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Merge branch 'develop' into features/new-task-layout

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This commit is contained in:
aignatov-bio 2020-04-23 14:07:40 +02:00
commit 10fdd0c1c7
43 changed files with 641 additions and 208 deletions
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2
VERSION
View file

@ -1 +1 @@
1.18.6
1.18.7

25
app/assets/javascripts/sidebar.js
View file

@ -28,6 +28,31 @@ var Sidebar = (function() {
}
function loadLastState() {
var currentProject = $(SIDEBAR_ID).attr('data-current-project');
var currentExperiment = $(SIDEBAR_ID).attr('data-current-experiment');
var currentTask = $(SIDEBAR_ID).attr('data-current-task');
if (currentProject) {
let projectBranch = $(`.tree-child[data-branch-id="pro${currentProject}"]`).attr('data-active', 'true');
projectBranch.prev().addClass('active');
if (!currentExperiment) projectBranch.closest('.branch').addClass('active');
}
if (currentExperiment) {
let experimentBranch = $(`.tree-child[data-branch-id="exp${currentExperiment}"]`).attr('data-active', 'true');
experimentBranch.prev().addClass('active');
if (!currentTask) {
experimentBranch.closest('.branch')
.addClass('show-canvas-handler')
.addClass('active');
}
}
if (currentTask) {
$(`.leaf[data-module-id="${currentTask}"]`).addClass('active');
}
toggleTree($(SIDEBAR_ID).find('.tree-child[data-active="true"]'));
toggleTree($(SIDEBAR_ID).find('.tree-child.hidden').filter(sessionStorage.getItem(STORAGE_TREE_KEY)));
PerfectSb().update_all();

23
app/assets/stylesheets/dashboard/calendar.scss
View file

@ -1,7 +1,10 @@
// scss-lint:disable SelectorDepth
// scss-lint:disable NestingDepth
.dashboard-container .calendar-widget {
--calendar-day-size: 32px;
grid-column: 10 / span 3;
grid-row: 1 / span 6;
min-height: 320px;
@ -57,12 +60,12 @@
animation-timing-function: $timing-function-sharp;
border-radius: 50%;
display: flex;
height: 32px;
height: var(--calendar-day-size);
justify-content: center;
position: relative;
transition: .3s;
user-select: none;
width: 32px;
width: var(--calendar-day-size);
&.adjacent-month {
color: $color-alto;
@ -75,9 +78,9 @@
border-radius: 50%;
cursor: pointer;
display: flex;
height: 30px;
height: calc(var(--calendar-day-size) - 2px);
justify-content: center;
width: 30px;
width: calc(var(--calendar-day-size) - 2px);
&:hover {
background: $color-concrete;
@ -91,9 +94,9 @@
border-radius: 50%;
content: "";
height: 4px;
left: 14px;
left: calc((var(--calendar-day-size) / 2) - 2px);
position: absolute;
top: 24px;
top: calc((var(--calendar-day-size) / 2) + 8px);
width: 4px;
}
}
@ -143,3 +146,11 @@
}
}
}
@media (max-width: 700px) {
.dashboard-container .calendar-widget {
--calendar-day-size: 28px;
grid-column: 1 / span 12;
grid-row: 2;
}
}

56
app/assets/stylesheets/dashboard/current_tasks.scss
View file

@ -335,3 +335,59 @@
}
}
}
@media (max-width: 700px) {
.dashboard-container .current-tasks-widget {
--widget-header-size: 72px;
grid-row: 1;
min-height: 450px;
.widget-title {
flex-basis: 100%;
line-height: 36px;
}
.actions-container {
flex-grow: 0;
padding: 0;
}
.current-tasks-navbar {
flex-basis: 0;
flex-grow: 1;
}
.search-container {
margin-right: 5px;
.task-search-field {
width: 150px;
&:focus {
width: 150px;
}
}
}
.current-tasks-list {
.current-task-item {
.item-row {
flex-wrap: wrap;
.task-due-date {
@include font-small;
.fas {
display: none;
}
}
.task-progress-container {
flex-basis: 100%;
max-width: none;
}
}
}
}
}
}

12
app/assets/stylesheets/dashboard/quick_start.scss
View file

@ -1,3 +1,6 @@
// scss-lint:disable SelectorDepth
// scss-lint:disable NestingDepth
.dashboard-container .quick-start-widget {
grid-column: 1 / span 2;
grid-row: 7 / span 6;
@ -34,3 +37,12 @@
grid-row: 5 / span 4;
}
}
@media (max-width: 700px) {
.dashboard-container .quick-start-widget {
--widget-header-size: 36px;
grid-column: 1 / span 12;
grid-row: 4;
min-height: 300px;
}
}

38
app/assets/stylesheets/dashboard/recent_work.scss
View file

@ -83,3 +83,41 @@
}
}
}
@media (max-width: 700px) {
.dashboard-container .recent-work-widget {
--widget-header-size: 72px;
grid-row: 3;
min-height: 450px;
.widget-title {
flex-basis: 100%;
line-height: 36px;
}
.recent-work-container {
.recent-work-item {
flex-wrap: wrap;
margin: 5px 0;
.object-name {
flex-basis: 100%;
line-height: 18px;
}
.object-type {
flex-basis: 0;
flex-grow: 1;
line-height: 18px;
}
.object-changed {
flex-basis: 0;
flex-grow: 1;
line-height: 18px;
text-align: right;
}
}
}
}
}

