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Code Issues Packages Projects Releases Wiki Activity

Optimize update canvas SQL and remove module group name [SCI-1642]

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This commit is contained in:
Oleksii Kriuchykhin 2017-10-05 16:19:25 +02:00
parent 03743a21f6
commit b26b963e54
19 changed files with 198 additions and 603 deletions
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113
app/assets/javascripts/projects/canvas.js.erb
View file

@ -163,7 +163,6 @@ function initializeEdit() {
// Read permissions from the data attributes of the form
var canEditModules = _.isEqual($("#update-canvas").data("can-edit-modules"), "yes");
var canEditModuleGroups = _.isEqual($("#update-canvas").data("can-edit-module-groups"), "yes");
var canCreateModules = _.isEqual($("#update-canvas").data("can-create-modules"), "yes");
var canCloneModules = _.isEqual($("#update-canvas").data("can-clone-modules"), "yes");
var canMoveModules = _.isEqual($("#update-canvas").data("can-move-modules"), "yes");
@ -211,11 +210,6 @@ function initializeEdit() {
$(".edit-module").on("click touchstart", editModuleHandler);
}
if (canEditModuleGroups) {
initEditModuleGroups();
$(".edit-module-group").on("click touchstart", editModuleGroupHandler);
}
if (canCloneModules) {
bindCloneModuleAction(
$(".module-options a.clone-module"),
@ -1220,22 +1214,6 @@ function updateModuleHtml(module, id, name, gridDistX, gridDistY) {
// Add click handler for the edit module
$(editModuleLink).on("click touchstart", editModuleHandler);
}
if (_.isEqual($("#update-canvas").data("can-edit-module-groups"), "yes")) {
var editModuleGroupItem = document.createElement("li");
$(editModuleGroupItem).appendTo(dropdownMenu);
$(editModuleGroupItem).hide();
var editModuleGroupLink = document.createElement("a");
$(editModuleGroupLink)
.attr("href", "")
.attr("data-module-id", id)
.addClass("edit-module-group")
.html($("#edit-group-link-placeholder").text().trim())
.appendTo(editModuleGroupItem);
// Add click handler for the edit module group
$(editModuleGroupLink).on("click touchstart", editModuleGroupHandler);
}
// Add clone links if neccesary
if (_.isEqual($("#update-canvas").data("can-clone-modules"), "yes")) {
@ -1636,95 +1614,11 @@ editModuleHandler = function(ev) {
/**
* Initialize editing of module groups.
*/
function initEditModuleGroups() {
function handleRenameConfirm(modal, ev) {
var input = modal.find("#edit-module-group-name-input");
// Validate module group name
var moduleNameValid = textValidator(ev, input, 1,
<%= Constants::NAME_MAX_LENGTH %>, true);
if (moduleNameValid) {
var newModuleGroupName = input.val();
var moduleId = modal.attr("data-module-id");
var moduleEl = $("#" + moduleId);
// Update the module group name for all modules
// currently in the module group
var ids = connectedComponents(graph, moduleEl.attr("data-module-id"));
_.each(ids, function(id) {
$("#" + id).attr("data-module-group-name", newModuleGroupName);
});
// Hide modal
modal.modal("hide");
}
}
$("#modal-edit-module-group")
.on("show.bs.modal", function (event) {
var modal = $(this);
var moduleId = modal.attr("data-module-id");
var moduleEl = $("#" + moduleId);
var input = modal.find("#edit-module-group-name-input");
// Set the input to the current module's name
input
.attr("value", moduleEl.attr("data-module-group-name"));
input.val(moduleEl.attr("data-module-group-name"));
// Bind on enter button
input.keydown(function(ev) {
if (ev.keyCode == 13) {
// "Submit" modal
handleRenameConfirm(modal, ev);
// In any case, prevent form submission
ev.preventDefault();
ev.stopPropagation();
return false;
}
});
})
.on("shown.bs.modal", function (event) {
$(this).find("#edit-module-group-name-input").focus();
})
