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fixes hound

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This commit is contained in:
zmagod 2017-01-31 13:33:55 +01:00
parent e59b2e039a
commit be5faad97c
9 changed files with 189 additions and 155 deletions
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4
app/assets/javascripts/users/settings/teams.js
View file

@ -1,4 +1,4 @@
function initLeaveOrganizations() {
function initLeaveTeams() {
// Bind the "leave team" buttons in teams table
$(document)
.on(
@ -56,4 +56,4 @@ function initLeaveOrganizations() {
);
}
initLeaveOrganizations();
initLeaveTeams();

33
app/controllers/users/settings_controller.rb
View file

@ -177,36 +177,37 @@ class Users::SettingsController < ApplicationController
def leave_user_team_html
respond_to do |format|
format.json {
format.json do
render json: {
html: render_to_string({
partial: "users/settings/teams/leave_user_team_modal_body.html.erb",
html: render_to_string(
partial: 'users/settings/teams/leave_user_team_modal_body.html.erb',
locals: { user_team: @user_team }
}),
),
heading: I18n.t(
"users.settings.teams.index.leave_uo_heading",
'users.settings.teams.index.leave_uo_heading',
team: escape_input(@user_team.team.name)
)
}
}
end
end
end
def destroy_user_team_html
respond_to do |format|
format.json {
format.json do
render json: {
html: render_to_string({
partial: "users/settings/teams/destroy_user_team_modal_body.html.erb",
html: render_to_string(
partial: 'users/settings/teams/' \
'destroy_user_team_modal_body.html.erb',
locals: { user_team: @user_team }
}),
),
heading: I18n.t(
"users.settings.teams.edit.destroy_uo_heading",
'users.settings.teams.edit.destroy_uo_heading',
user: escape_input(@user_team.user.full_name),
team: escape_input(@user_team.team.name)
)
}
}
end
end
end
@ -254,7 +255,7 @@ class Users::SettingsController < ApplicationController
if !invalid
if params[:leave] then
flash[:notice] = I18n.t(
"users.settings.teams.index.leave_flash",
'users.settings.teams.index.leave_flash',
team: @user_team.team.name
)
flash.keep(:notice)
@ -285,7 +286,7 @@ class Users::SettingsController < ApplicationController
.includes(team: :users)
.where(role: 1..2)
.order(created_at: :asc)
.map { |uo| uo.team }
.map(&:team)
@member_of = @teams.count
respond_to do |format|
@ -379,8 +380,8 @@ class Users::SettingsController < ApplicationController
@team = @user_team.team
# Don't allow the user to modify UserTeam-s if he's not admin,
# unless he/she is modifying his/her UserTeam
if current_user != @user_team.user and
!is_admin_of_team(@user_team.team)
if current_user != @user_team.user &&
!is_admin_of_team(@user_team.team)
render_403
end
end

11
app/datatables/sample_datatable.rb
View file

@ -253,12 +253,13 @@ class SampleDatatable < AjaxDatatablesRails::Base
.select('"samples"."id"')
.distinct
# grabs the ids that are not the previous one but are still of the same team
# grabs the ids that are not the previous one but are still
# of the same team
unassigned = Sample
.where('"samples"."team_id" = ?', @team.id)
.where('"samples"."id" NOT IN (?)', assigned)
.select('"samples"."id"')
.distinct
.where('"samples"."team_id" = ?', @team.id)
.where('"samples"."id" NOT IN (?)', assigned)
.select('"samples"."id"')
.distinct
# check the input param and merge the two arrays of ids
if params[:order].values[0]['dir'] == 'asc'