21
app/assets/stylesheets/dashboard/show.scss
View file

@ -1,6 +1,9 @@
// scss-lint:disable SelectorDepth
// scss-lint:disable NestingDepth
.dashboard-container {
--widget-header-size: 44px;
--dashboard-widgets-gap: 30px;
--widget-header-size: 44px;
display: grid;
grid-column-gap: var(--dashboard-widgets-gap);
grid-row-gap: var(--dashboard-widgets-gap);
@ -19,7 +22,6 @@
align-items: center;
border-bottom: $border-tertiary;
display: flex;
height: var(--widget-header-size);
padding-left: 16px;
@ -54,3 +56,18 @@
--dashboard-widgets-gap: 16px;
}
}
@media (max-width: 700px) {
.dashboard-container {
--widget-header-size: 72px;
grid-template-rows: auto;
.widget-header {
flex-wrap: wrap;
.sci-secondary-navbar {
height: 36px;
}
}
}
}

33
app/assets/stylesheets/forgot_password.scss Normal file
View file

@ -0,0 +1,33 @@
// scss-lint:disable SelectorDepth NestingDepth IdSelector
.forgot-password-layout {
#content-wrapper {
margin-left: 0;
.container:first-child {
padding: 0;
}
}
.forgot-password-container {
display: flex;
.forgot-password-form-wrapper {
flex-basis: 50%;
flex-grow: 1;
.center-block-narrow {
margin-top: 72px;
padding: 0 50px;
}
.forgot-password-title {
margin-bottom: 24px;
}
.sci-input-container {
margin-bottom: 24px;
}
}
}
}

13
app/assets/stylesheets/partials/_tree_view.scss
View file

@ -58,6 +58,7 @@
.canvas-center-on {
animation-timing-function: $timing-function-sharp;
color: $color-volcano;
display: none;
flex-basis: 36px;
flex-shrink: 0;
line-height: 50px;
@ -66,6 +67,12 @@
transition: .2s;
}
&.active {
.line-wrap {
font-weight: bold;
}
}
&:hover {
.line-wrap {
background-color: $color-alto;
@ -94,6 +101,12 @@
color: $brand-primary;
}
}
&.show-canvas-handler {
.canvas-center-on {
display: inline-block;
}
}
}
.leaf {

1
app/assets/stylesheets/shared_styles/constants.scss Normal file
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@ -0,0 +1 @@
@import "constants/*";

5
app/assets/stylesheets/shared_styles/elements/input_fields.scss
View file

@ -3,6 +3,7 @@
.sci-input-container {
display: inline-block;
position: relative;
width: 100%;
label {
@include font-small;
@ -14,8 +15,8 @@
.sci-input-field {
@include font-button;
animation-timing-function: $timing-function-sharp;
border: $border-default;
border-radius: $border-radius-default;
border: $border-secondary;
border-radius: $border-radius-default !important;
box-shadow: none;
height: 36px;
outline: 0;

2
app/assets/stylesheets/shared_styles/elements/navigation.scss
View file

@ -1,6 +1,7 @@
.sci-secondary-navbar {
display: flex;
height: 100%;
overflow-x: auto;
.navbar-link {
@include font-small;
@ -13,6 +14,7 @@
position: relative;
text-decoration: none;
text-transform: uppercase;
white-space: nowrap;
&:hover {
color: $color-volcano;

61
app/assets/stylesheets/sign_up.scss Normal file
View file

@ -0,0 +1,61 @@
// scss-lint:disable SelectorDepth NestingDepth IdSelector
.sign-up-layout {
#content-wrapper {
margin-left: 0;
.container:first-child {
padding: 0;
}
}
.sign-up-container {
display: flex;
.sign-up-form-wrapper {
flex-basis: 50%;
flex-grow: 1;
.center-block-narrow {
margin-top: 72px;
padding: 0 50px;
}
.sign-up-title {
margin-bottom: 24px;
}
.sci-input-container {
margin-bottom: 24px;
.minimum-password-length {
@include font-small;
}
}
.sign-up-button {
padding: 7px 32px;
}
.linkedin-container {
margin-bottom: 24px;
.linkedin-link {
margin-right: 15px;
&:hover {
text-decoration: none;
}
}
.linkedin-signin-button {
margin: 0;
}
span {
font-weight: bold;
}
}
}
}
}

73
app/assets/stylesheets/sing_in.scss Normal file
View file

@ -0,0 +1,73 @@
// scss-lint:disable SelectorDepth NestingDepth IdSelector
.sign-in-layout {
#content-wrapper {
margin-left: 0;
.container:first-child {
padding: 0;
}
}
.sign-in-container {
display: flex;
.sign-in-form-wrapper {
flex-basis: 50%;
flex-grow: 1;
.center-block-narrow {
margin-top: 72px;
padding: 0 50px;
}
.log-in-title {
margin-bottom: 24px;
}
.remember-me {
align-items: center;
display: flex;
margin-bottom: 24px;
label {
margin-left: 8px;
margin-bottom: 0;
}
}
.sci-input-container {
margin-bottom: 24px;
}
.linkedin-container {
margin-bottom: 24px;
.linkedin-link {
margin-right: 15px;
&:hover {
text-decoration: none;
}
}
.linkedin-signin-button {
margin: 0;
}
span {
font-weight: bold;
}
}
.log-in-button {
padding: 7px 32px;
}
.forgot-password-link {
display: inline-block;
margin-bottom: 16px;
}
}
}
}