.on("hide.bs.modal", function (event) {
// Remove potential error classes
$(this).find("#edit-module-group-name-input").parent().removeClass("has-error");
$(this).find("span.help-block").remove();
$(this).find("#edit-module-group-name-input").off("keydown");
// When hiding modal, re-enable events
toggleCanvasEvents(true);
});
// Bind the confirm button on modal
$("#modal-edit-module-group").find("button[data-action='confirm']").on("click", function(ev) {
var modal = $(this).closest(".modal");
handleRenameConfirm(modal, ev);
});
}
/**
* Handler when editing a module group.
*/
editModuleGroupHandler = function(ev) {
var modal = $("#modal-edit-module-group");
var moduleEl = $(this).closest(".module");
// Set modal's module id
modal.attr("data-module-id", moduleEl.attr("data-module-id"));
// Disable dragging & zooming events on canvas temporarily
toggleCanvasEvents(false);
// Show modal
modal.modal("show");
ev.preventDefault();
ev.stopPropagation();
return false;
};
function initMoveModules() {
function handleMoveConfirm(modal) {
@ -1978,7 +1872,6 @@ function deleteModule(id, linkConnections) {
_.each (ins, function(inEdge) {
if (graph.degree(inEdge[0]) === 0) {
tempModuleEl = $("#" + inEdge[0]);
tempModuleEl.find(".edit-module-group").parents("li").hide();
tempModuleEl.find(".clone-module-group").parents("li").hide();
tempModuleEl.find(".move-module-group").parents("li").hide();
tempModuleEl.find(".delete-module-group").parents("li").hide();
@ -1989,7 +1882,6 @@ function deleteModule(id, linkConnections) {
_.each (outs, function(outEdge) {
if (graph.degree(outEdge[1]) === 0) {
tempModuleEl = $("#" + outEdge[1]);
tempModuleEl.find(".edit-module-group").parents("li").hide();
tempModuleEl.find(".clone-module-group").parents("li").hide();
tempModuleEl.find(".move-module-group").parents("li").hide();
tempModuleEl.find(".delete-module-group").parents("li").hide();
@ -2361,7 +2253,6 @@ cloneModuleGroupHandler = function(moduleId, modulesSel, gridDistX, gridDistY) {
var nm = cloneModule(m, gridDistX, gridDistY, elLeft(m), elTop(m) + height + offset - gridDistY);
//Show module group options
nm.find(".edit-module-group").parents("li").show();
nm.find(".clone-module-group").parents("li").show();
nm.find(".move-module-group").parents("li").show();
nm.find(".delete-module-group").parents("li").show();
@ -2963,12 +2854,10 @@ function initJsPlumb(containerSel, containerChildSel, modulesSel, params) {
//Modules should belong to module group now
//Show module group options for target and source
srcModuleEl.find(".edit-module-group").parents("li").show();
srcModuleEl.find(".clone-module-group").parents("li").show();
srcModuleEl.find(".move-module-group").parents("li").show();
srcModuleEl.find(".delete-module-group").parents("li").show();
targetModuleEl.find(".edit-module-group").parents("li").show();
targetModuleEl.find(".clone-module-group").parents("li").show();
targetModuleEl.find(".move-module-group").parents("li").show();
targetModuleEl.find(".delete-module-group").parents("li").show();
@ -3001,13 +2890,11 @@ function initJsPlumb(containerSel, containerChildSel, modulesSel, params) {
var targetModuleEl = $("#" + c.targetId);
//First source
if (graph.degree(c.sourceId) === 0) {
srcModuleEl.find(".edit-module-group").parents("li").hide();
srcModuleEl.find(".clone-module-group").parents("li").hide();
srcModuleEl.find(".move-module-group").parents("li").hide();
srcModuleEl.find(".delete-module-group").parents("li").hide();
}
if (graph.degree(c.targetId) === 0) {
targetModuleEl.find(".edit-module-group").parents("li").hide();
targetModuleEl.find(".clone-module-group").parents("li").hide();
targetModuleEl.find(".move-module-group").parents("li").hide();
targetModuleEl.find(".delete-module-group").parents("li").hide();

