(organization_id: organization).where.not(id: assigned_samples)
def project_my_modules
MyModule.where('"experiment_id" IN (?)', experiments.select(:id))
end
def space_taken
st = 0
my_modules.find_each do |my_module|
project_my_modules.find_each do |my_module|
st += my_module.space_taken
end
st
end
def update_canvas(
to_archive,
to_add,
to_rename,
to_clone,
connections,
positions,
current_user,
module_groups
)
cloned_modules = []
begin
Project.transaction do
# First, add new modules
new_ids, cloned_pairs, originals = add_modules(
to_add, to_clone, current_user)
cloned_modules = cloned_pairs.collect { |mn, _| mn }
# Rename modules
rename_modules(to_rename)
# Add activities that modules were created
originals.each do |m|
Activity.create(
type_of: :create_module,
user: current_user,
project: self,
my_module: m,
message: I18n.t(
"activities.create_module",
user: current_user.full_name,
module: m.name
)
)
end
# Add activities that modules were cloned
cloned_pairs.each do |mn, mo|
Activity.create(
type_of: :clone_module,
project: mn.project,
my_module: mn,
user: current_user,
message: I18n.t(
"activities.clone_module",
user: current_user.full_name,
module_new: mn.name,
module_original: mo.name
)
)
end
# Then, archive modules that need to be archived
archive_modules(to_archive, current_user)
# Update connections, positions & module group variables
# with actual IDs retrieved from the new modules creation
updated_connections = []
connections.each do |a,b|
updated_connections << [new_ids.fetch(a, a), new_ids.fetch(b, b)]
end
updated_positions = Hash.new
positions.each do |id, pos|
updated_positions[new_ids.fetch(id, id)] = pos
end
updated_module_groups = {}
module_groups.each do |id, name|
updated_module_groups[new_ids.fetch(id, id)] = name
end
# Update connections
update_module_connections(updated_connections)
# Update module positions (no validation needed here)
update_module_positions(updated_positions)
# Normalize module positions
normalize_module_positions
# Finally, update module groups
update_module_groups(updated_module_groups, current_user)
end
rescue ActiveRecord::ActiveRecordError, ArgumentError, ActiveRecord::RecordNotSaved
return false
end
return true
end
# Writes to user log.
def log(message)
final = "[%s] %s" % [name, message]
organization.log(final)
end
private
# Archive all modules. Receives an array of module integer IDs.
def archive_modules(module_ids)
module_ids.each do |m_id|
my_module = my_modules.find_by_id(m_id)
unless my_module.blank?
my_module.archive!
end
end
my_modules.reload
end
# Archive all modules. Receives an array of module integer IDs and current user.
def archive_modules(module_ids, current_user)
module_ids.each do |m_id|
my_module = my_modules.find_by_id(m_id)
unless my_module.blank?
my_module.archive!(current_user)
end
end
my_modules.reload
end
# Add modules, and returns a map of "virtual" IDs with
# actual IDs of saved modules.
# to_add is an array of hashes, each containing 'name',
# 'x', 'y' and 'id'.
# to_clone is a hash, storing new cloned modules as keys,
# and original modules as values.
def add_modules(to_add, to_clone, current_user)
originals = []
cloned_pairs = {}
ids_map = Hash.new
to_add.each do |m|
original = MyModule.find_by_id(to_clone.fetch(m[:id], nil))
if original.present? then
my_module = original.deep_clone(current_user)
cloned_pairs[my_module] = original
else
my_module = MyModule.new(
project: self)
originals << my_module
end
my_module.name = m[:name]
my_module.x = m[:x]
my_module.y = m[:y]
my_module.created_by = current_user
my_module.last_modified_by = current_user
my_module.save!
ids_map[m[:id]] = my_module.id.to_s
end
my_modules.reload
return ids_map, cloned_pairs, originals
end
# Rename modules; this method accepts a map where keys
# represent IDs of modules, and values new names for
# such modules. If a module with given ID doesn't exist,
# it's obviously not updated.
def rename_modules(to_rename)
to_rename.each do |id, new_name|
my_module = MyModule.find_by_id(id)
if my_module.present?
my_module.name = new_name
my_module.save!
end
end
end
# Update connections for all modules in this project.
# Input is an array of arrays, where first element represents
# source node, and second element represents target node.
# Example input: [ [1, 2], [2, 3], [4, 5], [2, 5] ]
def update_module_connections(connections)
require 'rgl/base'
require 'rgl/adjacency'
require 'rgl/topsort'
dg = RGL::DirectedAdjacencyGraph.new
connections.each do |a,b|
# Check if both vertices exist
if (my_modules.find_all {|m| [a.to_i, b.to_i].include? m.id }).count == 2
dg.add_edge(a, b)
end
end
# Check if cycles exist!
topsort = dg.topsort_iterator.to_a
if topsort.length == 0 and dg.edges.size > 1
raise ArgumentError, "Cycles exist."
end
# First, delete existing connections
# but keep a copy of previous state
previous_sources = {}
previous_sources.default = []
my_modules.each do |m|
previous_sources[m.id] = []
m.inputs.each do |c|
previous_sources[m.id] << c.from
end
end
my_modules.each do |m|
unless m.outputs.destroy_all
raise ActiveRecord::ActiveRecordError
end
end
# Add new connections
filtered_edges = dg.edges.collect { |e| [e.source, e.target] }
filtered_edges.each do |a, b|
Connection.create!(:input_id => b, :output_id => a)
end
# Unassign samples from former downstream modules
# for all destroyed connections
unassign_samples_from_old_downstream_modules(previous_sources)
