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Merge branch 'features/protocol_versioning' into sb_SCI-8007

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sboursen-scinote 2023-03-08 11:36:22 +01:00
parent 6a885d4023 66ec451d5e
commit a25a49a051
52 changed files with 553 additions and 406 deletions
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4
app/assets/javascripts/access_permissions/user_assignments.js
View file

@ -8,7 +8,7 @@
let submitBtn = $(this).find('input[type="submit"]');
$(this).find('input:checked').each((_, el) => {
let select = $(el).closest('.row').find('select');
let select = $(el).closest('.new-member-item').find('select');
let selectValue = parseInt(select.val(), 10);
values.push(selectValue);
count += 1;
@ -48,7 +48,7 @@
$(document).on('click', '.user-assignment-dropdown .user-role-selector', function() {
let roleId = $(this).data('role-id');
$(this).closest('.dropdown').find('#user_assignment_user_role_id').val(roleId);
$(this).closest('.dropdown').find('#user_assignment_user_role_id, .default-public-user-role-id').val(roleId);
$(this).closest('form').trigger('submit');
});
}

23
app/assets/javascripts/protocols/index.js
View file

@ -403,8 +403,8 @@ var ProtocolsIndex = (function() {
let protocolsContainer = '.protocols-container';
let versionsModal = '#protocol-versions-modal';
protocolsTableEl.on('click', '.protocol-versions-link', function(e) {
$.get(this.href, function(data) {
function loadVersionModal(href) {
$.get(href, function(data) {
$(protocolsContainer).append($.parseHTML(data.html));
$(versionsModal).modal('show');
inlineEditing.init();
@ -415,12 +415,16 @@ var ProtocolsIndex = (function() {
$(versionsModal).remove();
});
});
}
protocolsTableEl.on('click', '.protocol-versions-link', function(e) {
loadVersionModal(this.href);
e.stopPropagation();
e.preventDefault();
});
$(protocolsContainer).on('click', '#protocolVersions', function() {
$(`tr[data-row-id=${rowsSelected[0]}] .protocol-versions-link`).click();
loadVersionModal($(`tr[data-row-id=${rowsSelected[0]}]`).data('versions-url'));
});
}
@ -512,13 +516,12 @@ var ProtocolsIndex = (function() {
url: $el.data('url'),
data: JSON.stringify({ ids: rowsSelected }),
contentType: 'application/json'
},
(data) => {
animateSpinner(null, false);
HelperModule.flashAlertMsg(data.message, 'success');
reloadTable();
}
).error((data) => {
).success((data) => {
animateSpinner(null, false);
HelperModule.flashAlertMsg(data.message, 'success');
reloadTable();
}).error((data) => {
animateSpinner(null, false);
HelperModule.flashAlertMsg(data.responseJSON.message, 'danger');
});
@ -691,6 +694,8 @@ var ProtocolsIndex = (function() {
actionToolbar.find('.btn').removeClass('btn-primary').addClass('btn-light');
actionToolbar.find('.btn:visible').first().addClass('btn-primary').removeClass('btn-light');
actionToolbar.find('.btn').removeClass('notransition');
actionToolbar.find('.emptyPlaceholder').toggleClass('hidden', actionToolbar.find('.btn:visible').length > 0);
}
/*

58
app/assets/javascripts/protocols/protocolsio.js
View file

@ -1,5 +1,5 @@
/* global animateSpinner PerfectSb initHandsOnTable */
/* global HelperModule */
/* global HelperModule dropdownSelector */
/* eslint-disable no-use-before-define, no-alert */
function applyClickCallbackOnProtocolCards() {
@ -34,6 +34,7 @@ function applyClickCallbackOnProtocolCards() {
$('.full-preview-panel').attr('data-url', currProtocolCard.data('url'));
$('.full-preview-panel').attr('data-protocol-source', currProtocolCard.data('protocol-source'));
$('.full-preview-panel').attr('data-id', currProtocolCard.data('id'));
$('.full-preview-panel').data('id', currProtocolCard.data('id'));
$('.convert-protocol').attr('disabled', false);
// Set base tag to account for relative links in the iframe
@ -194,6 +195,16 @@ function handleFormSubmit(modal) {
e.preventDefault(); // avoid to execute the actual submit of the form.
e.stopPropagation();
animateSpinner(modal, true);
const visibility = $('#protocol-preview-modal .modal-footer #visibility').prop('checked');
const defaultPublicUserRoleId = $('#protocol-preview-modal .modal-footer #default_public_user_role_id')
.prop('value');
const visibilityField = $('#protocol-preview-modal #protocol_visibility');
const defaultPublicUserRoleIdField = $('#protocol-preview-modal #protocol_default_public_user_role_id');
visibilityField.prop('value', visibility ? 'visible' : 'hidden');
defaultPublicUserRoleIdField.prop('value', defaultPublicUserRoleId);
$.ajax({
type: 'POST',
url: url,
@ -215,7 +226,7 @@ function handleFormSubmit(modal) {
function initLoadProtocolModalPreview() {
$('.convert-protocol').off('click').on('click', function(e) {
var link = $('.full-preview-panel');
const link = $('.full-preview-panel');
animateSpinner(null, true);
$.ajax({
url: link.data('url'),
@ -226,10 +237,11 @@ function initLoadProtocolModalPreview() {
},
dataType: 'json',
success: function(data) {
var modal = $('#protocol-preview-modal');
var modalTitle = modal.find('.modal-title');
var modalBody = modal.find('.modal-body');
var modalFooter = modal.find('.modal-footer');
$('#protocolsioModal').modal('hide');
const modal = $('#protocol-preview-modal');
const modalTitle = modal.find('.modal-title');
const modalBody = modal.find('.modal-body');
const modalFooter = modal.find('.modal-footer');
modalTitle.html(data.title);
modalBody.html(data.html);
@ -243,6 +255,7 @@ function initLoadProtocolModalPreview() {
showFormErrors(modal, data.validation_errors);
}
initProtocolModalPreview();
initFormSubmits();
handleFormSubmit(modal);
},
@ -272,3 +285,36 @@ applySearchCallback();
// Trigger initial retrieval of latest publications
$('form.protocols-search-bar').submit();
function initProtocolModalPreview() {
$('#protocol-preview-modal').on('change', '#visibility', function() {
const checkbox = this;
$('#protocol-preview-modal #roleSelectWrapper').toggleClass('hidden', !checkbox.checked);
});
const roleSelector = '#protocol-preview-modal #role_selector';
dropdownSelector.init(roleSelector, {
noEmptyOption: true,
singleSelect: true,
closeOnSelect: true,
selectAppearance: 'simple',
onChange: function() {
$('#protocol-preview-modal #default_public_user_role_id').val(dropdownSelector.getValues(roleSelector));
}
});
$('#protocol-preview-modal')
.on('ajax:error', 'form', function(e, error) {
let msg = error.responseJSON.error;
$('#protocol-preview-modal #protocol_name').parent().addClass('error').attr('data-error-text', msg);
})
.on('ajax:success', 'form', function(e, data) {
if (data.message) {
HelperModule.flashAlertMsg(data.message, 'success');
}
$('#protocol-preview-modal #protocol_name').parent().removeClass('error');
$('#protocol-preview-modal').modal('hide');
});
}

26
app/assets/stylesheets/access_permissions/access_modal.scss
View file

@ -1,4 +1,26 @@
#user_assignments_modal {
.btn-role-select {
padding: 0;
&:hover {
background-color: $color-white;
}
&:focus {
box-shadow: none;
}
&.disabled {
color: $color-black;
opacity: 1;
.caret {
opacity: 0;
}
}
}
.modal-body {
min-height: calc(100vh - 200px);
overflow: auto;
@ -7,9 +29,7 @@
.member-item {
border-bottom: 1px solid $modal-header-border-color;
margin: 0 .5em;
padding: .5em;
padding: .5em 0;
}
.user-assignment-role .dropdown-toggle,

1
app/assets/stylesheets/my_modules/protocols/index.scss
View file

@ -426,6 +426,7 @@
left: -125px;
max-width: 100vw;
width: 506px;
padding: 15px 0;
.dropdown-header,
.dropdown-body {

2
app/assets/stylesheets/partials/_sidebar.scss
View file

@ -162,7 +162,7 @@
&.selected {
background: $color-white;
color: $brand-primary;
font-weight: bold;
font-weight: normal;
}
.fas {

26
app/assets/stylesheets/protocols/index.scss
View file

@ -18,6 +18,15 @@
flex-direction: column;
height: 100%;
width: 100%;
tbody {
td:not(:first-child) {
max-width: 30rem;
overflow: hidden;
text-overflow: ellipsis;
white-space: nowrap;
}
}
}
.toolbar {
@ -46,10 +55,15 @@
flex-direction: column;
flex-grow: 1;
height: calc(100% - var(--datatable-pagination-row) - var(--protocol-toolbar-size));
padding-bottom: 12px;
}
.dataTables_scrollBody {
height: 100%;
td:not(:first-child) {
padding: 14px 8px;
}
}
// Cells
@ -123,6 +137,18 @@
width: 32px;
}
}
.select-block.has-draft {
align-items: center;
column-gap: 8px;
display: flex;
}
.input-field:focus-within,
.datetime-picker-container:focus-within {
border: 1px solid $brand-focus;
border-radius: 4px;
}
}
&.archived {