16
app/controllers/api/v1/inventory_columns_controller.rb
View file

@ -56,9 +56,7 @@ module Api
private
def check_manage_permissions
unless can_manage_repository_column?(@inventory_column)
raise PermissionError.new(RepositoryColumn, :manage)
end
raise PermissionError.new(RepositoryColumn, :manage) unless can_manage_repository_column?(@inventory_column)
end
def check_create_permissions
@ -66,12 +64,11 @@ module Api
end
def inventory_column_params
unless params.require(:data).require(:type) == 'inventory_columns'
raise TypeError
end
raise TypeError unless params.require(:data).require(:type) == 'inventory_columns'
params.require(:data).require(:attributes)
new_params = params
.permit(data: { attributes: %i(name data_type) })[:data]
.permit(data: { attributes: [:name, :data_type, metadata: {}] })[:data]
.merge(created_by: @current_user)
if new_params[:attributes][:data_type].present?
new_params[:attributes][:data_type] =
@ -82,9 +79,8 @@ module Api
end
def update_inventory_column_params
unless params.require(:data).require(:id).to_i == params[:id].to_i
raise IDMismatchError
end
raise IDMismatchError unless params.require(:data).require(:id).to_i == params[:id].to_i
if inventory_column_params[:attributes].include?(:data_type)
raise ActiveRecord::RecordInvalid,
I18n.t('api.core.errors.inventory_column_type.detail')

47
app/controllers/users/omniauth_callbacks_controller.rb
View file

@ -28,25 +28,40 @@ module Users
email = auth.info.email
email ||= auth.dig(:extra, :raw_info, :id_token_claims, :emails)&.first
user = User.from_omniauth(auth)
if user
# User found in database so just sign in him
sign_in_and_redirect(user)
elsif email.present?
user = User.find_by(email: email)
if user.blank?
# Create new user and identity
User.create_from_omniauth!(auth)
sign_in_and_redirect(user)
elsif provider_conf[:auto_link_on_sign_in]
# Link to existing local account
# User found in database so just signing in
return sign_in_and_redirect(user) if user.present?
if email.blank?
# No email in the token so can not link or create user
error_message = I18n.t('devise.azure.errors.no_email')
return redirect_to after_omniauth_failure_path_for(resource_name)
end
user = User.find_by(email: email)
if user.blank?
# Create new user and identity
full_name = "#{auth.info.first_name} #{auth.info.last_name}"
user = User.new(full_name: full_name,
initials: generate_initials(full_name),
email: email,
password: generate_user_password)
User.transaction do
user.save!
user.user_identities.create!(provider: auth.provider, uid: auth.uid)
sign_in_and_redirect(user)
else
# Cannot do anything with it, so just return an error
error_message = I18n.t('devise.azure.errors.no_local_user_map')
redirect_to after_omniauth_failure_path_for(resource_name)
user.update!(confirmed_at: user.created_at)
end
sign_in_and_redirect(user)
elsif provider_conf[:auto_link_on_sign_in]
# Link to existing local account
user.user_identities.create!(provider: auth.provider, uid: auth.uid)
sign_in_and_redirect(user)
else
# Cannot do anything with it, so just return an error
error_message = I18n.t('devise.azure.errors.no_local_user_map')
redirect_to after_omniauth_failure_path_for(resource_name)
end
rescue StandardError => e
Rails.logger.error e.message

3
app/helpers/form_tag_helper.rb
View file

@ -1,9 +1,10 @@
module FormTagHelper
def recaptcha_input_tag
if Rails.configuration.x.enable_recaptcha
res = "<div class='form-group "
res = "<div class='form-group sci-input-container"
res << 'has-error' if flash[:recaptcha_error]
res << "'>"
res << label_tag(:recaptcha_label, I18n.t('users.registrations.new.captcha_description'))
res << recaptcha_tags
if flash[:recaptcha_error]
res << "<span class='help-block'>"

4
app/models/application_settings.rb Normal file
View file

@ -0,0 +1,4 @@
# frozen_string_literal: true
class ApplicationSettings < Settings
end

2
app/models/experiment.rb
View file

@ -293,6 +293,8 @@ class Experiment < ApplicationRecord
my_module.last_modified_by = current_user
my_module.save!
my_module.assign_user(current_user)
ids_map[m[:id]] = my_module.id.to_s
end
my_modules.reload

15
app/models/my_module.rb
View file

@ -538,6 +538,21 @@ class MyModule < ApplicationRecord
end
end
def assign_user(user, assigned_by = nil)
user_my_modules.create(
assigned_by: assigned_by || user,
user: user
)
Activities::CreateActivityService
.call(activity_type: :assign_user_to_module,
owner: assigned_by || user,
team: experiment.project.team,
project: experiment.project,
subject: self,
message_items: { my_module: id,
user_target: user.id })
end
private
def create_blank_protocol

14
app/models/user.rb
View file

@ -354,20 +354,6 @@ class User < ApplicationRecord
.take
end
def self.create_from_omniauth!(auth)
full_name = "#{auth.info.first_name} #{auth.info.last_name}"
user = User.new(full_name: full_name,
initials: generate_initials(full_name),
email: email,
password: generate_user_password)
User.transaction do
user.save!
user.user_identities.create!(provider: auth.provider, uid: auth.uid)
user.update!(confirmed_at: user.created_at)
end
user
end
# Search all active users for username & email. Can
# also specify which team to ignore.
def self.search(

2
app/serializers/api/v1/inventory_column_serializer.rb
View file

@ -4,7 +4,7 @@ module Api
module V1
class InventoryColumnSerializer < ActiveModel::Serializer
type :inventory_columns
attributes :name, :data_type
attributes :name, :data_type, :metadata
has_many :repository_list_items,
key: :inventory_list_items,
serializer: InventoryListItemSerializer,

3
app/services/create_my_module_service.rb
View file

@ -32,6 +32,9 @@ class CreateMyModuleService
@my_module.save!
create_my_module_activity
@my_module.assign_user(@user)
@params[:experiment].generate_workflow_img
new_my_module = @my_module
end