212
app/controllers/canvas_controller.rb
View file

@ -29,58 +29,41 @@ class CanvasController < ApplicationController
end
def update
error = false
# Make sure that remove parameter is valid
to_archive = []
if can_archive_modules(@experiment) and
update_params[:remove].present? then
to_archive = update_params[:remove].split(",")
unless to_archive.all? { |id| is_int? id }
error = true
if can_archive_modules(@experiment) && update_params[:remove].present?
to_archive = update_params[:remove].split(',')
if to_archive.all? { |id| is_int? id }
to_archive.collect!(&:to_i)
else
to_archive.collect! { |id| id.to_i }
return render_403
end
end
if error then
render_403 and return
end
# Make sure connections parameter is valid
connections = []
if can_edit_connections(@experiment) and
update_params[:connections].present? then
conns = update_params[:connections].split(",")
unless conns.length % 2 == 0 and
conns.all? { |c| c.is_a? String } then
error = true
else
if can_edit_connections(@experiment) && update_params[:connections].present?
conns = update_params[:connections].split(',')
if conns.length.even? && conns.all? { |c| c.is_a? String }
conns.each_slice(2).each do |c|
connections << [c[0], c[1]]
end
else
return render_403
end
end
if error then
render_403 and return
end
# Make sure positions parameter is valid
positions = Hash.new
if can_reposition_modules(@experiment) and
update_params[:positions].present? then
poss = update_params[:positions].split(";")
center = ""
(poss.collect { |pos| pos.split(",") }).each_with_index do |pos, index|
unless pos.length == 3 &&
pos[0].is_a?(String) &&
float?(pos[1]) &&
float?(pos[2])
error = true
break
positions = {}
if can_reposition_modules(@experiment) && update_params[:positions].present?
poss = update_params[:positions].split(';')
center = ''
(poss.collect { |pos| pos.split(',') }).each_with_index do |pos, index|
unless pos.length == 3 && pos[0].is_a?(String) &&
float?(pos[1]) && float?(pos[2])
return render_403
end
if index == 0
if index.zero?
center = pos
x = 0
y = 0
@ -89,86 +72,59 @@ class CanvasController < ApplicationController
y = pos[2].to_i - center[2].to_i
end
# Multiple modules cannot have same position
if positions.any? { |k,v| v[:x] == x and v[:y] == y} then
error = true
break
end
return render_403 if positions.any? { |_, v| v[:x] == x && v[:y] == y }
positions[pos[0]] = { x: x, y: y }
end
end
if error then
render_403 and return
end
# Make sure that to_add is an array of strings,
# as well as that positions for newly added modules exist
to_add = []
if can_create_modules(@experiment) and
update_params[:add].present? and
update_params["add-names"].present? then
ids = update_params[:add].split(",")
names = update_params["add-names"].split("|")
unless ids.length == names.length and
ids.all? { |id| id.is_a? String and positions.include? id } and
names.all? { |name| name.is_a? String }
error = true
else
if can_create_modules(@experiment) && update_params[:add].present? &&
update_params['add-names'].present?
ids = update_params[:add].split(',')
names = update_params['add-names'].split('|')
if ids.length == names.length &&
ids.all? { |id| id.is_a?(String) && positions.include?(id) } &&
names.all? { |name| name.is_a? String }
ids.each_with_index do |id, i|
to_add << {
id: id,
name: names[i],
x: positions[id][:x],
y: positions[id][:y]
}
to_add << { id: id, name: names[i],
x: positions[id][:x], y: positions[id][:y] }
end
else
return render_403
end
end
if error then
render_403 and return
end
# Make sure rename parameter is valid
to_rename = Hash.new
if can_edit_modules(@experiment) and
update_params[:rename].present? then
to_rename = {}
if can_edit_modules(@experiment) && update_params[:rename].present?
begin
to_rename = JSON.parse(update_params[:rename])
# Okay, JSON parsed!
unless (
to_rename.is_a? Hash and
to_rename.keys.all? { |k| k.is_a? String } and
to_rename.values.all? { |k| k.is_a? String }
)
error = true
unless to_rename.is_a?(Hash) &&
to_rename.keys.all? { |k| k.is_a? String } &&
to_rename.values.all? { |k| k.is_a? String }
return render_403
end
rescue
error = true
return render_403
end
end
if error then
render_403 and return
end
# Make sure move parameter is valid
to_move = {}
if can_move_modules(@experiment) && update_params[:move].present?
begin
to_move = JSON.parse(update_params[:move])
# Okay, JSON parsed!
unless (
to_move.is_a? Hash and
to_move.keys.all? { |k| k.is_a? String } &&
to_move.values.all? { |k| k.is_a? String }
)
error = true
unless to_move.is_a?(Hash) &&
to_move.keys.all? { |k| k.is_a? String } &&
to_move.values.all? { |k| k.is_a? String }
return render_403
end
rescue
error = true
return render_403
end
end
@ -181,54 +137,21 @@ class CanvasController < ApplicationController
end
end
render_403 and return if error
# Make sure that to_clone is an array of pairs,
# as well as that all IDs exist
to_clone = Hash.new
if can_clone_modules(@experiment) and
update_params[:cloned].present? then
clones = update_params[:cloned].split(";")
(clones.collect { |v| v.split(",") }).each do |val|
unless (val.length == 2 and
is_int? val[0] and
val[1].is_a? String and
to_add.any? { |m| m[:id] == val[1] })
error = true
break
else
to_clone = {}
if can_clone_modules(@experiment) && update_params[:cloned].present?
clones = update_params[:cloned].split(';')
(clones.collect { |v| v.split(',') }).each do |val|
if val.length == 2 && is_int?(val[0]) && val[1].is_a?(String) &&
to_add.any? { |m| m[:id] == val[1] }
to_clone[val[1]] = val[0]
else
return render_403
end
end
end
if error then
render_403 and return
end
module_groups = Hash.new
if can_edit_module_groups(@experiment) and
update_params["module-groups"].present? then
begin
module_groups = JSON.parse(update_params["module-groups"])
# Okay, JSON parsed!
unless (
module_groups.is_a? Hash and
module_groups.keys.all? { |k| k.is_a? String } and
module_groups.values.all? { |k| k.is_a? String }
)
error = true
end
rescue
error = true
end
end
if error then
render_403 and return
end
# Call the "master" function to do all the updating for us
unless @experiment.update_canvas(
to_archive,
@ -239,36 +162,29 @@ class CanvasController < ApplicationController
to_clone,
connections,
positions,
current_user,
module_groups
current_user
)
render_403 and return
return render_403
end
#Save activities that modules were archived
# Save activities that modules were archived
to_archive.each do |module_id|
my_module = MyModule.find_by_id(module_id)
unless my_module.blank?
Activity.create(
type_of: :archive_module,
project: my_module.experiment.project,
experiment: my_module.experiment,
my_module: my_module,
user: current_user,
message: t(
'activities.archive_module',
user: current_user.full_name,
module: my_module.name
)
)
end
next if my_module.blank?
Activity.create(type_of: :archive_module,
project: my_module.experiment.project,
experiment: my_module.experiment,
my_module: my_module,
user: current_user,
message: t('activities.archive_module',
user: current_user.full_name,
module: my_module.name))
end
# Create workflow image
@experiment.delay.generate_workflow_img
flash[:success] = t(
"experiments.canvas.update.success_flash")
flash[:success] = t('experiments.canvas.update.success_flash')
redirect_to canvas_experiment_path(@experiment)
end