39
app/assets/stylesheets/protocols/preview_modal.scss
View file

@ -26,4 +26,43 @@
.general-error {
text-align: center;
}
.modal-footer {
.footer {
align-items: center;
display: flex;
justify-content: space-between;
.left-section {
column-gap: 32px;
display: flex;
justify-content: space-between;
.default-role-container {
align-items: center;
column-gap: 8px;
display: flex;
}
.sci-input-container {
display: flex;
align-items: center;
column-gap: 12px;
flex-grow: 1;
label {
margin-bottom: 0;
white-space: nowrap;
}
}
}
.right-section {
column-gap: 8px;
display: flex;
flex-basis: 0;
justify-content: flex-end;
}
}
}
}

5
app/assets/stylesheets/shared/datatable.scss
View file

@ -56,6 +56,11 @@
top: 0;
width: 100%;
.emptyPlaceholder {
color: $color-volcano;
margin-left: 12px;
}
.btn {
margin-right: .25em;
}

4
app/assets/stylesheets/shared_styles/elements/buttons.scss
View file

@ -233,6 +233,10 @@
float: left;
margin: 2px 4px 2px 0;
.fas {
margin-right: 8px;
}
&:nth-last-child(1) {
margin-right: 0;
}

4
app/assets/stylesheets/shared_styles/elements/dropdown.scss
View file

@ -2,6 +2,10 @@
@import "constants";
.dropdown-menu .divider {
margin: 5px 0;
}
.sci-dropdown {
[data-toggle="dropdown"] {
.caret {

18
app/assets/stylesheets/shared_styles/elements/modal.scss
View file

@ -7,6 +7,24 @@
}
.modal {
.modal-dialog {
.modal-body {
padding: 0;
}
.modal-content {
padding: 1.15em;
}
.modal-header {
padding: 0 0 1.15em 0;
}
.modal-footer {
padding: 1.15em 0 0 0;
}
}
.modal-absolute-close-button {
position: absolute;
right: 1em;

2
app/controllers/access_permissions/projects_controller.rb
View file

@ -38,7 +38,7 @@ module AccessPermissions
@user_assignment.update!(permitted_update_params)
log_activity(:change_user_role_on_project, @user_assignment)
propagate_job(user_assignment)
propagate_job(@user_assignment)
respond_to do |format|
format.json do

17
app/controllers/access_permissions/protocols_controller.rb
View file

@ -51,12 +51,17 @@ module AccessPermissions
permitted_create_params[:resource_members].each do |_k, user_assignment_params|
next unless user_assignment_params[:assign] == '1'
user_assignment = UserAssignment.new(user_assignment_params)
user_assignment.assignable = @protocol
user_assignment.assigned = :manually
user_assignment.team = current_team
user_assignment.assigned_by = current_user
user_assignment.save!
user_assignment = UserAssignment.find_or_initialize_by(
assignable: @protocol,
user_id: user_assignment_params[:user_id],
team: current_team
)
user_assignment.update!(
user_role_id: user_assignment_params[:user_role_id],
assigned_by: current_user,
assigned: :manually
)
created_count += 1
log_activity(:protocol_template_access_granted, user_assignment)

86
app/controllers/protocols_controller.rb
View file

@ -49,10 +49,6 @@ class ProtocolsController < ApplicationController
update_from_parent_modal
delete_steps
)
before_action :check_manage_parent_in_repository_permissions, only: %i(
update_parent
update_parent_modal
)
before_action :check_manage_all_in_repository_permissions, only: :make_private
before_action :check_restore_all_in_repository_permissions, only: :restore
before_action :check_archive_all_in_repository_permissions, only: :archive
@ -300,7 +296,7 @@ class ProtocolsController < ApplicationController
log_activity(:create_protocol_in_repository, nil, protocol: @protocol.id)
redirect_to protocol_path(@protocol)
else
render json: { error: @protocol.errors.full_messages.join(', ') }, status: :unprocessable_entity
render json: { error: @protocol.errors.messages.map { |_k, v| v }.join(', ') }, status: :unprocessable_entity
end
end
@ -393,6 +389,7 @@ class ProtocolsController < ApplicationController
flash[:error] = draft.errors.full_messages.join(', ')
redirect_to protocols_path
else
log_activity(:protocol_template_draft_created, nil, protocol: @protocol.id)
redirect_to protocol_path(draft)
end
rescue StandardError => e
@ -410,7 +407,7 @@ class ProtocolsController < ApplicationController
Protocol.transaction do
begin
@protocol.unlink
rescue Exception
rescue StandardError
transaction_error = true
raise ActiveRecord::Rollback
end
@ -477,47 +474,6 @@ class ProtocolsController < ApplicationController
end
end
def update_parent
respond_to do |format|
if @protocol.parent.can_destroy?
transaction_error = false
Protocol.transaction do
@protocol.update_parent(current_user)
rescue StandardError
transaction_error = true
raise ActiveRecord::Rollback
end
if transaction_error
# Bad request error
format.json do
render json: {
message: t('my_modules.protocols.update_parent_error')
},
status: :bad_request
end
else
# Everything good, record activity, display flash & render 200
log_activity(:update_protocol_in_repository_from_task,
@protocol.my_module.experiment.project,
my_module: @protocol.my_module.id,
protocol_repository: @protocol.parent.id)
flash[:success] = t(
'my_modules.protocols.update_parent_flash'
)
flash.keep(:success)
format.json { render json: {}, status: :ok }
end
else
format.json do
render json: {
message: t('my_modules.protocols.update_parent_error_locked')
}, status: :bad_request
end
end
end
end
def update_from_parent
protocol_can_destroy = @protocol.can_destroy?
respond_to do |format|
@ -530,7 +486,7 @@ class ProtocolsController < ApplicationController
else
@protocol.parent.parent
end
@protocol.update_from_parent(current_user, source_parent.latest_published_version)
@protocol.update_from_parent(current_user, source_parent.latest_published_version_or_self)
rescue StandardError
transaction_error = true
raise ActiveRecord::Rollback
@ -769,9 +725,9 @@ class ProtocolsController < ApplicationController
Protocol.transaction do
begin
protocol = @importer.import_new_protocol(@db_json)
rescue Exception
rescue StandardError
transaction_error = true
raise ActiveRecord:: Rollback
raise ActiveRecord::Rollback
end
end
p_name =
@ -813,7 +769,7 @@ class ProtocolsController < ApplicationController
# Create folder and xml file for each protocol and populate it
@protocols.each do |protocol|
protocol = protocol.latest_published_version || protocol
protocol = protocol.latest_published_version_or_self
protocol_dir = get_guid(protocol.id).to_s
ostream.put_next_entry("#{protocol_dir}/eln.xml")
ostream.print(generate_protocol_xml(protocol))
@ -912,19 +868,6 @@ class ProtocolsController < ApplicationController
end
end
def update_parent_modal
respond_to do |format|
format.json do
render json: {
title: t('my_modules.protocols.confirm_link_update_modal.update_parent_title'),
message: t('my_modules.protocols.confirm_link_update_modal.update_parent_message'),
btn_text: t('general.update'),
url: update_parent_protocol_path(@protocol)
}
end
end
end
def update_from_parent_modal
respond_to do |format|
format.json do
@ -1107,10 +1050,12 @@ class ProtocolsController < ApplicationController
begin
Protocol.transaction do
@protocols.find_each do |protocol|
protocol = protocol.parent if protocol.parent_id
protocol.method(action).call(current_user)
end
end
rescue
rescue StandardError => e
Rails.logger.error e.message
rollbacked = true
end
@ -1173,7 +1118,7 @@ class ProtocolsController < ApplicationController
def check_clone_permissions
load_team_and_type
protocol = Protocol.find_by(id: params[:ids][0])
@original = protocol.latest_published_version || protocol
@original = protocol.latest_published_version_or_self
if @original.blank? ||
!can_clone_protocol_in_repository?(@original) || @type == :archive
@ -1200,13 +1145,6 @@ class ProtocolsController < ApplicationController
can_delete_protocol_draft_in_repository?(@protocol)
end
def check_manage_parent_in_repository_permissions
@protocol = Protocol.find_by_id(params[:id])
render_403 unless @protocol.present? &&
can_read_protocol_in_module?(@protocol) &&
can_manage_protocol_in_repository?(@protocol.parent)
end
def check_manage_all_in_repository_permissions
@protocols = Protocol.where(id: params[:protocol_ids])
@protocols.find_each do |protocol|
@ -1251,7 +1189,7 @@ class ProtocolsController < ApplicationController
def check_load_from_repository_permissions
@protocol = Protocol.find_by(id: params[:id])
@source = Protocol.find_by(id: params[:source_id])&.latest_published_version
@source = Protocol.find_by(id: params[:source_id])&.latest_published_version_or_self
render_403 unless @protocol.present? && @source.present? &&
(can_manage_protocol_in_module?(@protocol) &&