8
app/services/spreadsheet_parser.rb
View file

@ -53,7 +53,13 @@ class SpreadsheetParser
def self.parse_row(row, sheet)
if sheet.is_a?(Roo::Excelx)
row.map { |cell| cell&.formatted_value }
row.map do |cell|
if cell.is_a?(Roo::Excelx::Cell::Number) && cell.format == 'General'
cell&.value&.to_d
else
cell&.formatted_value
end
end
else
row.map(&:to_s)
end

1
app/views/dashboards/_current_tasks.html.erb
View file

@ -13,7 +13,6 @@
<label><%= t("dashboard.current_tasks.filter.sort") %></label>
<select class="sort-filter">
<option value="date_asc" ><%= t("dashboard.current_tasks.filter.date_asc") %></option>
<option value="date_desc" ><%= t("dashboard.current_tasks.filter.date_desc") %></option>
<option value="atoz" ><%= t("dashboard.current_tasks.filter.atoz") %></option>
<option value="ztoa" ><%= t("dashboard.current_tasks.filter.ztoa") %></option>
</select>

5
app/views/shared/_sidebar.html.erb
View file

@ -12,10 +12,7 @@
<div class="tree perfect-scrollbar" data-scroll="<%= params[:scroll] %>">
<% cache [action_name, current_user, current_team] do %>
<%= render partial: 'shared/sidebar/projects', locals: {
current_project: current_project,
current_experiment: current_experiment,
current_task: current_task
} %>
} %>
<% end %>
</div>
</div>

13
app/views/shared/sidebar/_experiments.html.erb
View file

@ -1,8 +1,8 @@
<% if project.active_experiments.present? %>
<ul class="tree-child hidden" data-active="<%= project.id == current_project&.id %>" data-branch-id="pro<%= project.id %>">
<ul class="tree-child hidden" data-branch-id="pro<%= project.id %>">
<% project.active_experiments.each do |experiment| %>
<% cache [action_name, current_user, experiment] do %>
<li data-parent="candidate" class="branch <%= 'active' if experiment_page? && current_experiment == experiment %>">
<li data-parent="candidate" class="branch">
<span class="tree-link first-indent" title="<%= experiment.name %>">
<% if experiment.active_my_modules.any? %>
<i class="fas fa-caret-right tree-toggle"></i>
@ -10,15 +10,10 @@
<%= link_to experiment.name,
experiment_action_to_link_to(experiment),
class: 'overview_exp_label line-wrap',
style: (current_experiment == experiment ? 'font-weight: bold' : ''),
data: { type: 'experiment', id: experiment.id }
%>
%>
</span>
<%= render partial: 'shared/sidebar/my_modules', locals: {
experiment: experiment,
current_experiment: current_experiment,
current_task: current_task
} %>
<%= render partial: 'shared/sidebar/my_modules', locals: { experiment: experiment } %>
</li>
<% end %>
<% end %>

6
app/views/shared/sidebar/_my_modules.html.erb
View file

@ -1,13 +1,13 @@
<% if experiment.active_my_modules.present? %>
<ul class="tree-child hidden" data-active="<%= current_experiment&.id == experiment.id %>" data-branch-id="exp<%= experiment.id %>">
<ul class="tree-child hidden" data-branch-id="exp<%= experiment.id %>">
<% experiment.active_my_modules.each do |my_module| %>
<li class="leaf <%= 'active' if module_page? && current_task == my_module %>" data-module-id="<%= my_module.id %>">
<li class="leaf" data-module-id="<%= my_module.id %>">
<span class="tree-link task-tree-link second-indent" title="<%= my_module.name %>">
<%= link_to my_module.name,
module_action_to_link_to(my_module),
class: 'line-wrap',
data: { type: 'my_module', id: my_module.id } %>
<% if experiment_page? && current_experiment == experiment && action_name =='canvas' %>
<% if action_name =='canvas' %>
<a href="" class="canvas-center-on"><i class="fas fa-map-marker-alt"></i></a>
<% end %>
</span>

10
app/views/shared/sidebar/_projects.html.erb
View file

@ -2,7 +2,7 @@
<% @projects_tree.each do |project| %>
<% cache [action_name, current_user, project] do %>
<li data-parent="candidate"
class="branch <%= 'active' if project_page? && current_project == project %>" >
class="branch" >
<span class="tree-link no-indent" title="<%= project.name %>">
<% if project.active_experiments.any? %>
<i class="fas fa-caret-right tree-toggle"></i>
@ -11,15 +11,9 @@
project_action_to_link_to(project),
title: project.name,
class: 'line-wrap',
style: (current_project == project ? 'font-weight: bold' : ''),
data: { type: 'project', id: project.id } %>
</span>
<%= render partial: 'shared/sidebar/experiments', locals: {
project: project,
current_project: current_project,
current_experiment: current_experiment,
current_task: current_task
} %>
<%= render partial: 'shared/sidebar/experiments', locals: { project: project } %>
</li>
<% end %>
<% end %>