4
app/controllers/my_modules_controller.rb
View file

@ -291,7 +291,7 @@ class MyModulesController < ApplicationController
task_names = []
new_samples = []
@my_module.get_downstream_modules.each do |my_module|
@my_module.downstream_modules.each do |my_module|
new_samples = samples.select { |el| my_module.samples.exclude?(el) }
my_module.samples.push(*new_samples)
task_names << my_module.name
@ -330,7 +330,7 @@ class MyModulesController < ApplicationController
end
task_names = []
@my_module.get_downstream_modules.each do |my_module|
@my_module.downstream_modules.each do |my_module|
task_names << my_module.name
my_module.samples.destroy(samples & my_module.samples)
end

11
app/controllers/search_controller.rb
View file

@ -8,7 +8,6 @@ class SearchController < ApplicationController
search_projects if @search_category == :projects
search_experiments if @search_category == :experiments
search_workflows if @search_category == :workflows
search_modules if @search_category == :modules
search_results if @search_category == :results
search_tags if @search_category == :tags
@ -145,7 +144,6 @@ class SearchController < ApplicationController
def count_search_results
@project_search_count = count_by_name Project
@experiment_search_count = count_by_name Experiment
@workflow_search_count = count_by_name MyModuleGroup
@module_search_count = count_by_name MyModule
@result_search_count = count_by_name Result
@tag_search_count = count_by_name Tag
@ -161,7 +159,6 @@ class SearchController < ApplicationController
@search_results_count = @project_search_count
@search_results_count += @experiment_search_count
@search_results_count += @workflow_search_count
@search_results_count += @module_search_count
@search_results_count += @result_search_count
@search_results_count += @tag_search_count
@ -190,14 +187,6 @@ class SearchController < ApplicationController
@search_count = @experiment_search_count
end
def search_workflows
@workflow_results = []
if @workflow_search_count > 0
@workflow_results = search_by_name(MyModuleGroup)
end
@search_count = @workflow_search_count
end
def search_modules
@module_results = []
@module_results = search_by_name(MyModule) if @module_search_count > 0

6
app/helpers/permission_helper.rb
View file

@ -64,7 +64,6 @@ module PermissionHelper
:can_edit_connections,
:can_create_modules,
:can_edit_modules,
:can_edit_module_groups,
:can_clone_modules,
:can_archive_modules,
:can_view_reports,
@ -149,7 +148,6 @@ module PermissionHelper
:can_edit_connections,
:can_create_modules,
:can_edit_modules,
:can_edit_module_groups,
:can_clone_modules,
:can_archive_modules
] do |proxy, *args, &block|
@ -421,10 +419,6 @@ module PermissionHelper
is_user_or_higher_of_project(experiment.project)
end
def can_edit_module_groups(experiment)
is_user_or_higher_of_project(experiment.project)
end
def can_clone_modules(experiment)
is_user_or_higher_of_project(experiment.project)
end