6
app/controllers/users/settings/user_teams_controller.rb
View file

@ -193,9 +193,9 @@ module Users
Protocol.where(id: p_ids).find_each do |protocol|
protocol.record_timestamps = false
protocol.added_by = new_owner
protocol.archived_by = new_owner unless protocol.archived_by.nil?
protocol.restored_by = new_owner unless protocol.restored_by.nil?
protocol.save!
protocol.archived_by = new_owner if protocol.archived_by == user_assignment.user
protocol.restored_by = new_owner if protocol.restored_by == user_assignment.user
protocol.save!(validate: false)
protocol.user_assignments.find_by(user: new_owner)&.destroy!
protocol.user_assignments.create!(user: new_owner, user_role: UserRole.find_predefined_owner_role)
end

145
app/datatables/load_from_repository_protocols_datatable.rb
View file

@ -3,6 +3,8 @@ class LoadFromRepositoryProtocolsDatatable < CustomDatatable
include ActiveRecord::Sanitization::ClassMethods
include InputSanitizeHelper
PREFIXED_ID_SQL = "('#{Protocol::ID_PREFIX}' || COALESCE(\"protocols\".\"parent_id\", \"protocols\".\"id\"))".freeze
def initialize(view, team, user)
super(view)
@team = team
@ -12,8 +14,8 @@ class LoadFromRepositoryProtocolsDatatable < CustomDatatable
def sortable_columns
@sortable_columns ||= [
'Protocol.name',
'nr_of_versions',
'Protocol.id',
'Protocol.version_number',
'adjusted_parent_id',
'protocol_keywords_str',
'full_username_str',
'Protocol.published_on'
@ -23,20 +25,18 @@ class LoadFromRepositoryProtocolsDatatable < CustomDatatable
def searchable_columns
@searchable_columns ||= [
'Protocol.name',
'Protocol.id',
'Protocol.published_on'
"Protocol.#{PREFIXED_ID_SQL}",
'Protocol.published_on',
'Protocol.version_number',
'ProtocolKeyword.name'
]
end
# This hack is needed to display a correct amount of
# searched entries (needed for pagination).
# This is needed because of usage of GROUP operator in SQL.
# See https://github.com/antillas21/ajax-datatables-rails/issues/112
def as_json(options = {})
def as_json(_options = {})
{
draw: dt_params[:draw].to_i,
recordsTotal: get_raw_records.length,
recordsFiltered: filter_records(get_raw_records).length,
recordsTotal: get_raw_records_base.distinct.count,
recordsFiltered: records.present? ? records.first.filtered_count : 0,
data: data
}
end
@ -46,33 +46,55 @@ class LoadFromRepositoryProtocolsDatatable < CustomDatatable
# Returns json of current protocols (already paginated)
def data
records.map do |record|
parent = record.parent || record
{
'DT_RowId': record.id,
DT_RowId: parent.id,
'0': escape_input(record.name),
'1': record.nr_of_versions,
'2': record.code,
'1': record.version_number,
'2': parent.code,
'3': keywords_html(record),
'4': escape_input(record.full_username_str),
'4': escape_input(record.published_by.full_name),
'5': I18n.l(record.published_on, format: :full)
}
end
end
def get_raw_records_base
records =
Protocol
.where(team: @team)
.where(protocols: { protocol_type: Protocol.protocol_types[:in_repository_published_original] })
.joins("LEFT OUTER JOIN protocols protocol_versions "\
"ON protocol_versions.protocol_type = #{Protocol.protocol_types[:in_repository_published_version]} "\
"AND protocol_versions.parent_id = protocols.id")
.joins('LEFT OUTER JOIN "protocol_protocol_keywords" '\
'ON "protocol_protocol_keywords"."protocol_id" = "protocols"."id"')
.joins('LEFT OUTER JOIN "protocol_keywords"'\
'ON "protocol_protocol_keywords"."protocol_keyword_id" = "protocol_keywords"."id"')
.joins('LEFT OUTER JOIN users ON users.id = protocols.published_by_id').active
def new_search_condition(column, value)
model, column = column.split('.', 2)
model = model.constantize
records.group('"protocols"."id"')
casted_column = case column
when PREFIXED_ID_SQL
::Arel::Nodes::SqlLiteral.new(PREFIXED_ID_SQL)
when 'published_on'
::Arel::Nodes::NamedFunction.new(
'CAST', [Arel.sql("to_char( protocols.published_on, '#{formated_date}' ) AS VARCHAR")]
)
else
::Arel::Nodes::NamedFunction.new('CAST', [model.arel_table[column.to_sym].as(typecast)])
end
casted_column.matches("%#{ActiveRecord::Base.sanitize_sql_like(value)}%")
end
def fetch_records
super.select('COUNT("protocols"."id") OVER() AS filtered_count')
end
def get_raw_records_base
original_without_versions = @team.protocols
.left_outer_joins(:published_versions)
.where(protocol_type: Protocol.protocol_types[:in_repository_published_original])
.where(published_versions: { id: nil })
.select(:id)
published_versions = @team.protocols
.where(protocol_type: Protocol.protocol_types[:in_repository_published_version])
.order('parent_id, version_number DESC')
.select('DISTINCT ON (parent_id) id')
Protocol.where("protocols.id IN ((#{original_without_versions.to_sql}) UNION (#{published_versions.to_sql}))")
.active
.with_granted_permissions(@user, ProtocolPermissions::READ)
end
# OVERRIDE - query database for records (this will be
@ -80,10 +102,17 @@ class LoadFromRepositoryProtocolsDatatable < CustomDatatable
# will return json
def get_raw_records
get_raw_records_base
.preload(:parent, :protocol_keywords, user_assignments: %i(user user_role))
.joins('LEFT OUTER JOIN "protocol_protocol_keywords" ' \
'ON "protocol_protocol_keywords"."protocol_id" = "protocols"."id"')
.joins('LEFT OUTER JOIN "protocol_keywords" ' \
'ON "protocol_protocol_keywords"."protocol_keyword_id" = "protocol_keywords"."id"')
.joins('LEFT OUTER JOIN "users" ON "users"."id" = "protocols"."published_by_id"')
.group('"protocols"."id"')
.select(
'"protocols".*',
'STRING_AGG("protocol_keywords"."name", \', \') AS "protocol_keywords_str"',
'COUNT("protocol_versions"."id") + 1 AS "nr_of_versions"',
'COALESCE("protocols"."parent_id", "protocols"."id") AS adjusted_parent_id',
'STRING_AGG(DISTINCT("protocol_keywords"."name"), \', \') AS "protocol_keywords_str"',
'MAX("users"."full_name") AS "full_username_str"'
)
end
@ -91,59 +120,15 @@ class LoadFromRepositoryProtocolsDatatable < CustomDatatable
# Various helper methods
def keywords_html(record)
if record.protocol_keywords_str.blank?
if record.protocol_keywords.blank?
"<i>#{I18n.t('protocols.no_keywords')}</i>"
else
kws = record.protocol_keywords_str.split(', ')
res = []
kws.sort_by(&:downcase).each do |kw|
res << "<a href='#' data-action='filter' data-param='#{kw}'>#{kw}</a>"
record.protocol_keywords.sort_by { |kw| kw.name.downcase }.each do |kw|
sanitized_kw = sanitize_input(kw.name)
res << "<a href='#' data-action='filter' data-param='#{sanitized_kw}'>#{sanitized_kw}</a>"
end
sanitize_input(res.join(', '))
res.join(', ')
end
end
def timestamp_column_html(record)
if @type == :public
I18n.l(record.published_on, format: :full)
else
I18n.l(record.created_at, format: :full)
end
end
# OVERRIDE - This is only called when filtering results;
# when using GROUP BY function, SQL cannot perform a WHERE
# clause on aggregated columns (protocol keywords & users' full_name), but
# since we want those 2 columns to be searchable/filterable, we do an "inner"
# query where we select only protocol IDs which are filtered by those 2 columns
# using HAVING keyword (which is the correct way to filter aggregated columns).
# Another OR is then appended to the WHERE clause, checking if protocol is inside
# this list of IDs.
def build_conditions_for(query)
# Inner query to retrieve list of protocol IDs where concatenated
# protocol keywords string, or user's full_name contains searched query
search_val = dt_params[:search][:value]
records_having = get_raw_records_base.having(
::Arel::Nodes::NamedFunction.new(
'CAST',
[::Arel::Nodes::SqlLiteral.new("string_agg(\"protocol_keywords\".\"name\", ' ') AS #{typecast}")]
).matches("%#{sanitize_sql_like(search_val)}%").to_sql +
' OR ' +
::Arel::Nodes::NamedFunction.new(
'CAST',
[::Arel::Nodes::SqlLiteral.new("max(\"users\".\"full_name\") AS #{typecast}")]
).matches("%#{sanitize_sql_like(search_val)}%").to_sql +
' OR ' +
::Arel::Nodes::NamedFunction.new(
'CAST',
[::Arel::Nodes::SqlLiteral.new("COUNT(\"protocol_versions\".\"id\") + 1 AS #{typecast}")]
).matches("%#{sanitize_sql_like(search_val)}%").to_sql
).select(:id)
# Call parent function
criteria = super(query)
# Aight, now append another or
criteria.or(Protocol.arel_table[:id].in(records_having.arel))
end
end