42
app/views/users/passwords/new.html.erb
View file

@ -1,25 +1,29 @@
<% provide(:head_title, t("devise.passwords.new.head_title")) %>
<% content_for(:body_class, 'forgot-password-layout') %>
<div class="forgot-password-container">
<div class="forgot-password-form-wrapper">
<div class="center-block center-block-narrow">
<h1 class="forgot-password-title"><%=t "devise.passwords.new.title" %></h1>
<div class="center-block center-block-narrow">
<h2><%=t "devise.passwords.new.title" %></h2>
<%= form_for(resource, as: resource_name, url: password_path(resource_name), html: { method: :post }) do |f| %>
<%= form_for(resource, as: resource_name, url: password_path(resource_name), html: { method: :post }) do |f| %>
<% if not resource.errors.empty? %>
<div class="alert alert-danger" id="alert-flash">
<%= devise_error_messages! %>
</div>
<% end %>
<% if not resource.errors.empty? %>
<div class="alert alert-danger" id="alert-flash">
<%= devise_error_messages! %>
<div class="form-group sci-input-container">
<%= f.label :email %><br /actions>
<%= f.email_field :email, autofocus: true, class: "form-control sci-input-field" %>
</div>
<div class="form-group">
<%= f.submit t("devise.passwords.new.submit"), class: "btn btn-primary" %>
</div>
<% end %>
<%= render partial: 'users/shared/links', locals: {linkedin_skip: true} %>
</div>
<% end %>
<div class="form-group">
<%= f.label :email %><br /actions>
<%= f.email_field :email, autofocus: true, class: "form-control" %>
</div>
<div class="form-group">
<%= f.submit t("devise.passwords.new.submit"), class: "btn btn-primary" %>
</div>
<% end %>
<%= render "users/shared/links" %>
</div>
</div>

95
app/views/users/registrations/new.html.erb
View file

@ -1,53 +1,64 @@
<% provide(:head_title, t('users.registrations.new.head_title')) %>
<% content_for(:body_class, 'sign-up-layout') %>
<div class="sign-up-container">
<div class="sign-up-form-wrapper">
<div class="center-block center-block-narrow">
<h1 class="sign-up-title"><%= t 'users.registrations.new.head_title' %></h1>
<div class="center-block center-block-narrow">
<h1><%= t 'users.registrations.new.head_title' %></h1>
<div data-hook="sign-up-form-hook">
<%= form_for(:user, as: resource_name, url: registration_path(resource_name), html: { id: "sign-up-form" } ) do |f| %>
<%- if Rails.configuration.x.enable_user_registration && Rails.configuration.x.linkedin_signin_enabled && @oauth_authorize != true %>
<div class="linkedin-container">
<%= render partial: "users/shared/linkedin_sign_in_links", locals: { resource_name: resource_name } %>
<span><%= t("devise.sessions.new.or") %></span>
</div>
<% end -%>
<div class="form-group">
<%= f.label :full_name %>
<%= f.text_field :full_name, autofocus: true, class: 'form-control' %>
</div>
<div data-hook="sign-up-form-hook">
<%= form_for(:user, as: resource_name, url: registration_path(resource_name), html: { id: "sign-up-form" } ) do |f| %>
<div class="form-group">
<%= f.label :email %>
<%= f.email_field :email, class: 'form-control' %>
</div>
<div class="form-group sci-input-container">
<%= f.label :full_name, t('users.registrations.new.full_name_label') %>
<%= f.text_field :full_name, autofocus: true, class: 'form-control sci-input-field' %>
</div>
<div class="form-group">
<%= f.label :password %>
<% if @minimum_password_length %>
<em>(<%= @minimum_password_length %> characters minimum)</em>
<div class="form-group sci-input-container">
<%= f.label :email, t('users.registrations.new.email_label') %>
<%= f.email_field :email, class: 'form-control sci-input-field' %>
</div>
<div class="form-group sci-input-container">
<%= f.label :password, t('users.registrations.new.password_label') %>
<% if @minimum_password_length %>
<em class="minimum-password-length"><%= t('users.registrations.new.minimum_password_length', password_length: @minimum_password_length) %></em>
<% end %>
<%= f.password_field :password, autocomplete: 'off', class: 'form-control sci-input-field' %>
</div>
<div class="form-group sci-input-container" id="password_confirmation_form">
<%= f.label :password_confirmation, t('users.registrations.new.password_confirmation_label') %>
<%= f.password_field :password_confirmation, autocomplete: 'off', class: 'form-control sci-input-field' %>
</div>
<% if Rails.configuration.x.new_team_on_signup %>
<div class="form-group sci-input-container" id="team_name_form">
<%= label :team, :name, t('users.registrations.new.team_name_label') %>
<% if @team %>
<%= text_field :team, :name, class: 'form-control sci-input-field', value: @team.name,
placeholder: t('users.registrations.new.team_name_placeholder') %>
<% else %>
<%= text_field :team, :name, class: 'form-control sci-input-field',
placeholder: t('users.registrations.new.team_name_placeholder') %>
<% end %>
</div>
<% end %>
<%= recaptcha_input_tag %>
<div class="form-group" data-hook="sign-up-form-submit">
<%= f.submit 'Sign up', class: 'btn btn-primary sign-up-button' %>
</div>
<% end %>
<%= f.password_field :password, autocomplete: 'off', class: 'form-control' %>
</div>
<%= render partial: 'users/shared/links', locals: {linkedin_skip: true} %>
</div>
<div class="form-group" id="password_confirmation_form">
<%= f.label :password_confirmation %>
<%= f.password_field :password_confirmation, autocomplete: 'off', class: 'form-control' %>
</div>
<% if Rails.configuration.x.new_team_on_signup %>
<div class="form-group" id="team_name_form">
<%= label :team, :name, t('users.registrations.new.team_name_label') %>
<% if @team %>
<%= text_field :team, :name, class: 'form-control', value: @team.name,
placeholder: t('users.registrations.new.team_name_placeholder') %>
<% else %>
<%= text_field :team, :name, class: 'form-control',
placeholder: t('users.registrations.new.team_name_placeholder') %>
<% end %>
<span><small><%= t 'users.registrations.new.team_name_help' %></small></span>
</div>
<% end %>
<%= recaptcha_input_tag %>
<div class="form-group" data-hook="sign-up-form-submit">
<%= f.submit 'Sign up', class: 'btn btn-primary' %>
</div>
<% end %>
</div>
<%= render 'users/shared/links' %>
</div>
<% if resource and not resource.errors.empty? %>