206
app/models/protocol.rb
View file

@ -41,103 +41,148 @@ class Protocol < ActiveRecord::Base
end
with_options if: :in_repository_public? do |protocol|
# Public protocol must have unique name inside its team
protocol.validates_uniqueness_of :name, scope: [:team], conditions: -> { where(protocol_type: Protocol.protocol_types[:in_repository_public]) }
protocol
.validates_uniqueness_of :name,
scope: :team,
conditions: -> {
where(
protocol_type:
Protocol
.protocol_types[:in_repository_public]
)
}
protocol.validates :published_on, presence: true
end
with_options if: :in_repository_private? do |protocol|
# Private protocol must have unique name inside its team & user scope
protocol.validates_uniqueness_of :name, scope: [:team, :added_by], conditions: -> { where(protocol_type: Protocol.protocol_types[:in_repository_private]) }
protocol
.validates_uniqueness_of :name,
scope: [:team, :added_by],
conditions: -> {
where(
protocol_type:
Protocol
.protocol_types[:in_repository_private]
)
}
end
with_options if: :in_repository_archived? do |protocol|
# Archived protocol must have unique name inside its team & user scope
protocol.validates_uniqueness_of :name, scope: [:team, :added_by], conditions: -> { where(protocol_type: Protocol.protocol_types[:in_repository_archived]) }
protocol
.validates_uniqueness_of :name,
scope: [:team, :added_by],
conditions: -> {
where(
protocol_type:
Protocol
.protocol_types[:in_repository_archived]
)
}
protocol.validates :archived_by, presence: true
protocol.validates :archived_on, presence: true
end
belongs_to :added_by, foreign_key: 'added_by_id', class_name: 'User', inverse_of: :added_protocols
belongs_to :added_by,
foreign_key: 'added_by_id',
class_name: 'User',
inverse_of: :added_protocols
belongs_to :my_module, inverse_of: :protocols
belongs_to :team, inverse_of: :protocols
belongs_to :parent, foreign_key: 'parent_id', class_name: 'Protocol'
belongs_to :archived_by, foreign_key: 'archived_by_id', class_name: 'User', inverse_of: :archived_protocols
belongs_to :restored_by, foreign_key: 'restored_by_id', class_name: 'User', inverse_of: :restored_protocols
has_many :linked_children, class_name: 'Protocol', foreign_key: 'parent_id'
has_many :protocol_protocol_keywords, inverse_of: :protocol, dependent: :destroy
belongs_to :archived_by,
foreign_key: 'archived_by_id',
class_name: 'User',
inverse_of: :archived_protocols
belongs_to :restored_by,
foreign_key: 'restored_by_id',
class_name: 'User',
inverse_of: :restored_protocols
has_many :linked_children,
class_name: 'Protocol',
foreign_key: 'parent_id'
has_many :protocol_protocol_keywords,
inverse_of: :protocol,
dependent: :destroy
has_many :protocol_keywords, through: :protocol_protocol_keywords
has_many :steps, inverse_of: :protocol, dependent: :destroy
def self.search(user, include_archived, query = nil, page = 1)
team_ids =
Team
.joins(:user_teams)
.where("user_teams.user_id = ?", user.id)
.select("id")
.distinct
team_ids = Team.joins(:user_teams)
.where('user_teams.user_id = ?', user.id)
.select('id')
.distinct
module_ids =
MyModule
.search(user, include_archived, nil, Constants::SEARCH_NO_LIMIT)
.select("id")
module_ids = MyModule.search(user,
include_archived,
nil,
Constants::SEARCH_NO_LIMIT)
.select('id')
where_str =
"(protocol_type IN (?) AND my_module_id IN (?)) OR " +
"(protocol_type = ? AND protocols.team_id IN (?) AND added_by_id = ?) OR " +
"(protocol_type = ? AND protocols.team_id IN (?))"
'(protocol_type IN (?) AND my_module_id IN (?)) OR ' \
'(protocol_type = ? AND protocols.team_id IN (?) AND ' \
'added_by_id = ?) OR (protocol_type = ? AND protocols.team_id IN (?))'
if include_archived
where_str +=
" OR (protocol_type = ? AND protocols.team_id IN (?) AND added_by_id = ?)"
' OR (protocol_type = ? AND protocols.team_id IN (?) ' \
'AND added_by_id = ?)'
new_query = Protocol
.where(
where_str,
[Protocol.protocol_types[:unlinked], Protocol.protocol_types[:linked]],
module_ids,
Protocol.protocol_types[:in_repository_private],
team_ids,
user.id,
Protocol.protocol_types[:in_repository_public],
team_ids,
Protocol.protocol_types[:in_repository_archived],
team_ids,
user.id
)
.where(
where_str,
[Protocol.protocol_types[:unlinked],
Protocol.protocol_types[:linked]],
module_ids,
Protocol.protocol_types[:in_repository_private],
team_ids,
user.id,
Protocol.protocol_types[:in_repository_public],
team_ids,
Protocol.protocol_types[:in_repository_archived],
team_ids,
user.id
)
else
new_query = Protocol
.where(
where_str,
[Protocol.protocol_types[:unlinked], Protocol.protocol_types[:linked]],
module_ids,
Protocol.protocol_types[:in_repository_private],
team_ids,
user.id,
Protocol.protocol_types[:in_repository_public],
team_ids
)
.where(
where_str,
[Protocol.protocol_types[:unlinked],
Protocol.protocol_types[:linked]],
module_ids,
Protocol.protocol_types[:in_repository_private],
team_ids,
user.id,
Protocol.protocol_types[:in_repository_public],
team_ids
)
end
if query
a_query = query.strip
.gsub("_","\\_")
.gsub("%","\\%")
.split(/\s+/)
.map {|t| "%" + t + "%" }
.gsub('_', '\\_')
.gsub('%', '\\%')
.split(/\s+/)
.map { |t| '%' + t + '%' }
else
a_query = query
end
new_query = new_query
.distinct
.joins("LEFT JOIN protocol_protocol_keywords ON protocols.id = protocol_protocol_keywords.protocol_id")
.joins("LEFT JOIN protocol_keywords ON protocol_keywords.id = protocol_protocol_keywords.protocol_keyword_id")
.where_attributes_like(
[
"protocols.name",
"protocols.description",
"protocols.authors",
"protocol_keywords.name"
],
a_query
)
.distinct
.joins('LEFT JOIN protocol_protocol_keywords ON ' \
'protocols.id = protocol_protocol_keywords.protocol_id')
.joins('LEFT JOIN protocol_keywords ' \
'ON protocol_keywords.id = ' \
'protocol_protocol_keywords.protocol_keyword_id')
.where_attributes_like(
[
'protocols.name',
'protocols.description',
'protocols.authors',
'protocol_keywords.name'
],
a_query
)
# Show all results if needed
if page == Constants::SEARCH_NO_LIMIT
@ -271,9 +316,7 @@ class Protocol < ActiveRecord::Base
# Copy tables
step.tables.each do |table|
table2 = Table.new(
name: table.name,
contents: table.contents)
table2 = Table.new(name: table.name, contents: table.contents)
table2.created_by = current_user
table2.last_modified_by = current_user
step2.tables << table2
@ -288,38 +331,38 @@ class Protocol < ActiveRecord::Base
end
def in_repository_active?
in_repository_private? ||
in_repository_public?
in_repository_private? || in_repository_public?
end
def in_repository?
in_repository_active? ||
in_repository_archived?
in_repository_active? || in_repository_archived?
end
def in_module?
unlinked? ||
linked?
unlinked? || linked?
end
def linked_no_diff?
linked? && updated_at == parent_updated_at &&
parent.updated_at == parent_updated_at
linked? &&
updated_at == parent_updated_at &&
parent.updated_at == parent_updated_at
end
def newer_than_parent?
linked? && parent.updated_at == parent_updated_at &&
updated_at > parent_updated_at
updated_at > parent_updated_at
end
def parent_newer?
linked? && updated_at == parent_updated_at &&
parent.updated_at > parent_updated_at
linked? &&
updated_at == parent_updated_at &&
parent.updated_at > parent_updated_at
end
def parent_and_self_newer?
linked? && parent.updated_at > parent_updated_at &&
updated_at > parent_updated_at
linked? &&
parent.updated_at > parent_updated_at &&
updated_at > parent_updated_at
end
def number_of_steps
@ -327,7 +370,7 @@ class Protocol < ActiveRecord::Base
end
def completed_steps
steps.select { |step| step.completed }
steps.select(&:completed)
end
def space_taken
@ -602,15 +645,12 @@ class Protocol < ActiveRecord::Base
success = clone.save
end
unless success
raise ActiveRecord::RecordNotSaved
end
raise ActiveRecord::RecordNotSaved unless success
Protocol.clone_contents(self, clone, current_user, true)
clone.reload
return clone
clone
end
def update_linked_children