113
app/datatables/protocols_datatable.rb
View file

@ -30,7 +30,7 @@ class ProtocolsDatatable < CustomDatatable
'adjusted_parent_id',
'nr_of_versions',
'protocol_keywords_str',
'nr_of_linked_children',
'nr_of_linked_tasks',
'nr_of_assigned_users',
'full_username_str',
'published_on',
@ -54,8 +54,8 @@ class ProtocolsDatatable < CustomDatatable
def as_json(_options = {})
{
draw: dt_params[:draw].to_i,
recordsTotal: get_raw_records.length,
recordsFiltered: filter_records(get_raw_records).length,
recordsTotal: get_raw_records_base.distinct.count,
recordsFiltered: records.present? ? records.first.filtered_count : 0,
data: data
}
end
@ -79,7 +79,7 @@ class ProtocolsDatatable < CustomDatatable
casted_column = ::Arel::Nodes::NamedFunction.new('CAST',
[model.arel_table[column.to_sym].as(typecast)])
end
casted_column.matches("%#{value}%")
casted_column.matches("%#{ActiveRecord::Base.sanitize_sql_like(value)}%")
end
private
@ -91,7 +91,8 @@ class ProtocolsDatatable < CustomDatatable
{
DT_RowId: record.id,
DT_RowAttr: {
'data-permissions-url': permissions_protocol_path(parent)
'data-permissions-url': permissions_protocol_path(parent),
'data-versions-url': versions_modal_protocol_path(parent)
},
'1': name_html(parent),
'2': parent.code,
@ -108,6 +109,10 @@ class ProtocolsDatatable < CustomDatatable
end
end
def fetch_records
super.select('COUNT("protocols"."id") OVER() AS filtered_count')
end
def filter_protocols_records(records)
if params[:name_and_keywords].present?
records = records.where_attributes_like(['protocols.name', 'protocol_keywords.name'], params[:name_and_keywords])
@ -120,7 +125,13 @@ class ProtocolsDatatable < CustomDatatable
records = records.where('protocols.updated_at > ?', params[:modified_on_from]) if params[:modified_on_from].present?
records = records.where('protocols.updated_at < ?', params[:modified_on_to]) if params[:modified_on_to].present?
records = records.where(protocols: { published_by_id: params[:published_by] }) if params[:published_by].present?
records = records.where(all_user_assignments: { user_id: params[:members] }) if params[:members].present?
if params[:members].present?
records = records.joins('LEFT OUTER JOIN "user_assignments" "all_user_assignments" '\
'ON "all_user_assignments"."assignable_type" = \'Protocol\' '\
'AND "all_user_assignments"."assignable_id" = "protocols"."id"')
.where(all_user_assignments: { user_id: params[:members] })
end
if params[:archived_on_from].present?
records = records.where('protocols.archived_on > ?', params[:archived_on_from])
@ -144,6 +155,7 @@ class ProtocolsDatatable < CustomDatatable
.select(:id)
published_versions = @team.protocols
.where(protocol_type: Protocol.protocol_types[:in_repository_published_version])
.order(:parent_id, version_number: :desc)
.select('DISTINCT ON (parent_id) id')
new_drafts = @team.protocols
.where(protocol_type: Protocol.protocol_types[:in_repository_draft], parent_id: nil)
@ -157,38 +169,49 @@ class ProtocolsDatatable < CustomDatatable
"(#{new_drafts.to_sql}))"
)
records =
records
.preload(:parent, :latest_published_version, :draft, :protocol_keywords, user_assignments: %i(user user_role))
.joins("LEFT OUTER JOIN protocols protocol_versions " \
"ON protocol_versions.protocol_type = #{Protocol.protocol_types[:in_repository_published_version]} " \
"AND protocol_versions.parent_id = protocols.parent_id")
.joins('LEFT OUTER JOIN "protocol_protocol_keywords" ' \
'ON "protocol_protocol_keywords"."protocol_id" = "protocols"."id"')
.joins('LEFT OUTER JOIN "protocol_keywords" ' \
'ON "protocol_protocol_keywords"."protocol_keyword_id" = "protocol_keywords"."id"')
.with_granted_permissions(@user, ProtocolPermissions::READ)
records = records.joins('LEFT OUTER JOIN "users" "archived_users"
ON "archived_users"."id" = "protocols"."archived_by_id"')
records = records.joins('LEFT OUTER JOIN "users" ON "users"."id" = "protocols"."published_by_id"')
records = @type == :archived ? records.archived : records.active
records = filter_protocols_records(records)
records.group('"protocols"."id"')
records.with_granted_permissions(@user, ProtocolPermissions::READ)
end
# Query database for records (this will be later paginated and filtered)
# after that "data" function will return json
def get_raw_records
get_raw_records_base.select(
records =
get_raw_records_base
.preload(:parent, :latest_published_version, :draft, :protocol_keywords, user_assignments: %i(user user_role))
.joins("LEFT OUTER JOIN protocols protocol_versions " \
"ON protocol_versions.protocol_type = #{Protocol.protocol_types[:in_repository_published_version]} " \
"AND protocol_versions.parent_id = protocols.parent_id")
.joins("LEFT OUTER JOIN protocols self_linked_task_protocols " \
"ON self_linked_task_protocols.protocol_type = #{Protocol.protocol_types[:linked]} " \
"AND self_linked_task_protocols.parent_id = protocols.id")
.joins("LEFT OUTER JOIN protocols parent_linked_task_protocols " \
"ON parent_linked_task_protocols.protocol_type = #{Protocol.protocol_types[:linked]} " \
"AND parent_linked_task_protocols.parent_id = protocols.parent_id")
.joins("LEFT OUTER JOIN protocols version_linked_task_protocols " \
"ON version_linked_task_protocols.protocol_type = #{Protocol.protocol_types[:linked]} " \
"AND version_linked_task_protocols.parent_id = protocol_versions.id " \
"AND version_linked_task_protocols.parent_id != protocols.id")
.joins('LEFT OUTER JOIN "protocol_protocol_keywords" ' \
'ON "protocol_protocol_keywords"."protocol_id" = "protocols"."id"')
.joins('LEFT OUTER JOIN "protocol_keywords" ' \
'ON "protocol_protocol_keywords"."protocol_keyword_id" = "protocol_keywords"."id"')
.joins('LEFT OUTER JOIN "users" "archived_users" ON "archived_users"."id" = "protocols"."archived_by_id"')
.joins('LEFT OUTER JOIN "users" ON "users"."id" = "protocols"."published_by_id"')
.group('"protocols"."id"')
records = filter_protocols_records(records)
records.select(
'"protocols".*',
'COALESCE("protocols"."parent_id", "protocols"."id") AS adjusted_parent_id',
'STRING_AGG(DISTINCT("protocol_keywords"."name"), \', \') AS "protocol_keywords_str"',
"CASE WHEN protocols.protocol_type = #{Protocol.protocol_types[:in_repository_draft]}" \
"THEN COUNT(DISTINCT(\"protocol_versions\".\"id\")) ELSE COUNT(DISTINCT(\"protocol_versions\".\"id\")) + 1 " \
"CASE WHEN protocols.protocol_type = #{Protocol.protocol_types[:in_repository_draft]} " \
"THEN 0 ELSE COUNT(DISTINCT(\"protocol_versions\".\"id\")) + 1 " \
"END AS nr_of_versions",
'(COUNT(DISTINCT("self_linked_task_protocols"."id")) + ' \
'COUNT(DISTINCT("parent_linked_task_protocols"."id")) + ' \
'COUNT(DISTINCT("version_linked_task_protocols"."id"))) AS nr_of_linked_tasks',
'COUNT("user_assignments"."id") AS "nr_of_assigned_users"',
'MAX("users"."full_name") AS "full_username_str"', # "Hack" to get single username
'MAX("archived_users"."full_name") AS "archived_full_username_str"'
@ -222,8 +245,8 @@ class ProtocolsDatatable < CustomDatatable
def modules_html(record)
"<a href='#' data-action='load-linked-children'" \
"data-url='#{linked_children_protocol_path(record)}'>" \
"#{record.nr_of_linked_children}" \
"data-url='#{linked_children_protocol_path(record.parent || record)}'>" \
"#{record.nr_of_linked_tasks}" \
"</a>"
end
@ -251,36 +274,4 @@ class ProtocolsDatatable < CustomDatatable
def modified_timestamp(record)
I18n.l(record.updated_at, format: :full)
end
# OVERRIDE - This is only called when filtering results;
# when using GROUP BY function, SQL cannot perform a WHERE
# clause on aggregated columns (protocol keywords & users' full_name), but
# since we want those 2 columns to be searchable/filterable, we do an "inner"
# query where we select only protocol IDs which are filtered by those 2 columns
# using HAVING keyword (which is the correct way to filter aggregated columns).
# Another OR is then appended to the WHERE clause, checking if protocol is inside
# this list of IDs.
# def build_conditions_for(query)
# # Inner query to retrieve list of protocol IDs where concatenated
# # protocol keywords string, or user's full_name contains searched query
# search_val = dt_params[:search][:value]
# records_having = get_raw_records_base.having(
# ::Arel::Nodes::NamedFunction.new(
# 'CAST',
# [::Arel::Nodes::SqlLiteral.new("string_agg(\"protocol_keywords\".\"name\", ' ') AS #{typecast}")]
# ).matches("%#{sanitize_sql_like(search_val)}%").to_sql +
# " OR " +
# ::Arel::Nodes::NamedFunction.new(
# 'CAST',
# [::Arel::Nodes::SqlLiteral.new("max(\"users\".\"full_name\") AS #{typecast}")]
# ).matches("%#{sanitize_sql_like(search_val)}%").to_sql
# ).select(:id)
# # Call parent function
# criteria = super(query)
# # Aight, now append another or
# criteria = criteria.or(Protocol.arel_table[:id].in(records_having.arel))
# criteria
# end
end

2
app/javascript/vue/protocol/container.vue
View file

@ -158,7 +158,7 @@
<PublishProtocol v-if="publishing"
:protocol="protocol"
@publish="publishProtocol"
@close="closePublishModal"
@cancel="closePublishModal"
/>
</div>
</template>

4
app/javascript/vue/protocol/protocolMetadata.vue
View file

@ -13,11 +13,11 @@
</a>
</div>
<div class="actions-block">
<a class="btn btn-light icon-btn pull-right" data-toggle="modal" data-target="#print-protocol-modal" tabindex="0">
<a class="btn btn-light icon-btn pull-right" :href="protocol.attributes.urls.print_protocol_url" target="_blank">
<span class="fas fa-print" aria-hidden="true"></span>
</a>
<button class="btn btn-light" @click="openVersionsModal">{{ i18n.t("protocols.header.versions") }}</button>
<button v-if="!protocol.attributes.published" @click="$emit('publish')" class="btn btn-primary">{{ i18n.t("protocols.header.publish") }}</button>
<button v-if="protocol.attributes.urls.publish_url" @click="$emit('publish')" class="btn btn-primary">{{ i18n.t("protocols.header.publish") }}</button>
<button v-if="protocol.attributes.urls.save_as_draft_url" @click="saveAsdraft" class="btn btn-secondary">{{ i18n.t("protocols.header.save_as_draft") }}</button>
</div>
</div>

10
app/jobs/user_assignments/generate_user_assignments_job.rb
View file

@ -46,6 +46,16 @@ module UserAssignments
end
def assign_users_to_protocol(protocol)
if protocol.parent_id && protocol.in_repository_draft?
Protocol.transaction(requires_new: true) do
protocol.parent.user_assignments.find_each do |user_assignment|
protocol.parent.sync_child_protocol_user_assignment(user_assignment, protocol.id)
end
end
return
end
return unless protocol.visible?
protocol.create_public_user_assignments!(@assigned_by)

5
app/models/concerns/assignable.rb
View file

@ -60,6 +60,11 @@ module Assignable
private
def after_user_assignment_changed(user_assignment = nil)
# Optional, redefine in the assignable model.
# Will be called when an assignment is changed (save/destroy) for the assignable model.
end
def create_users_assignments
return if skip_user_assignments

8
app/models/my_module.rb
View file

@ -404,14 +404,6 @@ class MyModule < ApplicationRecord
clone_tinymce_assets(target_my_module, target_my_module.experiment.project.team)
target_my_module.protocols << protocol.deep_clone_my_module(self, current_user)
target_my_module.reload
# fixes linked protocols
target_my_module.protocols.each do |protocol|
next unless protocol.linked?
protocol.updated_at = protocol.parent_updated_at
protocol.save
end
end
# Find an empty position for the restored module. It's

130
app/models/protocol.rb
View file

@ -54,23 +54,22 @@ class Protocol < ApplicationRecord
validate :linked_parent_type_constrain
validates :added_by, presence: true
validates :parent, presence: true
validates :parent_updated_at, presence: true
end
with_options if: :in_repository? do
validates :name, presence: true
validates :added_by, presence: true
validates :my_module, absence: true
validates :parent_updated_at, absence: true
validate :version_number_constraint
end
with_options if: :in_repository_published_version? do
validates :parent, presence: true
validate :versions_same_name_constrain
validate :parent_type_constraint
validate :versions_same_name_constraint
end
with_options if: :in_repository_draft? do
# Only one draft can exist for each protocol
validate :ensure_single_draft
validate :versions_same_name_constrain
validate :versions_same_name_constraint
end
with_options if: -> { in_repository? && !parent } do |protocol|
# Active protocol must have unique name inside its team
@ -123,6 +122,7 @@ class Protocol < ApplicationRecord
class_name: 'User',
inverse_of: :published_protocols, optional: true
has_many :linked_children,
-> { linked },
class_name: 'Protocol',
foreign_key: 'parent_id'
has_one :next_version,
@ -222,11 +222,8 @@ class Protocol < ApplicationRecord
end
def self.viewable_by_user(user, teams)
where(my_module: MyModule.viewable_by_user(user, teams))
.or(where(team: teams)
.where('protocol_type = 3 OR '\
'(protocol_type = 2 AND added_by_id = :user_id)',
user_id: user.id))
where(team: teams, protocol_type: REPOSITORY_TYPES).with_granted_permissions(user, ProtocolPermissions::READ)
.or(where(my_module: MyModule.viewable_by_user(user, teams)))
end
def self.filter_by_teams(teams = [])
@ -260,6 +257,20 @@ class Protocol < ApplicationRecord
in_repository_draft? && parent.blank?
end
def newer_published_version_present?
if in_repository_published_original?
published_versions.any?
elsif in_repository_published_version?
parent.published_versions.where('version_number > ?', version_number).any?
else
false
end
end
def latest_published_version_or_self
latest_published_version || self
end
def permission_parent
in_module? ? my_module : team
end
@ -336,27 +347,12 @@ class Protocol < ApplicationRecord
unlinked? || linked?
end
def linked_no_diff?
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
linked? && updated_at > parent.published_on
end
def parent_newer?
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.newer_published_version_present?
end
def number_of_steps
@ -380,9 +376,6 @@ class Protocol < ApplicationRecord
end
def make_private(user)
# Don't update "updated_at" timestamp
self.record_timestamps = false
self.added_by = user
self.published_on = nil
self.archived_by = nil
@ -483,8 +476,6 @@ class Protocol < ApplicationRecord
result = true
begin
Protocol.transaction do
self.record_timestamps = false
# First, destroy all keywords
protocol_protocol_keywords.destroy_all
if keywords.present?
@ -503,31 +494,11 @@ class Protocol < ApplicationRecord
def unlink
self.parent = nil
self.parent_updated_at = nil
self.linked_at = nil
self.protocol_type = Protocol.protocol_types[:unlinked]
save!
end
def update_parent(current_user)
ActiveRecord::Base.no_touching do
# First, destroy parent's step contents
parent.destroy_contents
parent.reload
# Now, clone step contents
Protocol.clone_contents(self, parent, current_user, false)
end
# Lastly, update the metadata
parent.reload
parent.record_timestamps = false
parent.updated_at = updated_at
parent.save!
self.record_timestamps = false
self.parent_updated_at = updated_at
save!
end
def update_from_parent(current_user, source)
ActiveRecord::Base.no_touching do
# First, destroy step contents
@ -541,7 +512,6 @@ class Protocol < ApplicationRecord
reload
self.record_timestamps = false
self.updated_at = source.published_on
self.parent_updated_at = source.published_on
self.added_by = current_user
self.last_modified_by = current_user
self.parent = source
@ -564,7 +534,6 @@ class Protocol < ApplicationRecord
self.record_timestamps = false
self.updated_at = source.published_on
self.parent = source
self.parent_updated_at = source.published_on
self.added_by = current_user
self.last_modified_by = current_user
self.linked_at = Time.zone.now
@ -622,7 +591,6 @@ class Protocol < ApplicationRecord
if linked?
clone.added_by = current_user
clone.parent = parent
clone.parent_updated_at = parent_updated_at
end
deep_clone(clone, current_user)
@ -691,8 +659,50 @@ class Protocol < ApplicationRecord
end
end
def child_version_protocols
published_versions.or(Protocol.where(id: draft&.id))
end
def sync_child_protocol_user_assignment(user_assignment, child_protocol_id = nil)
# Copy user assignments to child protocol(s)
Protocol.transaction(requires_new: true) do
# Reload to ensure a potential new draft is also included in child versions
reload
(
# all or single child version protocol
child_protocol_id ? child_version_protocols.where(id: child_protocol_id) : child_version_protocols
).find_each do |child_protocol|
child_assignment = child_protocol.user_assignments.find_or_initialize_by(
user: user_assignment.user
)
if user_assignment.destroyed?
child_assignment.destroy! if child_assignment.persisted?
next
end
child_assignment.update!(
user_assignment.attributes.slice(
'user_role_id',
'assigned',
'assigned_by_id',
'team_id'
)
)
end
end
end
private
def after_user_assignment_changed(user_assignment)
return unless in_repository_published_original?
sync_child_protocol_user_assignment(user_assignment)
end
def auto_assign_protocol_members
UserAssignments::ProtocolGroupAssignmentJob.perform_now(
team,
@ -757,19 +767,13 @@ class Protocol < ApplicationRecord
end
end
def version_parent_type_constrain
def parent_type_constraint
unless parent.in_repository_published_original?
errors.add(:base, I18n.t('activerecord.errors.models.protocol.wrong_parent_type'))
end
end
def draft_parent_type_constrain
unless parent.in_repository_published_original?
errors.add(:base, I18n.t('activerecord.errors.models.protocol.wrong_parent_type'))
end
end
def versions_same_name_constrain
def versions_same_name_constraint
if parent.present? && !parent.name.eql?(name)
errors.add(:base, I18n.t('activerecord.errors.models.protocol.wrong_version_name'))
end

6
app/models/user_assignment.rb
View file

@ -7,6 +7,8 @@ class UserAssignment < ApplicationRecord
after_create :assign_team_child_objects, if: -> { assignable.is_a?(Team) }
after_update :update_team_children_assignments, if: -> { assignable.is_a?(Team) && saved_change_to_user_role_id? }
before_destroy :unassign_team_child_objects, if: -> { assignable.is_a?(Team) }
after_destroy :call_user_assignment_changed_hook
after_save :call_user_assignment_changed_hook
belongs_to :assignable, polymorphic: true, touch: true
belongs_to :user_role
@ -24,6 +26,10 @@ class UserAssignment < ApplicationRecord
private
def call_user_assignment_changed_hook
assignable.__send__(:after_user_assignment_changed, self)
end
def assign_team_child_objects
UserAssignments::CreateTeamUserAssignmentsService.new(self).call
end

14
app/serializers/protocol_serializer.rb
View file

@ -8,7 +8,7 @@ class ProtocolSerializer < ActiveModel::Serializer
attributes :name, :id, :urls, :description, :description_view, :updated_at, :in_repository,
:created_at_formatted, :updated_at_formatted, :added_by, :authors, :keywords, :version, :code,
:published, :version_comment
:published, :version_comment, :archived
def updated_at
object.updated_at.to_i
@ -75,7 +75,8 @@ class ProtocolSerializer < ActiveModel::Serializer
delete_steps_url: delete_steps_url,
publish_url: publish_url,
save_as_draft_url: save_as_draft_url,
versions_modal_url: versions_modal_url
versions_modal_url: versions_modal_url,
print_protocol_url: print_protocol_url
}
end
@ -115,6 +116,12 @@ class ProtocolSerializer < ActiveModel::Serializer
versions_modal_protocol_path(object.parent || object)
end
def print_protocol_url
return unless can_read_protocol_in_repository?(object)
print_protocol_path(object)
end
def reorder_steps_url
return unless can_manage_protocol_in_module?(object) || can_manage_protocol_in_repository?(object)
@ -140,8 +147,7 @@ class ProtocolSerializer < ActiveModel::Serializer
end
def update_protocol_url
return unless can_read_protocol_in_module?(object) && object.linked? &&
(object.parent_newer? || object.parent_and_self_newer?)
return unless can_read_protocol_in_module?(object) && object.linked? && object.parent_newer?
update_from_parent_modal_protocol_path(object, format: :json)
end

2
app/utilities/protocols_exporter.rb
View file

@ -27,7 +27,7 @@ module ProtocolsExporter
envelope_xml = "<envelope xmlns=\"http://www.scinote.net\" " \
"version=\"1.0\">\n"
protocols.each do |protocol|
protocol = protocol.latest_published_version || protocol
protocol = protocol.latest_published_version_or_self
protocol_name = get_protocol_name(protocol)
envelope_xml << "<protocol id=\"#{protocol.id}\" " \
"guid=\"#{get_guid(protocol.id)}\">#{protocol_name}" \

2
app/utilities/protocols_exporter_v2.rb
View file

@ -9,7 +9,7 @@ module ProtocolsExporterV2
envelope_xml = "<envelope xmlns=\"http://www.scinote.net\" " \
"version=\"1.1\">\n"
protocols.each do |protocol|
protocol = protocol.latest_published_version || protocol
protocol = protocol.latest_published_version_or_self
protocol_name = get_protocol_name(protocol)
envelope_xml << "<protocol id=\"#{protocol.id}\" " \
"guid=\"#{get_guid(protocol.id)}\">#{protocol_name}" \

16
app/views/access_permissions/modals/_edit_modal.html.erb
View file

@ -1,7 +1,7 @@
<% # frozen_string_literal: true %>
<div class="modal fade user-assignments-modal <%= assignable.class.name.parameterize(separator: '-') %>-assignments-modal" tabindex="-1" role="dialog" data-action="modal-close">
<div class="modal-dialog modal-lg" role="document">
<div class="modal-dialog" role="document">
<div class="modal-content" id="user_assignments_modal">
<div class="modal-header">
<button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">&times;</span></button>
@ -9,19 +9,19 @@
</div>
<div class="modal-body">
<% manually_assigned_users.order(full_name: :asc).each do |user| %>
<%= render('access_permissions/partials/member_field',
user: user,
assignable: assignable,
update_path: public_send("access_permissions_#{assignable.class.name.underscore}_path", assignable),
delete_path: public_send("access_permissions_#{assignable.class.name.underscore}_path", assignable, user_id: user.id)
) %>
<%
options = { user: user, with_inherit: !assignable.top_level_assignable?, assignable: assignable, update_path: public_send("access_permissions_#{assignable.class.name.underscore}_path", assignable) }
options.merge!(delete_path: public_send("access_permissions_#{assignable.class.name.underscore}_path", assignable, user_id: user.id)) if assignable == top_level_assignable
%>
<%= render('access_permissions/partials/member_field', options) %>
<% end %>
<%= render('access_permissions/partials/default_public_user_role_form', assignable: top_level_assignable, editable: assignable == top_level_assignable) if top_level_assignable.respond_to?(:visible?) && top_level_assignable.visible? %>
</div>
<% if assignable.top_level_assignable? %>
<div class="modal-footer">
<%= link_to new_assignment_path, class: 'btn btn-default pull-left', data: { action: 'swap-remote-container', target: '#user_assignments_modal' } do %>
<%= link_to new_assignment_path, class: 'btn btn-default pull-right', data: { action: 'swap-remote-container', target: '#user_assignments_modal' } do %>
<i class="fas fa-plus"></i>
<%= t('access_permissions.grant_access') %>
<% end %>

4
app/views/access_permissions/modals/_show_modal.html.erb
View file

@ -1,11 +1,11 @@
<% # frozen_string_literal: true %>
<div class="modal fade <%= assignable.class.name.parameterize(separator: '-') %>-assignments-modal" tabindex="-1" role="dialog" data-action="modal-close">
<div class="modal-dialog modal-lg" role="document">
<div class="modal-dialog" role="document">
<div class="modal-content" id="user_assignments_modal">
<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"><%= t "access_permissions.#{assignable.class.name.pluralize.underscore}.modals.show_modal.title", assignable_name: assignable.name %></h4>
<h4 class="modal-title"><%= t("access_permissions.#{assignable.class.name.pluralize.underscore}.modals.show_modal.title", resource_name: assignable.name) %></h4>
</div>
<div class="modal-body">
<% manually_assigned_users.order(full_name: :asc).each do |user| %>

2
app/views/access_permissions/my_modules/my_module_member.json.jbuilder
View file

@ -5,7 +5,7 @@ json.form controller.render_to_string(
formats: [:html],
locals: {
user: @user_assignment.user,
update_path: access_permissions_my_module_path(@my_module)
update_path: access_permissions_my_module_path(@my_module),
with_inherit: true,
assignable: @my_module
},

46
app/views/access_permissions/partials/_default_public_user_role_form.html.erb
View file

@ -1,5 +1,6 @@
<% editable ||= false %>
<% if assignable.visible? %>
<%= form_with(model: assignable, url: [:update_default_public_user_role, :access_permissions, assignable], method: :put, remote: true, html: { class: 'row member-item', id: 'public_assignments', data: { action: 'replace-form autosave-form', object_type: assignable.class.name.underscore.to_sym } }) do |f| %>
<%= form_with(model: assignable, url: [:update_default_public_user_role, :access_permissions, assignable], method: :put, remote: true, html: { class: 'member-item', id: 'public_assignments', data: { action: 'replace-form autosave-form', object_type: assignable.class.name.underscore.to_sym } }) do |f| %>
<div class="user-assignment-info">
<div class="global-avatar-container">
<%= image_tag "icon/team.png", class: 'img-circle pull-left' %>
@ -7,20 +8,43 @@
<div>
<%= t('access_permissions.everyone_else', team_name: assignable.team.name) %>
<%= render 'access_permissions/partials/public_members_dropdown', team: assignable.team, assignable: assignable %>
<br>
<small class="text-muted">
<%= assignable.default_public_user_role.name %>
<span class="permission-object-tag" title="<%= t("access_permissions.partials.#{assignable.class.name.underscore}_tooltip") %>"">
<%= t("access_permissions.partials.#{assignable.class.name.underscore}") %>
</span>
</small>
</div>
</div>
<div class="user-assignment-controls">
<div class="user-assignment-role">
<% if editable %>
<%= f.select :default_public_user_role_id, options_for_select(user_roles_collection + [[t('access_permissions.remove_access'), nil]], selected: assignable.default_public_user_role_id), {}, class: 'form-control selectpicker', title: t("user_assignment.change_#{assignable.class.name.underscore}_role"), data: { 'selected-text-format' => 'static' } %>
<% end %>
<div class="user-assignment-controls">
<div class="dropdown pull-right">
<% if editable %>
<button class="btn btn-light btn-role-select" type="button" id="defaultPublicUserRole" data-toggle="dropdown" aria-haspopup="true" aria-expanded="true">
<%= f.object.default_public_user_role.name %>
<span class="caret"></span>
</button>
<%= f.hidden_field :default_public_user_role_id, value: f.object.default_public_user_role.id, class: "default-public-user-role-id" %>
<ul class="dropdown-menu dropdown-menu-right user-assignment-dropdown" aria-labelledby="defaultPublicUserRole">
<% user_roles_collection.each do |role| %>
<li>
<a href="#" data-turbolinks="false" class="user-role-selector" data-role-id="<%= role[1] %>">
<%= role[0] %>
</a>
</li>
<% end %>
<% if assignable.top_level_assignable? %>
<li role="separator" class="divider" data-hook="support-dropdown-separator"></li>
<li>
<a href="#" data-turbolinks="false" class="user-role-selector" data-role-id="">
<%= t('access_permissions.remove_access') %>
</a>
</li>
<% end %>
</ul>
<% else %>
<button class="btn btn-light btn-role-select disabled" type="button">
<%= f.object.default_public_user_role.name %>
<span class="caret"></span>
</button>
<% end %>
</div>
</div>
</div>
</div>
<% end %>