74
app/views/users/sessions/new.html.erb
View file

@ -1,36 +1,46 @@
<% provide(:head_title, t("devise.sessions.new.head_title")) %>
<% content_for(:body_class, 'sign-in-layout') %>
<div class="sign-in-container">
<div class="sign-in-form-wrapper">
<div class="center-block center-block-narrow">
<h1 class="log-in-title"><%=t "devise.sessions.new.title" %></h1>
<div class="center-block center-block-narrow">
<h1><%=t "devise.sessions.new.title" %></h1>
<%- if Rails.configuration.x.enable_user_registration && Rails.configuration.x.linkedin_signin_enabled && @oauth_authorize != true %>
<div class="linkedin-container">
<%= render partial: "users/shared/linkedin_sign_in_links", locals: { resource_name: resource_name } %>
<span><%= t("devise.sessions.new.or") %></span>
</div>
<% end -%>
<%= form_for(resource, as: resource_name, url: session_path(resource_name)) do |f| %>
<div class="input-group">
<span class="input-group-addon" style="text-transform: capitalize;">
<%= :email %>
</span>
<%= f.email_field :email, autofocus: true, class: "form-control", placeholder: t("devise.sessions.new.email_placeholder") %>
<%= form_for(resource, as: resource_name, url: session_path(resource_name)) do |f| %>
<div class="input-group sci-input-container">
<%= f.label :email, t("devise.sessions.new.email_field") %>
<%= f.email_field :email, autofocus: true, class: "form-control sci-input-field", placeholder: t("devise.sessions.new.email_placeholder") %>
</div>
<div class="input-group sci-input-container">
<%= f.label :password, t("devise.sessions.new.password_field") %>
<%= f.password_field :password, autocomplete: "off", class: "form-control sci-input-field", placeholder: t("devise.sessions.new.password_placeholder") %>
</div>
<% if devise_mapping.rememberable? && !@simple_sign_in %>
<div class="field remember-me">
<div class="sci-checkbox-container">
<%= f.check_box :remember_me, class: "sci-checkbox" %>
<span class="sci-checkbox-label"></span>
</div>
<%= f.label :remember_me, t("devise.sessions.new.remember_me") %>
</div>
<% end %>
<%= hidden_field_tag(:simple_sign_in, @simple_sign_in) %>
<div class="actions" style="margin-top: 10px; margin-bottom: 10px;">
<%= f.submit t("devise.sessions.new.submit"), class: "btn btn-primary log-in-button" %>
</div>
<% end %>
<%= render partial: "users/shared/links", locals: {linkedin_skip: true} unless @simple_sign_in %>
</div>
<div class="input-group" style="margin-top: 10px;">
<span class="input-group-addon" style="text-transform: capitalize;">
<%= :password %>
</span>
<%= f.password_field :password, autocomplete: "off", class: "form-control", placeholder: t("devise.sessions.new.password_placeholder") %>
</div>
<% if devise_mapping.rememberable? && !@simple_sign_in %>
<div class="field" style="margin-top: 10px;">
<%= f.check_box :remember_me %>
<%= f.label :remember_me %>
</div>
<% end %>
<%= hidden_field_tag(:simple_sign_in, @simple_sign_in) %>
<div class="actions" style="margin-top: 10px; margin-bottom: 10px;">
<%= f.submit t("devise.sessions.new.submit"), class: "btn btn-primary" %>
</div>
<% end %>
<%= render "users/shared/links" unless @simple_sign_in %>
</div>
</div>
</div>

10
app/views/users/shared/_linkedin_sign_in_links.html.erb Normal file
View file

@ -0,0 +1,10 @@
<%- if devise_mapping.omniauthable? && resource_class.omniauth_providers.any? %>
<%= link_to omniauth_authorize_path(resource_name, :linkedin), method: :post, title: "Sign in with LinkedIn", class: 'linkedin-link' do %>
<%= image_tag('linkedin/Sign-in-Large---Default.png',
class: 'linkedin-signin-button',
alt: "Sign in with LinkedIn",
onmouseover: "src='#{image_path('linkedin/Sign-in-Large---Hover.png')}'",
onmouseout: "src='#{image_path('linkedin/Sign-in-Large---Default.png')}'",
onclick: "src='#{image_path('linkedin/Sign-in-Large---Active.png')}'") %>
<% end -%>
<% end -%>