visited = []
# Assign samples to all new downstream modules
filtered_edges.each do |a, b|
source = my_modules.find(a.to_i)
target = my_modules.find(b.to_i)
# Do this only for new edges
if previous_sources[target.id].exclude?(source)
# Go as high upstream as new edges take us
# and then assign samples to all downsteam samples
assign_samples_to_new_downstream_modules(previous_sources, visited, source)
end
end
# Save topological order of modules (for modules without workflow,
# leave them unordered)
my_modules.each do |m|
if topsort.include? m.id.to_s
m.workflow_order = topsort.find_index(m.id.to_s)
else
m.workflow_order = -1
end
m.save!
end
# Make sure to reload my modules, which now have updated connections and samples
my_modules.reload
true
end
# When connections are deleted, unassign samples that
# are not inherited anymore
def unassign_samples_from_old_downstream_modules(sources)
my_modules.each do |my_module|
sources[my_module.id].each do |s|
# Only do this for newly deleted connections
if s.outputs.map{|i| i.to}.exclude? my_module
my_module.get_downstream_modules.each do |dm|
# Get unique samples for all upstream modules
um = dm.get_upstream_modules
um.shift # remove current module
ums = um.map{|m| m.samples}.flatten.uniq
s.samples.each do |sample|
dm.samples.delete(sample) if ums.exclude? sample
end
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
if visited.include? (my_module)
return
end
visited << my_module
# Edge case, when module is source or it doesn't have any new input connections
if my_module.inputs.blank? or (
my_module.inputs.map{|c| c.from} -
sources[my_module.id]
).empty?
my_module.get_downstream_modules.each do |dm|
new_samples = my_module.samples.select { |el| dm.samples.exclude?(el) }
dm.samples.push(*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(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)
positions.each do |id, pos|
unless MyModule.update(id, x: pos[:x], y: pos[:y])
raise ActiveRecord::ActiveRecordError
end
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.collect { |m| m.x }).min
y_diff = (my_modules.collect { |m| m.y }).min
my_modules.each do |m|
unless
m.update_attribute(:x, m.x - x_diff) and
m.update_attribute(:y, m.y - y_diff)
raise ActiveRecord::ActiveRecordError
end
end
end
# Recalculate module groups in this project. Input is
# a hash of module ids and their corresponding module names.
def update_module_groups(module_groups, current_user)
require 'rgl/base'
require 'rgl/adjacency'
require 'rgl/connected_components'
dg = RGL::DirectedAdjacencyGraph[]
group_ids = Set.new
my_modules.where(archived: :false).each do |m|
unless m.my_module_group.blank?
group_ids << m.my_module_group.id
end
unless dg.has_vertex? m.id
dg.add_vertex m.id
end
m.outputs.each do |o|
dg.add_edge m.id, o.to.id
end
end
workflows = []
dg.to_undirected.each_connected_component { |w| workflows << w }
# Retrieve maximum allowed module group name
max_length = (MyModuleGroup.validators_on(:name).select { |v| v.class == ActiveModel::Validations::LengthValidator }).first.options[:maximum]
# For each workflow, generate new names
new_index = 1
wf_names = []
suffix = I18n.t("my_module_groups.new.suffix")
cut_index = -(suffix.length + 1)
workflows.each do |w|
modules = MyModule.find(w)
# Get an array of module names
names = []
modules.each do |m|
names << module_groups.fetch(m.id.to_s, "")
end
names = names.uniq
name = (names.select { |v| v != "" }).join(", ")
if w.length <= 1
name = nil
elsif name.blank?
name = I18n.t("my_module_groups.new.name", index: new_index)
new_index += 1
while MyModuleGroup.find_by(name: name).present?
name = I18n.t("my_module_groups.new.name", index: new_index)
new_index += 1
end
elsif name.length > max_length
# If length is too long, shorten it
name = name[0..(max_length + cut_index)] + suffix
end
wf_names << name
end
# Remove any existing module groups from modules
unless MyModuleGroup.destroy_all(:id => group_ids.to_a)
raise ActiveRecord::ActiveRecordError
end
# Second, create new groups
workflows.each_with_index do |w, i|
# Single modules are not considered part of any workflow
if w.length > 1
group = MyModuleGroup.new(
name: wf_names[i],
project: self,
my_modules: MyModule.find(w))
group.created_by = current_user
group.save!
end
end
my_module_groups.reload
true
end
end

4
app/models/protocol.rb
View file

@ -148,7 +148,7 @@ class Protocol < ActiveRecord::Base
def self.new_blank_for_module(my_module)
Protocol.new(
organization: my_module.project.organization,
organization: my_module.experiment.project.organization,
protocol_type: :unlinked,
my_module: my_module
)
@ -611,4 +611,4 @@ class Protocol < ActiveRecord::Base
self.parent.decrement!(:nr_of_linked_children) if self.parent.present?
end
end
end

2
app/models/step.rb
View file

@ -124,7 +124,7 @@ class Step < ActiveRecord::Base
if (protocol.my_module.present?) then
Activity.create(
type_of: :destroy_step,
project: protocol.my_module.project,
project: protocol.my_module.experiment.project,
my_module: protocol.my_module,
user: @current_user,
message: I18n.t(

2
app/models/user_project.rb
View file

@ -17,7 +17,7 @@ class UserProject < ActiveRecord::Base
def destroy_associations
# Destroy the user from all project's modules
project.my_modules.each do |my_module|
project.project_my_modules.each do |my_module|
um2 = (my_module.user_my_modules.select { |um| um.user == self.user }).first
if um2.present?
um2.destroy