7
app/views/access_permissions/partials/_member_field.html.erb
View file

@ -1,6 +1,7 @@
<% # frozen_string_literal: true %>
<%
with_inherit ||= false
assignment = assignable.user_assignments.find_by(user_id: user.id, team: current_team)
item_id = dom_id(user, :assignment_member)
%>
@ -18,15 +19,15 @@
</div>
</div>
<div class="user-assignment-controls">
<% unless defined?(with_inherit) && current_user == user %>
<% unless with_inherit && current_user == user %>
<div class="dropdown pull-right">
<button class="btn btn-light" type="button" id="userAccess_<%= user.id %>" data-toggle="dropdown" aria-haspopup="true" aria-expanded="true">
<button class="btn btn-light btn-role-select" type="button" id="userAccess_<%= user.id %>" data-toggle="dropdown" aria-haspopup="true" aria-expanded="true">
<%= f.object.user_role.name %>
<span class="caret"></span>
</button>
<%= f.hidden_field :user_role_id, value: f.object.user_role.id %>
<ul class="dropdown-menu dropdown-menu-right user-assignment-dropdown" aria-labelledby="userAccess_<%= user.id %>">
<% user_roles_collection(with_inherit: defined? with_inherit).each do |role| %>
<% user_roles_collection(with_inherit: with_inherit).each do |role| %>
<li>
<a href="#" data-turbolinks="false" class="user-role-selector" data-role-id="<%= role[1] %>">
<%= role[0] %>

2
app/views/access_permissions/partials/_new_assignments_form.html.erb
View file

@ -1,6 +1,6 @@
<% # frozen_string_literal: true %>
<div class="modal-content" id="user_assignments_modal" data-action="modal-close" data-target="<%= projects_path %>">
<div class="modal-content" id="user_assignments_modal" data-action="modal-close" data-target="<%= public_send("#{assignable.class.name.pluralize.underscore}_path") %>">
<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">

2
app/views/access_permissions/partials/_user_assignment_field.html.erb
View file

@ -5,7 +5,7 @@
id = dom_id(user, :new_protocol_member)
%>
<div class="row member-item new-member-item" data-filter-item="<%= user.full_name %>">
<div class="member-item new-member-item" data-filter-item="<%= user.full_name %>">
<%= user_form.hidden_field :user_id, value: user.id, name:"access_permissions_new_user_form[resource_members][#{user.id}][user_id]" %>
<div class="user-assignment-info">
<div class="sci-checkbox-container">

3
app/views/access_permissions/projects/show.json.jbuilder
View file

@ -6,8 +6,7 @@ json.modal controller.render_to_string(
locals: {
assignable: @project,
manually_assigned_users: @project.manually_assigned_users,
top_level_assignable: @project,
users: @project.manually_assigned_users
top_level_assignable: @project
},
layout: false
)

2
app/views/access_permissions/protocols/new.json.jbuilder
View file

@ -6,7 +6,7 @@ json.html controller.render_to_string(
locals: {
assignable: @protocol,
form_object: @user_assignment,
users: current_team.users.where.not(id: @protocol.assigned_users.select(:id)),
users: current_team.users.where.not(id: @protocol.manually_assigned_users.select(:id)),
create_path: access_permissions_protocols_path(id: @protocol.id),
assignable_path: edit_access_permissions_protocol_path(@protocol)
},

8
app/views/access_permissions/protocols/show.json.jbuilder
View file

@ -1,12 +1,12 @@
# frozen_string_literal: true
json.modal controller.render_to_string(
partial: 'access_permissions/protocols/modals/show_modal',
partial: 'access_permissions/modals/show_modal',
formats: [:html],
locals: {
protocol: @protocol,
users: @protocol.assigned_users,
can_manage_resource: can_manage_protocol_users?(@protocol)
assignable: @protocol,
top_level_assignable: @protocol,
manually_assigned_users: @protocol.manually_assigned_users
},
layout: false
)

4
app/views/my_modules/protocols/_protocol_status_bar.html.erb
View file

@ -9,7 +9,7 @@
</span>
<% end %>
<a href="#" id="my-module-protocol-info-button" class="status-info
<%= 'parent-newer' if @protocol.parent_newer? || @protocol.parent_and_self_newer? %>
<%= 'parent-newer' if @protocol.parent_newer? %>
<%= 'protocol-newer' if @protocol.newer_than_parent? %>
" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
<i class="fas fa-info-circle"></i>
@ -47,7 +47,7 @@
<div class="value"><%= I18n.l(@protocol&.parent&.published_on, format: :full) %></div>
</div>
<div class="dropdown-footer">
<% if @protocol.parent_newer? || @protocol.parent_and_self_newer? %>
<% if @protocol.parent_newer? %>
<div class="notification-line new-parent-version">
<i class="fas fa-info-circle"></i>
<div class="description"><%= t("my_modules.protocols.protocol_status_bar.messages.template_updated_html") %></div>

2
app/views/protocol_importers/_import_form.html.erb
View file

@ -32,6 +32,8 @@
<%= f.hidden_field(:published_on, value: protocol.published_on) %>
<%= f.hidden_field(:description, value: protocol.description) %>
<%= f.hidden_field(:protocol_type, value: protocol.protocol_type) %>
<%= f.hidden_field(:visibility) %>
<%= f.hidden_field(:default_public_user_role_id) %>
<% end %>

28
app/views/protocol_importers/_preview_modal_footer.html.erb
View file

@ -1,3 +1,25 @@
<button type="button" class="btn btn-secondary" data-dismiss="modal"><%=t "general.cancel" %></button>
<button type="button" class="btn btn-primary" data-action="import_protocol" data-import_type="in_repository_draft"><%=t "protocols.import_export.import_modal.import_to_team_protocols_label" %></button>
<button type="button" class="btn btn-primary" data-action="import_protocol" data-import_type="in_repository_draft"><%=t "protocols.import_export.import_modal.import_to_private_protocols_label" %></button>
<div class="footer">
<div class="left-section">
<div class="default-role-container">
<div class="sci-checkbox-container">
<%= check_box_tag "visibility", "visible", false, class: "sci-checkbox" %>
<span class="sci-checkbox-label"></span>
</div>
<div class="default-role-description">
<%= t("protocols.new_protocol_modal.access_label") %>
</div>
</div>
<div class="hidden" id="roleSelectWrapper">
<div class="sci-input-container">
<%= label_tag :default_public_user_role_id, t("protocols.new_protocol_modal.role_label") %>
<% default_role = UserRole.find_by(name: I18n.t('user_roles.predefined.viewer')).id %>
<%= hidden_field_tag :default_public_user_role_id, value: default_role %>
<%= select_tag :role_selector, options_for_select(user_roles_collection, default_role) %>
</div>
</div>
</div>
<div class="right-section">
<button type="button" class="btn btn-secondary" data-dismiss="modal"><%=t "general.cancel" %></button>
<button type="button" class="btn btn-primary" data-action="import_protocol" data-import_type="in_repository_draft"><%=t "protocols.import_export.import_modal.import_protocols_label" %></button>
</div>
</div>

3
app/views/protocols/index.html.erb
View file

@ -14,7 +14,7 @@
<div class="content-pane flexible protocols-index <%= @type %>">
<div class="content-header sticky-header">
<div class="title-row">
<% if templates_view_mode_archived? %>
<% if templates_view_mode_archived?(type: @type) %>
<h1>
<i class="fas fa-archive"></i>
<%= t('protocols.index.head_title_archived') %>
@ -43,6 +43,7 @@
<%= render partial: "protocols/index/linked_children_modal.html.erb" %>
<%= render partial: "protocols/index/protocolsio_modal.html.erb" %>
<%= render partial: "protocols/index/new_protocol_modal.html.erb", locals: {type: 'new'} %>
<%= render partial: "protocols/index/protocol_preview_modal.html.erb" %>
<%= render partial: "protocols/import_export/import_elements.html.erb" %>