10
app/models/sample.rb
View file

@ -26,12 +26,10 @@ class Sample < ActiveRecord::Base
page = 1,
current_team = nil
)
team_ids =
Team
.joins(:user_teams)
.where("user_teams.user_id = ?", user.id)
.select("id")
.distinct
team_ids = Team.joins(:user_teams)
.where('user_teams.user_id = ?', user.id)
.select('id')
.distinct
if query
a_query = '%' + query.strip.gsub('_', '\\_').gsub('%', '\\%') + '%'

4
app/models/team.rb
View file

@ -128,7 +128,7 @@ class Team < ActiveRecord::Base
# We need to have sample saved before messing with custom fields (they
# need sample id)
if index == stype_index
stype = SampleType.where(name: value, team_id: id).take();
stype = SampleType.where(name: value, team_id: id).take
if stype
sample.sample_type = stype
@ -140,7 +140,7 @@ class Team < ActiveRecord::Base
end
sample.save
elsif index == sgroup_index
sgroup = SampleGroup.where(name: value, team_id: id).take();
sgroup = SampleGroup.where(name: value, team_id: id).take
if sgroup
sample.sample_group = sgroup

2
app/models/user_team.rb
View file

@ -13,7 +13,7 @@ class UserTeam < ActiveRecord::Base
after_create :create_samples_table_state
def role_str
I18n.t("user_teams.enums.role.#{role.to_s}")
I18n.t("user_teams.enums.role.#{role}")
end
def create_samples_table_state

2
db/seeds.rb
View file

@ -7,6 +7,6 @@ create_user(
'admin@scinote.net',
admin_password,
true,
Constants::DEFAULT_PRIVATE_ORG_NAME,
Constants::DEFAULT_PRIVATE_TEAM_NAME,
[]
)

72
lib/tasks/db_users.rake
View file

@ -21,82 +21,78 @@ namespace :db do
begin
ActiveRecord::Base.transaction do
# Parse user & team hashes from YAML
teams = yaml.select{ |k, v| /team_[0-9]+/ =~ k }
users = yaml.select{ |k, v| /user_[0-9]+/ =~ k }
teams = yaml.select { |k, v| /team_[0-9]+/ =~ k }
users = yaml.select { |k, v| /user_[0-9]+/ =~ k }
# Create teams
teams.each do |k, team_hash|
team = Team.order(created_at: :desc).where(name: team_hash["name"]).first
if team.blank?
team = Team.create({
name: team_hash["name"][0..99]
})
end
team_hash["id"] = team.id
team = Team.order(created_at: :desc)
.where(name: team_hash['name'])
.first
team = Team.create(name: team_hash['name'][0..99]) if team.blank?
team_hash['id'] = team.id
end
# Create users
puts "Created users"
puts 'Created users'
users.each do |k, user_hash|
password = user_hash["password"]
if password.blank?
password = generate_user_password
end
password = user_hash['password']
password = generate_user_password if password.blank?
user_teams = user_hash["teams"]
if user_teams.blank?
user_teams = ""
end
user_teams = user_hash['teams']
user_teams = '' if user_teams.blank
team_ids =
user_teams
.split(",")
.collect{ |o| o.strip }
.split(',')
.collect(&:strip)
.uniq
.select{ |o| teams.include? o }
.collect{ |o| teams[o]["id"] }
.select { |o| teams.include? o }
.collect { |o| teams[o]['id'] }
user = create_user(
user_hash["full_name"],
user_hash["email"],
user_hash['full_name'],
user_hash['email'],
password,
true,
create_teams ? Constants::DEFAULT_PRIVATE_ORG_NAME : nil,
team_ids
)
if user.id.present? then
puts ""
if user.id.present?
puts ''
print_user(user, password)
end
end
puts ""
puts ''
end
rescue ActiveRecord::ActiveRecordError, ArgumentError
puts "Error creating all users, transaction reverted"
puts 'Error creating all users, transaction reverted'
end
end
desc "Add a single user to the database"
desc 'Add a single user to the database'
task :add_user => :environment do
puts "Type in user's full name (e.g. 'Steve Johnson')"
puts 'Type in user\'s full name (e.g. \'Steve Johnson\')'
full_name = $stdin.gets.to_s.strip
puts "Type in user's email (e.g. 'steve.johnson@gmail.com')"
puts 'Type in user\'s email (e.g. \'steve.johnson@gmail.com\')'
email = $stdin.gets.to_s.strip
puts "Type in user's password (e.g. 'password'), or leave blank to let Rails generate password"
puts 'Type in user\'s password (e.g. \'password\'), or ' \
'leave blank to let Rails generate password'
password = $stdin.gets.to_s.strip
if password.empty?
password = generate_user_password
end
puts "Do you want Rails to create default user's team? (T/F)"
create_team = $stdin.gets.to_s.strip == "T"
puts "Type names of any additional teams you want the user to be admin of (delimited with ','), or leave blank"
puts 'Do you want Rails to create default user\'s team? (T/F)'
create_team = $stdin.gets.to_s.strip == 'T'
puts 'Type names of any additional teams you want the user ' \
'to be admin of (delimited with \',\'), or leave blank'
team_names = $stdin.gets.to_s.strip
if team_names.empty?
team_names = []
else
team_names = team_names.split(",").collect { |n| n.strip }
team_names = team_names.split(',').collect(&:strip)
end
begin
@ -105,9 +101,7 @@ namespace :db do
team_ids = []
team_names.each do |team_name|
team = Team.order(created_at: :desc).where(name: team_name).first
if team.blank? then
team = Team.create({ name: team_name[0..99] })
end
team = Team.create(name: team_name[0..99]) if team.blank
team_ids << team.id
end