21
app/views/users/shared/_links.html.erb
View file

@ -5,12 +5,12 @@
<%= link_to login, new_session_path(resource_name) %><br />
<% end -%>
<%- if devise_mapping.registerable? && Rails.configuration.x.enable_user_registration && controller_name != 'registrations' %>
<%= link_to t("devise.links.signup"), new_registration_path(resource_name) %><br />
<%- if devise_mapping.recoverable? && controller_name != 'passwords' && controller_name != 'registrations' %>
<%= link_to t("devise.links.forgot"), new_password_path(resource_name), class: 'forgot-password-link' %><br />
<% end -%>
<%- if devise_mapping.recoverable? && controller_name != 'passwords' && controller_name != 'registrations' %>
<%= link_to t("devise.links.forgot"), new_password_path(resource_name) %><br />
<%- if devise_mapping.registerable? && Rails.configuration.x.enable_user_registration && controller_name != 'registrations' %>
<%= link_to t("devise.links.signup"), new_registration_path(resource_name), class: 'signup-link' %><br />
<% end -%>
<%- if Rails.configuration.x.enable_email_confirmations && devise_mapping.confirmable? && controller_name != 'confirmations' %>
@ -25,16 +25,9 @@
<div data-hook="omniauth-sign-in-links"></div>
<% end -%>
<%- if Rails.configuration.x.enable_user_registration && Rails.configuration.x.linkedin_signin_enabled && @oauth_authorize != true %>
<%- if devise_mapping.omniauthable? && resource_class.omniauth_providers.any? && controller_name != 'registrations' %>
<%= link_to omniauth_authorize_path(resource_name, :linkedin), method: :post, :title => "Sign in with LinkedIn" do %>
<%= image_tag('linkedin/Sign-in-Large---Default.png',
class: 'linkedin-signin-button',
alt: "Sign in with LinkedIn",
onmouseover: "src='#{image_path('linkedin/Sign-in-Large---Hover.png')}'",
onmouseout: "src='#{image_path('linkedin/Sign-in-Large---Default.png')}'",
onclick: "src='#{image_path('linkedin/Sign-in-Large---Active.png')}'") %>
<% end -%>
<%- unless defined?(linkedin_skip) %>
<%- if Rails.configuration.x.enable_user_registration && Rails.configuration.x.linkedin_signin_enabled && @oauth_authorize != true %>
<%= render partial: "users/shared/linkedin_sign_in_links", locals: { resource_name: resource_name } %>
<% end -%>
<% end -%>

35
config/initializers/azure_ad.rb
View file

@ -34,4 +34,39 @@ Rails.application.configure do
config.x.azure_ad_apps[value][:sign_in_policy] = ENV["#{app_name}_AZURE_AD_SIGN_IN_POLICY"]
end
end
# Checking additional configurations in ApplicationSettings JSON. Key and values should be strings there.
begin
if ApplicationSettings.instance.values['azure_ad_apps']&.is_a?(Array)
config.x.azure_ad_apps ||= HashWithIndifferentAccess.new
settings = ApplicationSettings.instance
settings.values['azure_ad_apps'].each do |azure_ad_app|
app_config = {}
app_id = azure_ad_app['app_id']
Rails.logger.error('No app_id present for the entry in Azure app settings') && next unless app_id
app_config[:iss] = azure_ad_app['iss']
Rails.logger.error("No iss for #{app_id} Azure app") && next unless app_config[:iss]
app_config[:conf_url] = azure_ad_app['conf_url']
Rails.logger.error("No conf_url for #{app_id} Azure app") && next unless app_config[:conf_url]
app_config[:provider] = azure_ad_app['provider_name']
Rails.logger.error("No provider_name for #{app_id} Azure app") && next unless app_config[:provider]
app_config[:enable_sign_in] = azure_ad_app['enable_sign_in'] == 'true'
if app_config[:enable_sign_in]
app_config[:sign_in_label] = azure_ad_app['sign_in_label'] || 'Sign in with Azure AD'
app_config[:auto_link_on_sign_in] = azure_ad_app['auto_link_on_sign_in'] == 'true'
app_config[:sign_in_policy] = azure_ad_app['sign_in_policy'] if azure_ad_app['sign_in_policy']
end
config.x.azure_ad_apps[app_id] = app_config
end
end
rescue ActiveRecord::ActiveRecordError, PG::ConnectionBad
Rails.logger.info('Not connected to database, skipping additional Azure AD configuration')
end
end

3
config/locales/dashboard/en.yml
View file

@ -10,8 +10,7 @@ en:
title: "Filters"
clear: "Clear"
sort: "Sort by"
date_asc: "Due Date Ascending"
date_desc: "Due Date Descending"
date_asc: "Due Date"
atoz: "From A to Z"
ztoa: "From Z to A"
display: "Display"

18
config/locales/en.yml
View file

@ -19,15 +19,19 @@ en:
new:
head_title: "Forgot password"
title: "Forgot your password?"
submit: "Send me reset password instructions"
submit: "Reset password"
registrations:
password_changed: "Password successfully updated."
sessions:
new:
head_title: "Log in"
title: "Log in"
email_placeholder: "username@email.com"
password_placeholder: "pass****"
or: "OR"
email_field: "E-mail"
email_placeholder: "john.doe@email.com"
password_field: "Password"
password_placeholder: "Enter password"
remember_me: "Remember me"
submit: "Log in"
create:
team_name: "%{user}'s projects"
@ -56,6 +60,7 @@ en:
errors:
generic: "Failed to sign in user"
no_local_user_map: "No local user record found"
no_email: "Email is missing in auth token"
failed_to_save: "Failed to create new user"
doorkeeper:
@ -1573,7 +1578,12 @@ en:
head_title: "Sign up"
team_name_label: "Team name"
team_name_placeholder: "e.g. John's lab"
team_name_help: "This is the name of your lab or your group. You can invite other members to your team if needed."
email_label: "E-mail"
full_name_label: "Full name"
password_label: "Password"
minimum_password_length: "(%{password_length} characters minimum)"
password_confirmation_label: "Password confirmation"
captcha_description: "Let us know you’re human. Enter the captcha below."
new_with_provider:
head_title: "Complete the Sign up"
statistics:

4
features/sessions/forgot_password.feature
View file

@ -14,14 +14,14 @@ Background:
Scenario: User forgot their password and requests for new password
Given I am on reset password page
Then I fill in "nonadmin@myorg.com" in "#user_email" field
And I click "Send me reset password instruction" button
And I click "Reset password" button
Then I should see "You will receive an email with instructions on how to reset your password in a few minutes." flash message
@javascript
Scenario: User forgot their password and enters non valid email
Given I am on reset password page
Then I fill in "nonuser@myorg.com" in "#user_email" field
And I click "Send me reset password instruction" button
And I click "Reset password" button
Then I should see "Email not found"
@javascript