6
app/models/connection.rb
View file

@ -1,4 +1,6 @@
class Connection < ActiveRecord::Base
belongs_to :to, :class_name => 'MyModule', :foreign_key => 'input_id', inverse_of: :inputs
belongs_to :from, :class_name => 'MyModule', :foreign_key => 'output_id', inverse_of: :outputs
belongs_to :to, class_name: 'MyModule', foreign_key: 'input_id',
inverse_of: :inputs
belongs_to :from, class_name: 'MyModule', foreign_key: 'output_id',
inverse_of: :outputs
end

288
app/models/experiment.rb
View file

@ -87,26 +87,27 @@ class Experiment < ActiveRecord::Base
end
def modules_without_group
MyModule.where(experiment_id: id).where(my_module_group: nil)
.where(archived: false)
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
my_module_groups.joins(:my_modules)
.where('my_modules.archived = ?', false)
.distinct
end
def active_modules
my_modules.where(:archived => false)
my_modules.where(archived: false)
end
def archived_modules
my_modules.where(:archived => true)
my_modules.where(archived: true)
end
def assigned_samples
Sample.joins(:my_modules).where(my_modules: {id: my_modules} )
Sample.joins(:my_modules).where(my_modules: { id: my_modules })
end
def unassigned_samples(assigned_samples)
@ -122,15 +123,15 @@ class Experiment < ActiveRecord::Base
to_clone,
connections,
positions,
current_user,
module_groups
current_user
)
cloned_modules = []
begin
Experiment.transaction do
with_lock do
# First, add new modules
new_ids, cloned_pairs, originals = add_modules(
to_add, to_clone, current_user)
to_add, to_clone, current_user
)
cloned_modules = cloned_pairs.collect { |mn, _| mn }
# Rename modules
@ -138,39 +139,31 @@ class Experiment < ActiveRecord::Base
# Add activities that modules were created
originals.each do |m|
Activity.create(
type_of: :create_module,
Activity.create(type_of: :create_module,
user: current_user,
project: self.project,
project: project,
experiment: m.experiment,
my_module: m,
message: I18n.t(
"activities.create_module",
user: current_user.full_name,
module: m.name
)
)
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,
Activity.create(type_of: :clone_module,
project: mn.experiment.project,
experiment: mn.experiment,
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
)
)
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)
archive_modules(to_archive, current_user) if to_archive.any?
# Update connections, positions & module group variables
# with actual IDs retrieved from the new modules creation
@ -187,17 +180,13 @@ class Experiment < ActiveRecord::Base
updated_to_move_groups[mapped] = value
end
updated_connections = []
connections.each do |a,b|
connections.each do |a, b|
updated_connections << [new_ids.fetch(a, a), new_ids.fetch(b, b)]
end
updated_positions = Hash.new
updated_positions = {}
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)
@ -209,7 +198,7 @@ class Experiment < ActiveRecord::Base
normalize_module_positions
# Finally, update module groups
update_module_groups(updated_module_groups, current_user)
update_module_groups(current_user)
# Finally move any modules to another experiment
move_modules(updated_to_move)
@ -217,11 +206,12 @@ class Experiment < ActiveRecord::Base
# Everyhing is set, now we can move any module groups
move_module_groups(updated_to_move_groups)
end
rescue ActiveRecord::ActiveRecordError, ArgumentError, ActiveRecord::RecordNotSaved
rescue ActiveRecord::ActiveRecordError,
ArgumentError,
ActiveRecord::RecordNotSaved
return false
end
return true
true
end
# This method generate the workflow image and saves it as
@ -422,22 +412,15 @@ class Experiment < ActiveRecord::Base
# 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
my_modules.where(id: module_ids).each(&:archive!)
my_modules.reload
end
# Archive all modules. Receives an array of module integer IDs and current user.
# 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
my_modules.where(id: module_ids).each do |m|
m.archive!(current_user)
end
my_modules.reload
end
@ -451,15 +434,14 @@ class Experiment < ActiveRecord::Base
def add_modules(to_add, to_clone, current_user)
originals = []
cloned_pairs = {}
ids_map = Hash.new
ids_map = {}
to_add.each do |m|
original = MyModule.find_by_id(to_clone.fetch(m[:id], nil))
if original.present? then
if original.present?
my_module = original.deep_clone(current_user)
cloned_pairs[my_module] = original
else
my_module = MyModule.new(
experiment: self)
my_module = MyModule.new(experiment: self)
originals << my_module
end
@ -528,7 +510,7 @@ class Experiment < ActiveRecord::Base
# to bottom left corner.
def move_module_groups(to_move)
to_move.each do |ids, experiment_id|
modules = my_modules.where(id: ids)
modules = my_modules.find(ids)
groups = Set.new(modules.map(&:my_module_group))
experiment = project.experiments.find_by_id(experiment_id)
@ -568,10 +550,8 @@ class Experiment < ActiveRecord::Base
# Generates workflow img when the workflow or module is moved
# to other experiment
def generate_workflow_img_for_moved_modules(to_move)
to_move.values.uniq.each do |id|
experiment = Experiment.find_by_id(id)
next unless experiment
experiment.delay.generate_workflow_img
Experiment.where(id: to_move.values.uniq).each do |exp|
exp.delay.generate_workflow_img
end
end
@ -583,42 +563,39 @@ class Experiment < ActiveRecord::Base
require 'rgl/base'
require 'rgl/adjacency'
require 'rgl/topsort'
dg = RGL::DirectedAdjacencyGraph.new
connections.each do |a,b|
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
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."
if topsort.length.zero? && 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|
my_modules.includes(inputs: { from: [:inputs, outputs: :to] }).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
# There are no callbacks in Connection, so delete_all should be safe
Connection.delete_all(output_id: my_modules)
# 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)
Connection.create!(input_id: b, output_id: a)
end
# Unassign samples from former downstream modules
@ -628,47 +605,49 @@ class Experiment < ActiveRecord::Base
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)
source = my_modules.includes({ inputs: :from }, :samples).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
next unless 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
# 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
my_modules.includes(:my_module_group).each do |m|
m.workflow_order =
if topsort.include? m.id.to_s
topsort.find_index(m.id.to_s)
else
-1
end
m.save!
end
# Make sure to reload my modules, which now have updated connections and samples
self.my_modules.reload
# 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)
self.my_modules.each do |my_module|
sources[my_module.id].each do |s|
my_modules.each do |my_module|
sources[my_module.id].each do |src|
# 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.destroy(sample) if ums.exclude? sample
end
next unless src.outputs.map(&:to).exclude? my_module
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.each do |sample|
dm.samples.destroy(sample) if ums.exclude? sample
end
end
end
@ -678,24 +657,21 @@ class Experiment < ActiveRecord::Base
# 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
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? 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)
# 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(input.from)
assign_samples_to_new_downstream_modules(sources, visited, input.from)
end
end
end
@ -705,104 +681,58 @@ class Experiment < ActiveRecord::Base
# 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
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
self.my_modules.reload
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
x_diff = my_modules.collect(&:x).min
y_diff = my_modules.collect(&: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
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(module_groups, current_user)
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.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
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 { |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
dg.to_undirected.each_connected_component do |w|
workflows << my_modules.find(w)
end
# Remove any existing module groups from modules
unless MyModuleGroup.destroy_all(:id => group_ids.to_a)
unless MyModuleGroup.destroy_all(id: group_ids.to_a)
raise ActiveRecord::ActiveRecordError
end
# Second, create new groups
workflows.each_with_index do |w, i|
workflows.each do |modules|
# Single modules are not considered part of any workflow
if w.length > 1
group = MyModuleGroup.new(
name: wf_names[i],
experiment: self,
my_modules: MyModule.find(w))
group.created_by = current_user
group.save!
end
next unless modules.length > 1
MyModuleGroup.create!(experiment: self,
my_modules: modules,
created_by: current_user)
end
my_module_groups.reload

16
app/models/my_module.rb
View file

@ -252,28 +252,24 @@ class MyModule < ActiveRecord::Base
end
# Treat this module as root, get all modules of that subtree
def get_downstream_modules
def downstream_modules
final = []
modules = [self]
while !modules.empty?
until modules.empty?
my_module = modules.shift
if !final.include?(my_module)
final << my_module
end
final << my_module unless final.include?(my_module)
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
def upstream_modules
final = []
modules = [self]
while !modules.empty?
until modules.empty?
my_module = modules.shift
if !final.include?(my_module)
final << my_module
end
final << my_module unless final.include?(my_module)
modules.push(*my_module.my_module_antecessors.flatten)
end
final

31
app/models/my_module_group.rb
View file

@ -1,49 +1,18 @@
class MyModuleGroup < ActiveRecord::Base
include SearchableModel
auto_strip_attributes :name, nullify: false
validates :name,
presence: true,
length: { maximum: Constants::NAME_MAX_LENGTH }
validates :experiment, presence: true
belongs_to :experiment, inverse_of: :my_module_groups
belongs_to :created_by, foreign_key: 'created_by_id', class_name: 'User'
has_many :my_modules, inverse_of: :my_module_group, dependent: :nullify
def self.search(user,
include_archived,
query = nil,
page = 1,
_current_team = nil,
options = {})
exp_ids =
Experiment
.search(user, include_archived, nil, Constants::SEARCH_NO_LIMIT)
.pluck(:id)
new_query = MyModuleGroup
.distinct
.where('my_module_groups.experiment_id IN (?)', exp_ids)
.where_attributes_like('my_module_groups.name', query, options)
# Show all results if needed
if page == Constants::SEARCH_NO_LIMIT
new_query
else
new_query
.limit(Constants::SEARCH_LIMIT)
.offset((page - 1) * Constants::SEARCH_LIMIT)
end
end
def ordered_modules
my_modules.order(workflow_order: :asc)
end
def deep_clone_to_experiment(current_user, experiment)
clone = MyModuleGroup.new(
name: name,
created_by: created_by,
experiment: experiment
)

5
app/utilities/first_time_data_generator.rb
View file

@ -150,7 +150,6 @@ module FirstTimeDataGenerator
# Create a module group
my_module_group = MyModuleGroup.create(
name: 'Potato qPCR workflow',
experiment: experiment
)
@ -317,7 +316,7 @@ module FirstTimeDataGenerator
samples_to_assign << sample
end
my_modules[1].get_downstream_modules.each do |mm|
my_modules[1].downstream_modules.each do |mm|
samples_to_assign.each do |s|
SampleMyModule.create(
sample: s,
@ -881,7 +880,7 @@ module FirstTimeDataGenerator
).sneaky_save
# create thumbnail
experiment.generate_workflow_img
experiment.delay.generate_workflow_img
# Lastly, create cookie with according ids
# so tutorial steps can be properly positioned

7
app/views/canvas/_edit.html.erb
View file

@ -1,7 +1,6 @@
<div id="update-canvas"
data-can-create-modules="<%= can_create_modules(@experiment) ? "yes" : "no" %>"
data-can-edit-modules="<%= can_edit_modules(@experiment) ? "yes" : "no" %>"
data-can-edit-module-groups="<%= can_edit_module_groups(@experiment) ? "yes" : "no" %>"
data-can-clone-modules="<%= can_clone_modules(@experiment) ? "yes" : "no" %>"
data-can-move-modules="<%= can_move_modules(@experiment) ? "yes" : "no" %>"
data-can-delete-modules="<%= can_archive_modules(@experiment) ? "yes" : "no" %>"
@ -49,9 +48,6 @@
<span style="display: none;" id="edit-link-placeholder">
<%=t "experiments.canvas.edit.edit_module" %>
</span>
<span style="display: none;" id="edit-group-link-placeholder">
<%=t "experiments.canvas.edit.edit_module_group" %>
</span>
<span style="display: none;" id="clone-link-placeholder">
<%=t "experiments.canvas.edit.clone_module" %>
</span>
@ -87,9 +83,6 @@
<% if can_edit_modules(@experiment) %>
<%= render partial: "canvas/edit/modal/edit_module", locals: {experiment: @experiment } %>
<% end %>
<% if can_edit_module_groups(@experiment) %>
<%= render partial: "canvas/edit/modal/edit_module_group", locals: {experiment: @experiment } %>
<% end %>
<% if can_move_modules(@experiment) %>
<%= render partial: "canvas/edit/modal/move_module", locals: {experiment: @experiment } %>
<%= render partial: "canvas/edit/modal/move_module_group", locals: {experiment: @experiment } %>

10
app/views/canvas/edit/_my_module.html.erb
View file

@ -2,11 +2,6 @@
id="<%= my_module.id %>"
data-module-id="<%= my_module.id %>"
data-module-name="<%= my_module.name %>"
<% if my_module.my_module_group.present? %>
data-module-group-name="<%= my_module.my_module_group.name %>"
<% else %>
data-module-group-name=""
<% end %>
data-module-x="<%= my_module.x %>"
data-module-y="<%= my_module.y %>"
data-module-conns="<%= construct_module_connections(my_module) %>">
@ -26,11 +21,6 @@
<a class="edit-module" href="" data-module-id="<%= my_module.id %>"><%=t "experiments.canvas.edit.edit_module" %></a>
</li>
<% end %>
<% if can_edit_module_groups(my_module.experiment) %>
<li <%= 'style=display:none;' if my_module.my_module_group.blank? %>>
<a class="edit-module-group" href="" data-module-id="<%= my_module.id %>"><%=t "experiments.canvas.edit.edit_module_group" %></a>
</li>
<% end %>
<% if can_clone_modules(my_module.experiment) %>
<li>
<a class ="clone-module" href="" data-module-id="<%= my_module.id %>"><%=t "experiments.canvas.edit.clone_module" %></a>

19
app/views/canvas/edit/modal/_edit_module_group.html.erb
View file

@ -1,19 +0,0 @@
<div class="modal fade" id="modal-edit-module-group" tabindex="-1" role="dialog" aria-labelledby="modal-edit-module-group-label">
<div class="modal-dialog" role="document">
<div class="modal-content">
<div class="modal-header">
<button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">&times;</span></button>
<h4 class="modal-title" id="modal-edit-module-group-label"><%=t "experiments.canvas.edit.modal_edit_module_group.title" %></h4>
</div>
<div class="modal-body">
<%= bootstrap_form_tag do |f| %>
<%= f.text_field t("experiments.canvas.edit.modal_edit_module_group.name"), id: "edit-module-group-name-input" %>
<% end %>
</div>
<div class="modal-footer">
<button type="button" class="btn btn-primary" data-action="confirm"><%=t "experiments.canvas.edit.modal_edit_module_group.confirm" %></button>
<button type="button" class="btn btn-default" data-dismiss="modal"><%=t "general.cancel" %></button>
</div>
</div>
</div>
</div>

16
app/views/search/index.html.erb
View file

@ -70,19 +70,6 @@
<%= t'Experiments' %>
</a>
</li>
<li role="presentation"
class="
<%= "active" if @search_category.present? and @search_category == :workflows %>
<%= "disabled" if @workflow_search_count == 0 %>"
>
<a href="?<%= {category: 'workflows', q: @search_query,
whole_word: @search_whole_word, whole_phrase: @search_whole_phrase,
match_case: @search_case, utf8: '✓'}.to_query %>">
<span class="badge pull-right"><%= @workflow_search_count %></span>
<span class="glyphicon glyphicon-random"></span>
<%= t'Workflows' %>
</a>
</li>
<li role="presentation"
class="
<%= "active" if @search_category.present? and @search_category == :modules %>
@ -268,9 +255,6 @@
<% if @search_category == :experiments and @experiment_search_count > 0 %>
<%= render 'search/results/experiments', search_query: @search_query, results: @experiment_results %>
<% end %>
<% if @search_category == :workflows and @workflow_search_count > 0 %>
<%= render 'search/results/workflows', search_query: @search_query, results: @workflow_results %>
<% end %>
<% if @search_category == :modules and @module_search_count > 0 %>
<%= render 'search/results/modules', search_query: @search_query, results: @module_results %>
<% end %>

33
app/views/search/results/_workflows.html.erb
View file

@ -1,33 +0,0 @@
<% results.each do |workflow| %>
<h5>
<span class="glyphicon glyphicon-random"></span>
<%= highlight workflow.name, search_query.strip.split(/\s+/) %>
</h5>
<p>
<span>
<%=t 'search.index.created_at' %>
<%=l workflow.created_at, format: :full %>
</span>
<br>
<span>
<%=t 'search.index.experiment' %>
<%= render partial: 'search/results/partials/experiment_text.html.erb',
locals: { experiment: workflow.experiment } %>
</span>
<br>
<span>
<%=t 'search.index.project' %>
<%= render partial: 'search/results/partials/project_text.html.erb',
locals: { project: workflow.experiment.project, link_to_page: :show } %>
</span>
<br>
<span>
<%=t 'search.index.team' %>
<%= render partial: 'search/results/partials/team_text.html.erb',
locals: { team: workflow.experiment.project.team } %>
</span>
</p>
<hr>
<% end %>

5
config/locales/en.yml
View file

@ -703,7 +703,6 @@ en:
drag_connections: "Drag connection/s from here"
options_header: "Options"
edit_module: "Rename task"
edit_module_group: "Rename workflow"
clone_module: "Copy task as template (only Protocols steps copied)"
clone_module_group: "Copy workflow as template (only Protocols steps copied)"
move_module: "Move task to another experiment"
@ -719,10 +718,6 @@ en:
title: "Rename task"
name: "Task name"
confirm: "Rename task"
modal_edit_module_group:
title: "Rename workflow"
name: "Workflow name"
confirm: "Rename workflow"
modal_move_module:
title: "Move task to experiment"
confirm: "Move task"

6
db/migrate/20171003082333_add_indexes_to_connections.rb Normal file
View file

@ -0,0 +1,6 @@
class AddIndexesToConnections < ActiveRecord::Migration
def change
add_index :connections, :input_id
add_index :connections, :output_id
end
end

5
db/migrate/20171005135350_update_my_module_groups.rb Normal file
View file

@ -0,0 +1,5 @@
class UpdateMyModuleGroups < ActiveRecord::Migration
def change
remove_column :my_module_groups, :name, :string
end
end

8
test/models/my_module_group_test.rb
View file

@ -8,15 +8,7 @@ class MyModuleGroupTest < ActiveSupport::TestCase
@module_group = my_module_groups(:wf1)
end
should validate_presence_of(:name)
should validate_length_of(:name)
.is_at_most(Constants::NAME_MAX_LENGTH)
test "should validate with valid data" do
assert @module_group.valid?
end
test "where_attributes_like should work" do
attributes_like_test(MyModuleGroup, :name, "expression")
end
end