3
app/views/protocols/index/_action_toolbar.html.erb
View file

@ -23,4 +23,7 @@
<i class="fas fa-undo"></i>
<span class="button-text"><%= t("protocols.index.action_toolbar.restore") %></span>
</button>
<div class="emptyPlaceholder hidden">
<%= t("protocols.index.action_toolbar.empty_placeholder") %>
</div>
</template>

2
app/views/protocols/index/_protocol_filters.html.erb
View file

@ -22,7 +22,7 @@
data-placeholder="Select who has access">
</select>
</div>
<div class="select-block folders">
<div class="select-block has-draft">
<span class="sci-checkbox-container">
<%= check_box_tag :has_draft, 'accepted', false, {class: "sci-checkbox"} %>
<span class="sci-checkbox-label"></span>

2
app/views/protocols/index/_protocolsio_modal_body.html.erb
View file

@ -98,7 +98,5 @@
<button type="button" class="btn btn-primary convert-protocol" disabled><%= t('protocols.index.protocolsio.convert') %></button>
</div>
<%= render partial: "protocols/index/protocol_preview_modal.html.erb" %>
<%= javascript_include_tag "protocols/steps" %>
<%= javascript_include_tag "protocols/protocolsio.js" %>

3
app/views/protocols/show.html.erb
View file

@ -22,6 +22,9 @@
config: @inline_editable_title_config
} %>
<% else %>
<% if @protocol.archived %>
<i class="fas fa-archive"></i>&nbsp;
<% end %>
<div class="name-readonly-placeholder">
<%= @protocol.name %>
</div>

5
config/initializers/extends.rb
View file

@ -436,7 +436,8 @@ class Extends
protocol_template_access_granted: 233,
protocol_template_access_changed: 234,
protocol_template_access_revoked: 235,
task_protocol_save_to_template: 236
task_protocol_save_to_template: 236,
protocol_template_draft_created: 237
}
ACTIVITY_GROUPS = {
@ -453,7 +454,7 @@ class Extends
78, 96, 107, 113, 114, *133..136, 180, 181, 182],
protocol_repository: [80, 103, 89, 87, 79, 90, 91, 88, 85, 86, 84, 81, 82,
83, 101, 112, 123, 125, 117, 119, 129, 131, 170, 173, 179, 187, 186,
190, 191, *204..215, 220, 221, 223, 227, 228, 229, *230..235],
190, 191, *204..215, 220, 221, 223, 227, 228, 229, *230..235, 237],
team: [92, 94, 93, 97, 104],
label_repository: [*216..219]
}

30
config/locales/en.yml
View file

@ -156,6 +156,8 @@ en:
attributes:
step_order:
invalid: "Invalid step order."
name:
taken: "This protocol template name has to be unique inside a team (this includes the archive)."
step:
attributes:
step_orderable_element_order:
@ -313,7 +315,7 @@ en:
templates:
sidebar_title: "TEMPLATES"
protocol_templates: "Protocol templates"
label_templates: "Label Templates"
label_templates: "Label templates"
nav2:
all_projects:
@ -1085,8 +1087,6 @@ en:
revert_title: "Revert protocol template"
revert_message: "This will override any changes you made. We can’t recover them once you revert."
revert_btn_text: "Yes, revert it"
update_parent_title: "Update templates version"
update_parent_message: "Are you sure you want to update the templates protocol with this version? This will override any other changes made in the templates version."
update_self_title: "Update from protocol templates"
update_self_message: "This will override any changes you made. We can’t recover them once you update this protocol with the new version."
update_self_btn_text: "Yes, update it"
@ -1099,7 +1099,7 @@ en:
update_parent_flash: "Protocol in templates was successfully updated with the version from the task."
update_parent_error: "Failed to update templates version of the protocol."
update_parent_error_locked: "Failed to update templates version of the protocol. One or more files in the protocol are currently being edited."
update_from_parent_flash: "Version in the templates was successfully updated."
update_from_parent_flash: "Protocol was successfully updated."
update_from_parent_error: "Failed to update the protocol with the version in the templates."
update_from_parent_error_locked: "Failed to update the protocol with the version in the templates. One or more files in the protocol are currently being edited."
load_from_repository_flash: "Successfully loaded the protocol from the templates."
@ -1130,7 +1130,7 @@ en:
link_label: "Link task to this protocol in templates"
link_text: "<strong>Warning!</strong>&nbsp;This will unlink the currently linked protocol."
error_400: "Due to unknown error, protocol could not be copied to templates."
success_message: "New protocol template was successfully saved. You can see it in protocol templates."
success_message: "Protocol was successfully saved as a new protocol template."
confirm: "Save"
load_from_file_flash: "Successfully loaded the protocol from the file."
load_from_file_error: "Failed to load the protocol from file."
@ -2641,6 +2641,7 @@ en:
import: "Load"
import_to_team_protocols_label: "Import to Team Protocols"
import_to_private_protocols_label: "Import to My Protocols"
import_protocols_label: "Import"
export:
export_results:
title: "Export results"
@ -2718,6 +2719,7 @@ en:
export: "Export"
archive: "Archive"
restore: "Restore"
empty_placeholder: "There is no action available"
public_description: "Team protocols are visible and can be used by everyone from the team."
private_description: "My protocols are only visible to you."
create_new: "New protocol"
@ -2850,7 +2852,7 @@ en:
import:
public: "Team protocols"
private: "My protocols"
success_flash: 'Protocol <strong>%{name}</strong> successfully imported to %{type}.'
success_flash: 'Protocol <strong>%{name}</strong> successfully imported.'
steps:
placeholder: 'Enter step name'
@ -3216,9 +3218,9 @@ en:
access_permissions:
everyone_else: "Everyone else at %{team_name}"
reset: "The inherited role will be applied"
reset: "Inherit role"
remove_access: "Remove access"
grant_access: "Grant access"
grant_access: "Grant new access"
create:
success:
one: "You have successfully granted access to %{count} member to the project."
@ -3233,15 +3235,15 @@ en:
new_resource_assignments: "Grant new access to %{resource}"
new_assignments_form:
title: "Select members"
submit: "Grant access"
submit_singular: "Grant access to 1 user"
submit_plural: "Grant access to {num} users"
submit: "Grant new access"
submit_singular: "Grant access to 1 member"
submit_plural: "Grant access to {num} members"
find_people_html: "Find people"
new_protocol_assignments_form:
title: "Select members"
submit: "Grant access"
submit_singular: "Grant access to 1 user"
submit_plural: "Grant access to {num} users"
submit: "Grant new access"
submit_singular: "Grant access to 1 member"
submit_plural: "Grant access to {num} members"
find_people_html: "Find people"
experiment_member_field:
reset: "Inherit role"

2
config/locales/global_activities/en.yml
View file

@ -257,6 +257,7 @@ en:
protocol_template_published_html: "%{user} published protocol template %{protocol} version %{version_number}"
protocol_template_revision_notes_updated_html: "%{user} edited revision notes of %{protocol}"
protocol_template_draft_deleted_html: "%{user} deleted draft of %{protocol}"
protocol_template_draft_created_html: "%{user} created draft of %{protocol}"
protocol_template_access_granted_html: "%{user} granted access to %{user_target} with user role %{role} to protocol template %{protocol}"
protocol_template_access_changed_html: "%{user} changed %{user_target}’s role on protocol template %{protocol} to %{role}"
protocol_template_access_revoked_html: "%{user} removed %{user_target} with user role %{role} from protocol template %{protocol}"
@ -472,6 +473,7 @@ en:
protocol_template_published: "Protocol template published"
protocol_template_revision_notes_updated: "Revision notes edited"
protocol_template_draft_deleted: "Deleting draft"
protocol_template_draft_created: "Creating draft"
protocol_template_access_granted: "User granted access to protocol template"
protocol_template_access_changed: "User role changed on a protocol"
protocol_template_access_revoked: "User removed from a protocol"

17
spec/controllers/protocols_controller_spec.rb
View file

@ -180,23 +180,6 @@ describe ProtocolsController, type: :controller do
.to(change { Activity.count })
end
end
describe 'POST update_parent' do
let(:action) { put :update_parent, params: params, format: :json }
it 'calls create activity for updating protocol in repository from task' do
expect(Activities::CreateActivityService)
.to(receive(:call)
.with(hash_including(activity_type:
:update_protocol_in_repository_from_task)))
action
end
it 'adds activity in DB' do
expect { action }
.to(change { Activity.count })
end
end
end
describe 'POST load_from_repository' do

1
spec/factories/protocols.rb
View file

@ -15,7 +15,6 @@ FactoryBot.define do
protocol_type { :linked }
parent { create :protocol }
added_by { create :user }
parent_updated_at { Time.now }
end
end
end

3
spec/services/model_importers/team_importer_spec.rb
View file

@ -187,9 +187,6 @@ describe TeamImporter do
expect(db_protocol.restored_on).to be_nil
expect(db_protocol.authors).to eq json_protocol['authors']
expect(db_protocol.parent_id).to eq json_protocol['parent_id']
expect(db_protocol.parent_updated_at).to eq(
json_protocol['parent_updated_at']
)
expect(db_protocol.protocol_type).to eq(
json_protocol['protocol_type']
)