8
features/sessions/sign_up.feature
View file

@ -14,7 +14,7 @@ Feature: Sign up
Scenario: Sign up for an existing user
Given I visit the sign up page
Then I fill the sign up form with
| Full name | Email | Password | Password confirmation | Team name |
| Full name | E-mail | Password | Password confirmation | Team name |
| Magnus | tusk@gmail.com | asdf1234 | asdf1234 | SpliceGirls |
And I click on "Sign up"
Then I should see "has already been taken"
@ -23,7 +23,7 @@ Feature: Sign up
Scenario: Sign up for an non-existent user
Given I visit the sign up page
Then I fill the sign up form with
| Full name | Email | Password | Password confirmation | Team name |
| Full name | E-mail | Password | Password confirmation | Team name |
| Magnus | magnus@gmail.com | asdf1234 | asdf1234 | SpliceGirls |
And I click on "Sign up"
Then I should be on homepage
@ -32,7 +32,7 @@ Feature: Sign up
Scenario: Unsuccessful sign up, password confirmation does not match
Given I visit the sign up page
Then I fill the sign up form with
| Full name | Email | Password | Password confirmation | Team name |
| Full name | E-mail | Password | Password confirmation | Team name |
| Magnus | magnus@gmail.com | asdf1234 | asdf1234567 | SpliceGirls |
And I click on "Sign up"
Then I should see "doesn't match Password"
@ -41,7 +41,7 @@ Feature: Sign up
Scenario: Unsuccessful sign up, team name is missing
Given I visit the sign up page
Then I fill the sign up form with
| Full name | Email | Password | Password confirmation |
| Full name | E-mail | Password | Password confirmation |
| Magnus | magnus@gmail.com | asdf1234 | asdf1234 |
And I click on "Sign up"
Then I should see "is too short (minimum is 2 characters)"

2
features/step_definitions/users_steps.rb
View file

@ -36,7 +36,7 @@ end
Given("I click on Reset Password link in the reset password email for user {string}") do |email|
visit new_user_password_path
fill_in 'user_email', with: email
click_button 'Send me reset password instruction'
click_button 'Reset password'
Delayed::Worker.new.work_off
sleep 1

2
lib/omniauth/strategies/custom_azure_active_directory.rb
View file

@ -25,7 +25,7 @@ module OmniAuth
response_mode: response_mode,
response_type: response_type,
nonce: new_nonce,
scope: 'openid'
scope: 'openid profile email'
}
params[:p] = options[:sign_in_policy] if options[:sign_in_policy].present?

11
spec/models/experiment_spec.rb
View file

@ -103,7 +103,9 @@ describe Experiment, type: :model do
expect(Activities::CreateActivityService)
.to(receive(:call)
.with(hash_including(activity_type: :create_module)))
expect(Activities::CreateActivityService)
.to(receive(:call)
.with(hash_including(activity_type: :assign_user_to_module)))
function_call
end
@ -137,12 +139,15 @@ describe Experiment, type: :model do
.to(receive(:call)
.with(hash_including(activity_type:
:clone_module))).exactly(3).times
expect(Activities::CreateActivityService)
.to(receive(:call)
.with(hash_including(activity_type:
:assign_user_to_module))).exactly(3).times
function_call
end
it 'creats 3 new activities in DB' do
expect { function_call }.to change { Activity.all.count }.by(3)
expect { function_call }.to change { Activity.all.count }.by(6)
end
end

10
yarn.lock
View file

@ -1136,7 +1136,7 @@ adjust-sourcemap-loader@^1.1.0:
object-path "^0.9.2"
regex-parser "^2.2.9"
agent-base@4, agent-base@^4.1.0:
agent-base@4, agent-base@^4.3.0:
version "4.3.0"
resolved "https://registry.yarnpkg.com/agent-base/-/agent-base-4.3.0.tgz#8165f01c436009bccad0b1d122f05ed770efc6ee"
integrity sha512-salcGninV0nPrwpGNn4VTXBb1SOuXQBiqbrNXoeizJsHrsL6ERFM2Ne3JUSBWRE6aeNJI2ROP/WEEIDUiDe3cg==
@ -4659,11 +4659,11 @@ https-browserify@^1.0.0:
integrity sha1-7AbBDgo0wPL68Zn3/X/Hj//QPHM=
https-proxy-agent@^2.2.0:
version "2.2.1"
resolved "https://registry.yarnpkg.com/https-proxy-agent/-/https-proxy-agent-2.2.1.tgz#51552970fa04d723e04c56d04178c3f92592bbc0"
integrity sha512-HPCTS1LW51bcyMYbxUIOO4HEOlQ1/1qRaFWcyxvwaqUS9TY88aoEuHUY33kuAh1YhVVaDQhLZsnPd+XNARWZlQ==
version "2.2.4"
resolved "https://registry.yarnpkg.com/https-proxy-agent/-/https-proxy-agent-2.2.4.tgz#4ee7a737abd92678a293d9b34a1af4d0d08c787b"
integrity sha512-OmvfoQ53WLjtA9HeYP9RNrWMJzzAz1JGaSFr1nijg0PVR1JaD/xbJq1mdEIIlxGpXp9eSe/O2LgU9DJmTPd0Eg==
dependencies:
agent-base "^4.1.0"
agent-base "^4.3.0"
debug "^3.1.0"
iconv-lite@0.4.24, iconv-lite@^0.4.17, iconv-lite@^0.4.24, iconv-lite@^0.4.4, iconv-lite@~0.4.13: