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Merge branch 'activestorage_migration' into features/marvinjs-integration

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This commit is contained in:
Anton Ignatov 2019-07-12 11:34:41 +02:00
commit 57a273d5d0
66 changed files with 489 additions and 1134 deletions
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2
Gemfile
View file

@ -12,7 +12,7 @@ gem 'bootstrap_form', '~> 2.7.0'
gem 'devise', '~> 4.6.2'
gem 'devise_invitable'
gem 'figaro'
gem 'pg', '~> 0.18'
gem 'pg', '~> 1.1'
gem 'pg_search' # PostgreSQL full text search
gem 'rails', '~> 5.2.3'
gem 'recaptcha', require: 'recaptcha/rails'

6
Gemfile.lock
View file

@ -364,7 +364,9 @@ GEM
parallel (1.17.0)
parser (2.6.3.0)
ast (~> 2.4.0)
pg (0.21.0)
pg (1.1.4)
activerecord (>= 4.2)
activesupport (>= 4.2)
pg_search (2.2.0)
activerecord (>= 4.2)
activesupport (>= 4.2)
@ -627,7 +629,7 @@ DEPENDENCIES
omniauth-linkedin-oauth2
overcommit
paperclip (~> 6.1)
pg (~> 0.18)
pg (~> 1.1)
pg_search
phantomjs
poltergeist

76
app/assets/javascripts/assets.js
View file

@ -1,76 +0,0 @@
/* global animateSpinner FilePreviewModal */
var Assets = (function() {
var DELAY = 5000;
var REPETITIONS_LIMIT = 30;
function finalizeAsset(element) {
var $el = $(element);
$el.attr('data-status', 'asset-failed');
if ($el.data('filename')) {
$el.html($el.data('filename'));
}
}
function refreshAsset(element) {
var $el = $(element);
if ($el.data('refreshCounter') > REPETITIONS_LIMIT) {
finalizeAsset($el);
return;
}
// Perform an AJAX call to present URL
// to check if file already exists
$.ajax({
url: $el.data('present-url'),
type: 'GET',
dataType: 'json',
success: function(data) {
if (data.processing === true) {
setTimeout(function() {
refreshAsset($el);
}, DELAY);
}
if (data.processing === false) {
$el.html(data.placeholder_html);
$el.attr('data-status', 'asset-loaded');
animateSpinner($el, false);
FilePreviewModal.init();
}
},
error: function() {
animateSpinner(null, false);
}
});
$el.data().refreshCounter += 1;
}
function setupAssetsLoading() {
var elements = $("[data-status='asset-loading']");
if (!elements.length) {
return;
}
$.each(elements, function(_, el) {
var $el = $(el);
if ($el.data('refreshIsRunning') === true) return;
$el.data('refreshCounter', 1);
$el.data('refreshIsRunning', true);
setTimeout(function() {
refreshAsset($el);
}, DELAY);
});
}
return Object.freeze({
setupAssetsLoading: setupAssetsLoading
});
}());

3
app/assets/javascripts/my_modules/results.js.erb
View file

@ -1,5 +1,3 @@
//= require assets
(function(global) {
'use strict';
@ -112,7 +110,6 @@
});
_renderTable($(result).find('div.step-result-hot-table'));
animateSpinner(null, false);
Assets.setupAssetsLoading();
}
function _renderTable(table) {

6
app/assets/javascripts/protocols/steps.js.erb
View file

@ -1,6 +1,5 @@
//= require Sortable.min
//= require canvas-to-blob.min
//= require assets
(function(global) {
'use strict';
@ -246,7 +245,6 @@
$new_step.find("[data-role='step-hot-table']").each(function() {
renderTable($(this));
});
Assets.setupAssetsLoading();
})
.on("ajax:error", function(e, xhr, status, error) {
$form.renderFormErrors('step', xhr.responseJSON, true, e);
@ -609,7 +607,10 @@
$(this).handsontable("render");
});
animateSpinner(null, false);
<<<<<<< HEAD
Assets.setupAssetsLoading();
=======
>>>>>>> activestorage_migration
DragNDropSteps.clearFiles();
FilePreviewModal.init();
$.initTooltips();
@ -688,7 +689,6 @@
initCallBacks();
initHandsOnTable($(document));
expandAllSteps();
Assets.setupAssetsLoading();
FilePreviewModal.init();
TinyMCE.highlight();
SmartAnnotation.preventPropagation('.atwho-user-popover');

6
app/assets/javascripts/repositories/forms/repository_item_edit.js
View file

@ -71,7 +71,7 @@
$.each(itemData.repository_row.repository_cells, function(i, cell) {
var tableCellId = 'colId-' + cell.cell_column_id;
if(cell.type === 'RepositoryAssetValue') {
formBindingsData[tableCellId] = new File([""], cell.value.file_file_name);
formBindingsData[tableCellId] = new File([""], cell.value.file_name);
} else {
formBindingsData[tableCellId] = cell.value;
}
@ -193,7 +193,7 @@
* @returns (String)
*/
function changeToInputFileField(object, name, value, id) {
var fileName = (value.file_file_name) ? value.file_file_name : I18n.t('general.file.no_file_chosen');
var fileName = (value.file_name) ? value.file_name : I18n.t('general.file.no_file_chosen');
var buttonLabel = I18n.t('general.file.choose');
var html = "<div class='repository-input-file-field'>" +
"<div class='form-group'><div><input type='file' name='" + name + "' id='" +
@ -202,7 +202,7 @@
"' data-id='" + id + "'>" + buttonLabel +
"</button></div><div><p class='file-name-label'>" + truncateLongString(fileName, 20) +
"</p></div>";
if(value.file_file_name) {
if(value.file_name) {
html += "<div><a data-action='removeAsset' ";
html += "onClick='clearFileInput(this)'><i class='fas fa-times'></i></a>";
} else {

2
app/assets/javascripts/repositories/repository_datatable.js.erb
View file

@ -1002,7 +1002,7 @@ var RepositoryDatatable = (function(global) {
if (cell.value != null) {
const dT = new ClipboardEvent('').clipboardData || // Firefox workaround exploiting https://bugzilla.mozilla.org/show_bug.cgi?id=1422655
new DataTransfer(); // specs compliant (as of March 2018 only Chrome)
dT.items.add(new File([_], cell.value.file_file_name));
dT.items.add(new File([_], cell.value.file_name));
input.files = dT.files;
}
$(input).on('change', function(){

13
app/assets/javascripts/sitewide/file_preview.js
View file

@ -3,7 +3,7 @@
/* eslint-disable no-underscore-dangle */
/* global Uint8Array fabric tui animateSpinner Assets
I18n PerfectScrollbar MarvinJsEditor refreshProtocolStatusBar */
//= require assets
var FilePreviewModal = (function() {
'use strict';
@ -397,7 +397,16 @@ var FilePreviewModal = (function() {
dataUpload.append('image', imageBlob);
animateSpinner(null, true);
function closeEditor() {
$.ajax({
type: 'POST',
url: '/files/' + data.id + '/update_image',
data: dataUpload,
contentType: false,
processData: false,
success: function(res) {
$('#modal_link' + data.id).parent().html(res.html);
}
}).done(function() {
animateSpinner(null, false);
imageEditor.destroy();
imageEditor = {};

5
app/assets/javascripts/users/registrations/edit.js
View file

@ -82,8 +82,8 @@
croppieContainer.croppie({ viewport: { type: 'circle' } });
$('.new-avatar-preview-container').off('update.croppie').on('update.croppie', function() {
croppieContainer.croppie('result', { type: 'base64', format: 'jpeg', circle: false })
.then(function(html) {
$('#user_avatar').val(html);
.then(function(image) {
$('#user_avatar').val(image);
});
});
};
@ -98,5 +98,6 @@
// Local file uploading
animateSpinner();
}
$fileInput[0].value = '';
});
}());

85
app/controllers/assets_controller.rb
View file

@ -13,43 +13,16 @@ class AssetsController < ApplicationController
include FileIconsHelper
before_action :load_vars, except: :create_wopi_file
before_action :check_read_permission, except: :file_present
before_action :check_edit_permission, only: %i(edit create_start_edit_image_activity)
def file_present
return render_403 unless @asset.team == current_team
respond_to do |format|
format.json do
if @asset.file.processing?
render json: { processing: true }
else
# Only if file is ready, check_read_permission
check_read_permission
# If check_read_permission already rendered error, stop execution
return if performed?
placeholder_html =
if @assoc.class == Step
render_to_string(partial: 'steps/attachments/placeholder.html.erb',
locals: { asset: @asset, edit_page: false })
else
render_to_string(partial: 'shared/asset_link_placeholder.html.erb',
locals: { asset: @asset, display_image_tag: true })
end
render json: { placeholder_html: placeholder_html, processing: false }
end
end
end
end
before_action :check_read_permission
before_action :check_edit_permission, only: :edit
def file_preview
response_json = {
'id' => @asset.id,
'type' => (@asset.image? ? 'image' : 'file'),
'filename' => truncate(escape_input(@asset.file_file_name),
'filename' => truncate(escape_input(@asset.file_name),
length: Constants::FILENAME_TRUNCATION_LENGTH),
'download-url' => download_asset_path(@asset, timestamp: Time.now.to_i)
}
@ -63,22 +36,18 @@ class AssetsController < ApplicationController
end
if @asset.image?
if ['image/jpeg', 'image/pjpeg'].include? @asset.file.content_type
if ['image/jpeg', 'image/pjpeg'].include? @asset.content_type
response_json['quality'] = @asset.file_image_quality || 90
end
response_json.merge!(
'editable' => @asset.editable_image? && can_edit,
'mime-type' => @asset.file.content_type,
'processing' => @asset.file.processing?,
'large-preview-url' => @asset.url(:large),
'processing-img' => image_tag('medium/processing.gif')
'large-preview-url' => @asset.large_preview
)
else
response_json['processing'] = @asset.file.processing?
response_json['preview-icon'] = render_to_string(
partial: 'shared/file_preview_icon.html.erb',
locals: { asset: @asset }
)
response_json['preview-icon'] = render_to_string(partial: 'shared/file_preview_icon.html.erb',
locals: { asset: @asset })
end
if wopi_enabled? && wopi_file?(@asset)
@ -102,7 +71,7 @@ class AssetsController < ApplicationController
# Check whether the wopi file can be edited and return appropriate response
def wopi_file_edit_button_status
file_ext = @asset.file_file_name.split('.').last
file_ext = @asset.file_name.split('.').last
if Constants::WOPI_EDITABLE_FORMATS.include?(file_ext)
edit_supported = true
title = ''
@ -120,20 +89,16 @@ class AssetsController < ApplicationController
end
def download
if !@asset.file_present
render_404 and return
elsif @asset.file.is_stored_on_s3?
redirect_to @asset.presigned_url(download: true), status: 307
if !@asset.file.attached?
render_404
else
send_file @asset.file.path, filename: URI.unescape(@asset.file_file_name),
type: @asset.file_content_type
redirect_to rails_blob_path(@asset.file, disposition: 'attachment')
end
end
def edit
action = @asset.file_file_size.zero? && !@asset.locked? ? 'editnew' : 'edit'
@action_url = append_wd_params(@asset
.get_action_url(current_user, action, false))
action = @asset.file_size.zero? && !@asset.locked? ? 'editnew' : 'edit'
@action_url = append_wd_params(@asset.get_action_url(current_user, action, false))
@favicon_url = @asset.favicon_url('edit')
tkn = current_user.get_wopi_token
@token = tkn.token
@ -146,8 +111,7 @@ class AssetsController < ApplicationController
end
def view
@action_url = append_wd_params(@asset
.get_action_url(current_user, 'view', false))
@action_url = append_wd_params(@asset.get_action_url(current_user, 'view', false))
@favicon_url = @asset.favicon_url('view')
tkn = current_user.get_wopi_token
@token = tkn.token
@ -162,12 +126,11 @@ class AssetsController < ApplicationController
def update_image
@asset = Asset.find(params[:id])
orig_file_size = @asset.file_file_size
orig_file_name = @asset.file_file_name
orig_file_size = @asset.file_size
orig_file_name = @asset.file_name
return render_403 unless can_read_team?(@asset.team)
@asset.file = params[:image]
@asset.file_file_name = orig_file_name
@asset.file.attach(io: params.require(:image), filename: orig_file_name)
@asset.save!
create_edit_image_activity(@asset, current_user, :finish_editing)
# release previous image space
@ -212,10 +175,10 @@ class AssetsController < ApplicationController
render_403 && return unless %w(docx xlsx pptx).include?(params[:file_type])
# Asset validation
file = Paperclip.io_adapters.for(StringIO.new)
file.original_filename = "#{params[:file_name]}.#{params[:file_type]}"
file.content_type = wopi_content_type(params[:file_type])
asset = Asset.new(file: file, created_by: current_user, file_present: true)
asset = Asset.new(created_by: current_user)
asset.file.attach(io: StringIO.new,
filename: "#{params[:file_name]}.#{params[:file_type]}",
content_type: wopi_content_type(params[:file_type]))
unless asset.valid?(:wopi_file_creation)
render json: {
@ -302,9 +265,7 @@ class AssetsController < ApplicationController
end
def asset_params
params.permit(
:file
)
params.permit(:file)
end
def asset_data_type(asset)

7
app/controllers/experiments_controller.rb
View file

@ -238,14 +238,13 @@ class ExperimentsController < ApplicationController
end
def updated_img
if @experiment.workflowimg.present? && !@experiment.workflowimg.exists?
@experiment.workflowimg = nil
@experiment.save
if @experiment.workflowimg.attached? && !@experiment.workflowimg_exists?
@experiment.workflowimg.purge
@experiment.generate_workflow_img
end
respond_to do |format|
format.json do
if @experiment.workflowimg.present?
if @experiment.workflowimg.attached?
render json: {}, status: 200
else
render json: {}, status: 404

9
app/controllers/protocols_controller.rb
View file

@ -794,14 +794,11 @@ class ProtocolsController < ApplicationController
step_dir = "#{protocol_dir}/#{step_guid}"
if step.assets.exists?
step.assets.order(:id).each do |asset|
next unless asset.file.exists?
next unless asset.file.attached?
asset_guid = get_guid(asset.id)
asset_file_name = asset_guid.to_s +
File.extname(asset.file_file_name).to_s
asset_file_name = asset_guid.to_s + File.extname(asset.file_name).to_s
ostream.put_next_entry("#{step_dir}/#{asset_file_name}")
input_file = asset.open
ostream.print(input_file.read)
input_file.close
ostream.print(asset.file.download)
end
end
ostream = step.tiny_mce_assets.save_to_eln(ostream, step_dir)

4
app/controllers/result_assets_controller.rb
View file

@ -194,10 +194,10 @@ class ResultAssetsController < ApplicationController
success = true
results = []
params[:results_files].values.each_with_index do |file, index|
asset = Asset.new(file: file,
created_by: current_user,
asset = Asset.new(created_by: current_user,
last_modified_by: current_user,
team: current_team)
asset.file.attach(file)
result = Result.new(user: current_user,
my_module: @my_module,
name: params[:results_names][index.to_s],

178
app/controllers/teams_controller.rb
View file

@ -1,13 +1,6 @@
class TeamsController < ApplicationController
before_action :load_vars, only: %i(parse_sheet import_samples
export_samples export_projects
export_projects_modal)
before_action :check_create_samples_permissions, only: %i(parse_sheet
import_samples)
before_action :check_view_samples_permission, only: [:export_samples]
before_action :check_export_projects_permissions,
only: %i(export_projects_modal export_projects)
before_action :load_vars, only: %i(parse_sheet export_projects export_projects_modal)
before_action :check_export_projects_permissions, only: %i(export_projects_modal export_projects)
def parse_sheet
session[:return_to] ||= request.referer
@ -66,167 +59,6 @@ class TeamsController < ApplicationController
end
end
def import_samples
session[:return_to] ||= request.referer
respond_to do |format|
if import_params[:file_id]
@temp_file = TempFile.find_by_id(import_params[:file_id])
if @temp_file
# Check if session_id is equal to prevent file stealing
if @temp_file.session_id == session.id
# Check if mappings exists or else we don't have anything to parse
if import_params[:mappings]
@sheet = SpreadsheetParser.open_spreadsheet(@temp_file.file)
# Check for duplicated values
h1 = import_params[:mappings].clone.delete_if { |_, v| v.empty? }
if h1.length == h1.invert.length
# Check if there exist mapping for sample name (it's mandatory)
if import_params[:mappings].value?('-1')
result = @team.import_samples(@sheet,
import_params[:mappings],
current_user)
nr_of_added = result[:nr_of_added]
total_nr = result[:total_nr]
if result[:status] == :ok
# If no errors are present, redirect back
# to samples table
flash[:success] = t(
"teams.import_samples.success_flash",
nr: nr_of_added,
samples: t(
"teams.import_samples.sample",
count: total_nr
)
)
@temp_file.destroy
format.html {
redirect_to session.delete(:return_to)
}
format.json {
flash.keep(:success)
render json: { status: :ok }
}
else
# Otherwise, also redirect back,
# but display different message
flash[:alert] = t(
"teams.import_samples.partial_success_flash",
nr: nr_of_added,
samples: t(
"teams.import_samples.sample",
count: total_nr
)
)
@temp_file.destroy
format.html {
redirect_to session.delete(:return_to)
}
format.json {
flash.keep(:alert)
render json: { status: :unprocessable_entity }
}
end
else
# This is currently the only AJAX error response
flash_alert = t(
"teams.import_samples.errors.no_sample_name")
format.html {
flash[:alert] = flash_alert
redirect_to session.delete(:return_to)
}
format.json {
render json: {
html: render_to_string({
partial: "parse_error.html.erb",
locals: { error: flash_alert }
})
},
status: :unprocessable_entity
}
end
else
# This code should never execute unless user tampers with
# JS (selects same column in more than one dropdown)
flash_alert = t(
"teams.import_samples.errors.duplicated_values")
format.html {
flash[:alert] = flash_alert
redirect_to session.delete(:return_to)
}
format.json {
render json: {
html: render_to_string({
partial: "parse_error.html.erb",
locals: { error: flash_alert }
})
},
status: :unprocessable_entity
}
end
else
@temp_file.destroy
flash[:alert] = t(
"teams.import_samples.errors.no_data_to_parse")
format.html {
redirect_to session.delete(:return_to)
}
format.json {
flash.keep(:alert)
render json: { status: :unprocessable_entity }
}
end
else
@temp_file.destroy
flash[:alert] = t(
"teams.import_samples.errors.session_expired")
format.html {
redirect_to session.delete(:return_to)
}
format.json {
flash.keep(:alert)
render json: { status: :unprocessable_entity }
}
end
else
# No temp file to begin with, so no need to destroy it
flash[:alert] = t(
"teams.import_samples.errors.temp_file_not_found")
format.html {
redirect_to session.delete(:return_to)
}
format.json {
flash.keep(:alert)
render json: { status: :unprocessable_entity }
}
end
else
flash[:alert] = t(
"teams.import_samples.errors.temp_file_not_found")
format.html {
redirect_to session.delete(:return_to)
}
format.json {
flash.keep(:alert)
render json: { status: :unprocessable_entity }
}
end
end
end
def export_samples
if export_params[:sample_ids] && export_params[:header_ids]
generate_samples_zip
else
flash[:alert] = t('zip_export.export_error')
end
redirect_back(fallback_location: root_path)
end
def export_projects
if current_user.has_available_exports?
current_user.increase_daily_exports_counter!
@ -318,12 +150,6 @@ class TeamsController < ApplicationController
render_403 unless can_create_samples?(@team)
end
def check_view_samples_permission
unless can_read_team?(@team)
render_403
end
end
def check_export_projects_permissions
render_403 unless can_read_team?(@team)

20
app/controllers/tiny_mce_assets_controller.rb
View file

@ -3,13 +3,17 @@
class TinyMceAssetsController < ApplicationController
def create
image = params.fetch(:file) { render_404 }
tiny_img = TinyMceAsset.new(image: image,
team_id: current_team.id,
saved: false)
if tiny_img.save
tiny_img = TinyMceAsset.new(team_id: current_team.id, saved: false)
tiny_img.transaction do
tiny_img.save!
tiny_img.image.attach(io: image, filename: image.original_filename)
end
if tiny_img.persisted?
render json: {
image: {
url: view_context.image_url(tiny_img.url(:large)),
url: url_for(tiny_img.image),
token: Base62.encode(tiny_img.id)
}
}, content_type: 'text/html'
@ -19,10 +23,4 @@ class TinyMceAssetsController < ApplicationController
}, status: :unprocessable_entity
end
end
def update
image = TinyMceAsset.find_by_id(Base62.decode(params[:id]))
image.update(image: params[:image], image_file_name: image.image_file_name)
render json: { url: view_context.image_url(image.url) }
end
end

102
app/controllers/users/registrations_controller.rb
View file

@ -8,40 +8,8 @@ class Users::RegistrationsController < Devise::RegistrationsController
def avatar
user = User.find_by_id(params[:id]) || current_user
style = params[:style] || "icon_small"
# TODO: Maybe avatar should be an Asset, so it's methods could be used,
# e.g. presigned_url in this case
redirect_to user.avatar.url(style.to_sym), status: 307
end
# Validates asset and then generates S3 upload posts, because
# otherwise untracked files could be uploaded to S3
def signature
respond_to do |format|
format.json {
# Changed avatar values are only used for pre-generating S3 key
# and user object is not persisted with this values.
current_user.empty_avatar avatar_params[:file].original_filename,
avatar_params[:file].size
validation_asset = Asset.new(avatar_params)
if current_user.valid? && validation_asset.valid?
render json: {
posts: generate_upload_posts
}
else
if validation_asset.errors[:file].any?
# Add file content error
current_user.errors[:avatar] << validation_asset.errors[:file].first
end
render json: {
status: 'error',
errors: current_user.errors
}, status: :bad_request
end
}
end
style = params[:style] || :icon_small
redirect_to user.avatar_url(style)
end
def update_resource(resource, params)
@ -50,12 +18,10 @@ class Users::RegistrationsController < Devise::RegistrationsController
if params.include? :change_password
# Special handling if changing password
params.delete(:change_password)
if (
resource.valid_password?(params[:current_password]) and
params.include? :password and
params.include? :password_confirmation and
params[:password].blank?
) then
if resource.valid_password?(params[:current_password]) &&
params.include?(:password) &&
params.include?(:password_confirmation) &&
params[:password].blank?
# If new password is blank and we're in process of changing
# password, add error to the resource and return false
resource.errors.add(:password, :blank)
@ -65,16 +31,26 @@ class Users::RegistrationsController < Devise::RegistrationsController
end
elsif params.include? :change_avatar
params.delete(:change_avatar)
unless params.include? :avatar
if !params.include?(:avatar)
resource.errors.add(:avatar, :blank)
false
else
temp_file = Tempfile.new('avatar', Rails.root.join('tmp'))
begin
temp_file.binmode
temp_file.write(Base64.decode64(params[:avatar].sub(%r{^data:image\/jpeg\;base64,}, '')))
temp_file.rewind
resource.avatar.attach(io: temp_file, filename: 'avatar.jpg')
ensure
temp_file.close
temp_file.unlink
end
params.delete(:avatar)
resource.update_without_password(params)
end
elsif params.include? :email or params.include? :password
elsif params.include?(:email) || params.include?(:password)
# For changing email or password, validate current_password
resource.update_with_password(params)
else
# For changing some attributes, no current_password validation
# is required
@ -235,7 +211,6 @@ class Users::RegistrationsController < Devise::RegistrationsController
:full_name,
:initials,
:avatar,
:avatar_file_name,
:email,
:password,
:password_confirmation,
@ -251,45 +226,6 @@ class Users::RegistrationsController < Devise::RegistrationsController
)
end
# Generates posts for uploading files (many sizes of same file)
# to S3 server
def generate_upload_posts
posts = []
file_size = current_user.avatar_file_size
content_type = current_user.avatar_content_type
s3_post = S3_BUCKET.presigned_post(
key: current_user.avatar.path[1..-1],
success_action_status: '201',
acl: 'private',
storage_class: "STANDARD",
content_length_range: file_size..file_size,
content_type: content_type
)
posts.push({
url: s3_post.url,
fields: s3_post.fields
})
current_user.avatar.options[:styles].each do |style, option|
s3_post = S3_BUCKET.presigned_post(
key: current_user.avatar.path(style)[1..-1],
success_action_status: '201',
acl: 'public-read',
storage_class: "REDUCED_REDUNDANCY",
content_length_range: 1..Rails.configuration.x.file_max_size_mb.megabytes,
content_type: content_type
)
posts.push({
url: s3_post.url,
fields: s3_post.fields,
style_option: option,
mime_type: content_type
})
end
posts
end
private
def layout

6
app/controllers/wopi_controller.rb
View file

@ -52,9 +52,9 @@ class WopiController < ActionController::Base
asset_owner_id = @asset.created_by_id.to_s if @asset.created_by_id
msg = {
BaseFileName: @asset.file_file_name,
BaseFileName: @asset.file_name,
OwnerId: asset_owner_id,
Size: @asset.file_file_size,
Size: @asset.file_size,
UserId: @user.id.to_s,
Version: @asset.version.to_s,
SupportsExtendedLockLength: true,
@ -218,7 +218,7 @@ class WopiController < ActionController::Base
response.headers['X-WOPI-Lock'] = @asset.lock
render body: nil, status: 409 and return
end
elsif !@asset.file_file_size.nil? && @asset.file_file_size.zero?
elsif !@asset.file_size.nil? && @asset.file_size.zero?
logger.warn 'WOPI: initializing empty file'
@team.release_space(@asset.estimated_size)

8
app/controllers/zip_exports_controller.rb
View file

@ -5,12 +5,10 @@ class ZipExportsController < ApplicationController
before_action :check_download_permissions, except: :file_expired
def download
if @zip_export.stored_on_s3?
redirect_to @zip_export.presigned_url(download: true), status: 307
if !@zip_export.zip_file.attached?
render_404
else
send_file @zip_export.zip_file.path,
filename: URI.unescape(@zip_export.zip_file_file_name),
type: 'application/zip'
redirect_to rails_blob_path(@zip_export.zip_file, disposition: 'attachment')
end
end

7
app/helpers/application_helper.rb
View file

@ -196,7 +196,12 @@ module ApplicationHelper
# No more dirty hack
def user_avatar_absolute_url(user, style)
begin
return user.avatar_base64(style) unless missing_avatar(user, style)
unless missing_avatar(user, style)
image = File.open(user.avatar_variant(style))
encoded_data = Base64.strict_encode64(image)
avatar_base64 = "data:#{user.avatar_content_type};base64,#{encoded_data}"
return avatar_base64
end
rescue StandardError => e
Rails.logger.error e.message
end

17
app/helpers/file_icons_helper.rb
View file

@ -1,11 +1,12 @@
module FileIconsHelper
def wopi_file?(asset)
file_ext = asset.file_file_name.split('.').last
%w(csv ods xls xlsb xlsm xlsx odp pot potm potx pps ppsm ppsx ppt pptm pptx doc docm docx dot dotm dotx odt rtf).include?(file_ext)
file_ext = asset.file_name.split('.').last
%w(csv ods xls xlsb xlsm xlsx odp pot potm potx pps ppsm
ppsx ppt pptm pptx doc docm docx dot dotm dotx odt rtf).include?(file_ext)
end
def file_fa_icon_class(asset)
file_ext = asset.file_file_name.split('.').last
file_ext = asset.file_name.split('.').last
if Extends::FILE_FA_ICON_MAPPINGS[file_ext] # Check for custom mappings or possible overrides
return Extends::FILE_FA_ICON_MAPPINGS[file_ext]
@ -28,7 +29,7 @@ module FileIconsHelper
# For showing next to file
def file_extension_icon(asset)
file_ext = asset.file_file_name.split('.').last
file_ext = asset.file_name.split('.').last
if Constants::FILE_TEXT_FORMATS.include?(file_ext)
image_link = 'office/Word-docx_20x20x32.png'
elsif Constants::FILE_TABLE_FORMATS.include?(file_ext)
@ -38,9 +39,7 @@ module FileIconsHelper
end
# Now check for custom mappings or possible overrides
if Extends::FILE_ICON_MAPPINGS[file_ext]
image_link = Extends::FILE_ICON_MAPPINGS[file_ext]
end
image_link = Extends::FILE_ICON_MAPPINGS[file_ext] if Extends::FILE_ICON_MAPPINGS[file_ext]
if image_link
image_tag image_link
@ -51,7 +50,7 @@ module FileIconsHelper
# For showing in view/edit buttons (WOPI)
def file_application_icon(asset)
file_ext = asset.file_file_name.split('.').last
file_ext = asset.file_name.split('.').last
if Constants::FILE_TEXT_FORMATS.include?(file_ext)
image_link = 'office/Word-color_16x16x32.png'
elsif Constants::FILE_TABLE_FORMATS.include?(file_ext)
@ -69,7 +68,7 @@ module FileIconsHelper
# Shows correct WOPI application text (Word Online/Excel ..)
def wopi_button_text(asset, action)
file_ext = asset.file_file_name.split('.').last
file_ext = asset.file_name.split('.').last
if Constants::FILE_TEXT_FORMATS.include?(file_ext)
app = 'Word Online'
elsif Constants::FILE_TABLE_FORMATS.include?(file_ext)

11
app/helpers/my_modules_helper.rb
View file

@ -30,12 +30,11 @@ module MyModulesHelper
end
def az_ordered_assets_index(step, asset_id)
assets = []
assets += step.assets
assets += step.marvin_js_assets
assets.sort! do |a, b|
(a[asset_name_sort_field(a)]).downcase <=> (b[asset_name_sort_field(b)]).downcase
end.pluck(:id).index(asset_id)
step.assets
.joins(file_attachment: :blob)
.order(Arel.sql('LOWER(active_storage_blobs.filename)'))
.pluck(:id)
.index(asset_id)
end
def number_of_samples(my_module)

7
app/helpers/reports_helper.rb
View file

@ -97,8 +97,9 @@ module ReportsHelper
end
# "Hack" to omit file preview URL because of WKHTML issues
def report_image_asset_url(asset, _type = :asset, klass = nil)
image_tag(asset.generate_base64(:medium), class: klass)
def report_image_asset_url(asset, type = :asset, klass = nil)
url = type == :tiny_mce_asset ? asset.preview : asset.large_preview
image_tag(url, class: klass)
end
# "Hack" to load Glyphicons css directly from the CDN
@ -147,7 +148,7 @@ module ReportsHelper
def obj_name_to_filename(obj, filename_suffix = '')
obj_name = if obj.class == Asset
obj_name, extension = obj.file_file_name.split('.')
obj_name, extension = obj.file_name.split('.')
extension&.prepend('.')
obj_name
elsif obj.class.in? [Table, Result, Repository]

283
app/models/asset.rb
View file

@ -1,4 +1,5 @@
class Asset < ApplicationRecord
include ActiveStorage::Downloading
include SearchableModel
include DatabaseHelper
include Encryptor
@ -78,30 +79,9 @@ class Asset < ApplicationRecord
has_many :report_elements, inverse_of: :asset, dependent: :destroy
has_one :asset_text_datum, inverse_of: :asset, dependent: :destroy
# Specific file errors propagate to "file" error hash key,
# so use just these errors
after_validation :filter_paperclip_errors
# Needed because Paperclip validatates on creation
after_initialize :filter_paperclip_errors, if: :new_record?
before_destroy :paperclip_delete, prepend: true
after_save { result&.touch; step&.touch }
attr_accessor :file_content, :file_info, :preview_cached, :in_template
def file_empty(name, size)
file_ext = name.split(".").last
self.file_file_name = name
self.file_content_type = Rack::Mime.mime_type(".#{file_ext}")
self.file_file_size = size
self.file_updated_at = DateTime.now
self.file_present = false
end
def self.new_empty(name, size)
asset = self.new
asset.file_empty name, size
asset
end
attr_accessor :file_content, :file_info, :in_template
def self.search(
user,
@ -136,6 +116,7 @@ class Asset < ApplicationRecord
assets_in_steps, assets_in_results, assets_in_inventories)
new_query = Asset.left_outer_joins(:asset_text_datum)
.left_outer_joins(file_attachment: :blob)
.from(assets, 'assets')
a_query = s_query = ''
@ -160,7 +141,7 @@ class Asset < ApplicationRecord
s_query = s_query.tr('\'', '"')
new_query = new_query.where(
"(trim_html_tags(assets.file_file_name) #{like} ? " \
"(active_storage_blobs.filename #{like} ? " \
"OR asset_text_data.data_vector @@ to_tsquery(?))",
a_query,
s_query
@ -181,7 +162,7 @@ class Asset < ApplicationRecord
.join('|')
.tr('\'', '"')
new_query = new_query.where(
"(trim_html_tags(assets.file_file_name) #{like} ANY (array[?]) " \
"(active_storage_blobs.filename #{like} ANY (array[?]) " \
"OR asset_text_data.data_vector @@ to_tsquery(?))",
a_query,
s_query
@ -203,34 +184,69 @@ class Asset < ApplicationRecord
end
end
def blob
file&.blob
end
def previewable?
return false unless file.attached?
previewable_document? || previewable_image?
end
def medium_preview
return file.variant(resize: Constants::MEDIUM_PIC_FORMAT) if previewable_image?
'medium/processing.gif'
'/images/medium/processing.gif'
# file.preview(resize: Constants::MEDIUM_PIC_FORMAT)
end
def large_preview
return file.variant(resize: Constants::LARGE_PIC_FORMAT) if previewable_image?
'large/processing.gif'
'/images/large/processing.gif'
# file.preview(resize: Constants::LARGE_PIC_FORMAT)
end
def file_name
return '' unless file.attached?
file.blob&.filename&.to_s
end
def file_size
return 0 unless file.attached?
file.blob&.byte_size
end
def content_type
file&.blob&.content_type
end
def file_size
file&.blob&.byte_size
end
def duplicate
new_asset = dup
return unless new_asset.save
return new_asset unless file.attached?
duplicate_file(new_asset)
new_asset
end
def duplicate_file(to_asset)
download_blob_to_tempfile do |tmp_file|
to_asset.file.attach(io: tmp_file.open, filename: file_name)
end
new_asset.post_process_file(new_asset.team)
end
def extract_image_quality
return unless ['image/jpeg', 'image/pjpeg'].include? file_content_type
return unless ['image/jpeg', 'image/pjpeg'].include? content_type
tempfile = file.queued_for_write[:original]
unless tempfile.nil?
@ -242,30 +258,18 @@ class Asset < ApplicationRecord
end
def image?
file.blob.content_type == %r{^image/#{Regexp.union(Constants::WHITELISTED_IMAGE_TYPES)}}
content_type == %r{^image/#{Regexp.union(Constants::WHITELISTED_IMAGE_TYPES)}}
end
def text?
Constants::TEXT_EXTRACT_FILE_TYPES.any? do |v|
file_content_type.start_with? v
file&.blob&.content_type&.start_with? v
end
end
# TODO: get the current_user
# before_save do
# if current_user
# self.created_by ||= current_user
# self.last_modified_by = current_user if self.changed?
# end
# end
def is_stored_on_s3?
file.options[:storage].to_sym == :s3
end
def post_process_file(team = nil)
# Update self.empty
self.update(file_present: true)
update(file_present: true)
# Extract asset text if it's of correct type
if text?
@ -273,80 +277,56 @@ class Asset < ApplicationRecord
# The extract_asset_text also includes
# estimated size calculation
Asset.delay(queue: :assets, run_at: 20.minutes.from_now)
.extract_asset_text(id, in_template)
.extract_asset_text_delayed(id, in_template)
else
# Update asset's estimated size immediately
update_estimated_size(team)
end
end
def self.extract_asset_text(asset_id, in_template = false)
def self.extract_asset_text_delayed(asset_id, in_template = false)
asset = find_by_id(asset_id)
return unless asset.present? && asset.file.present?
asset.in_template = in_template
return unless asset.present? && asset.file.attached?
begin
file_path = asset.file.path
asset.extract_asset_text(in_template)
end
if asset.file.is_stored_on_s3?
fa = asset.file.fetch
file_path = fa.path
end
def extract_asset_text(in_template = false)
self.in_template = in_template
download_blob_to_tempfile do |tmp_file|
# Start Tika as a server
if !ENV['NO_TIKA_SERVER'] && Yomu.class_variable_get(:@@server_pid).nil?
Yomu.server(:text)
end
Yomu.server(:text) if !ENV['NO_TIKA_SERVER'] && Yomu.class_variable_get(:@@server_pid).nil?
y = Yomu.new file_path
text_data = y.text
text_data = Yomu.new(tmp_file.path).text
if asset.asset_text_datum.present?
if asset_text_datum.present?
# Update existing text datum if it exists
asset.asset_text_datum.update(data: text_data)
asset_text_datum.update(data: text_data)
else
# Create new text datum
AssetTextDatum.create(data: text_data, asset: asset)
AssetTextDatum.create(data: text_data, asset: self)
end
Rails.logger.info "Asset #{asset.id}: Asset file successfully extracted"
Rails.logger.info "Asset #{id}: Asset file successfully extracted"
# Finally, update asset's estimated size to include
# the data vector
asset.update_estimated_size(asset.team)
update_estimated_size(team)
rescue StandardError => e
Rails.logger.fatal(
"Asset #{asset.id}: Error extracting contents from asset "\
"file #{asset.file.path}: #{e.message}"
"Asset #{id}: Error extracting contents from asset "\
"file #{file.blob.key}: #{e.message}"
)
ensure
File.delete file_path if fa
end
end
# Workaround for making Paperclip work with asset deletion (might be because
# of how the asset models are implemented)
def paperclip_delete
report_elements.destroy_all
asset_text_datum.destroy if asset_text_datum.present?
# Nullify needed to force paperclip file deletion
file = nil
save && reload
end
def destroy
super()
# Needed, otherwise the object isn't deleted, because of how the asset
# models are implemented
delete
end
# If team is provided, its space_taken
# is updated as well
def update_estimated_size(team = nil)
return if file_file_size.blank? || in_template
return if file_size.blank? || in_template
es = file_file_size
es = file_size
if asset_text_datum.present? && asset_text_datum.persisted?
asset_text_datum.reload
es += get_octet_length_record(asset_text_datum, :data)
@ -363,66 +343,18 @@ class Asset < ApplicationRecord
end
end
def url(style = :original, timeout: Constants::URL_SHORT_EXPIRE_TIME)
if file.is_stored_on_s3? && !file.processing?
presigned_url(style, timeout: timeout)
else
file.url(style)
end
end
# When using S3 file upload, we can limit file accessibility with url signing
def presigned_url(style = :original,
download: false,
timeout: Constants::URL_SHORT_EXPIRE_TIME)
if file.is_stored_on_s3?
if download
download_arg = 'attachment; filename=' + URI.escape(file_file_name)
else
download_arg = nil
end
signer = Aws::S3::Presigner.new(client: S3_BUCKET.client)
signer.presigned_url(:get_object,
bucket: S3_BUCKET.name,
key: file.path(style)[1..-1],
expires_in: timeout,
# this response header forces object download
response_content_disposition: download_arg)
end
end
def open
if file.is_stored_on_s3?
Kernel.open(presigned_url, "rb")
else
File.open(file.path, "rb")
end
end
# Preserving attachments (on client-side) between failed validations
# (only usable for small/few files!).
# Needs to be called before save method and view needs to have
# :file_content and :file_info hidden field.
# If file is an image, it can be viewed on front-end
# using @preview_cached with image_tag tag.
def preserve(file_data)
if file_data[:file_content].present?
restore_cached(file_data[:file_content], file_data[:file_info])
end
cache
end
def can_perform_action(action)
if ENV['WOPI_ENABLED'] == 'true'
file_ext = file_file_name.split('.').last
file_ext = file_name.split('.').last
if file_ext == 'wopitest' &&
(!ENV['WOPI_TEST_ENABLED'] || ENV['WOPI_TEST_ENABLED'] == 'false')
return false
end
action = get_action(file_ext, action)
return false if action.nil?
true
else
false
@ -430,7 +362,7 @@ class Asset < ApplicationRecord
end
def get_action_url(user, action, with_tokens = true)
file_ext = file_file_name.split('.').last
file_ext = file_name.split('.').last
action = get_action(file_ext, action)
if !action.nil?
action_url = action.urlsrc
@ -453,7 +385,7 @@ class Asset < ApplicationRecord
)
action_url += "WOPISrc=#{rest_url}"
if with_tokens
token = user.get_wopi_token
token = user.get_wopi_token
action_url + "&access_token=#{token.token}"\
"&access_token_ttl=#{(token.ttl * 1000)}"
else
@ -465,7 +397,7 @@ class Asset < ApplicationRecord
end
def favicon_url(action)
file_ext = file_file_name.split('.').last
file_ext = file_name.split('.').last
action = get_action(file_ext, action)
action.wopi_app.icon if action.try(:wopi_app)
end
@ -507,8 +439,8 @@ class Asset < ApplicationRecord
def update_contents(new_file)
new_file.class.class_eval { attr_accessor :original_filename }
new_file.original_filename = file_file_name
self.file = new_file
new_file.original_filename = file_name
file.attach(io: new_file, filename: original_filename)
self.version = version.nil? ? 1 : version + 1
save
end
@ -517,6 +449,7 @@ class Asset < ApplicationRecord
!locked? && %r{^image/#{Regexp.union(Constants::WHITELISTED_IMAGE_TYPES_EDITABLE)}} =~ file.content_type
end
<<<<<<< HEAD
def generate_base64(style)
image = if file.options[:storage].to_sym == :s3
URI.parse(url(style)).open.to_a.join
@ -528,22 +461,19 @@ class Asset < ApplicationRecord
end
protected
=======
private
>>>>>>> activestorage_migration
# Checks if attachments is an image (in post processing imagemagick will
# generate styles)
def allow_styles_on_images
if !(file.content_type =~ %r{^(image|(x-)?application)/(x-png|pjpeg|jpeg|jpg|png|gif)$})
return false
end
def tempdir
Rails.root.join('tmp')
end
private
def previewable_document?
previewable = Constants::PREVIEWABLE_FILE_TYPES.include?(file.blob&.content_type)
previewable = Constants::PREVIEWABLE_FILE_TYPES.include?(file.content_type)
filename = file.blob&.filename
content_type = file.blob&.content_type
filename = file.filename.to_s
content_type = file.content_type
extensions = %w(.xlsx .docx .pptx .xls .doc .ppt)
# Mimetype sometimes recognizes Office files as zip files
@ -562,29 +492,6 @@ class Asset < ApplicationRecord
file.blob&.content_type =~ %r{^image/#{Regexp.union(Constants::WHITELISTED_IMAGE_TYPES)}}
end
def filter_paperclip_errors
if errors.size > 1
temp_errors = errors[:file]
errors.clear
errors.add(:file, temp_errors)
end
end
def file_changed?
previous_changes.present? and
(
(
previous_changes.key? "file_file_name" and
previous_changes["file_file_name"].first !=
previous_changes["file_file_name"].last
) or (
previous_changes.key? "file_file_size" and
previous_changes["file_file_size"].first !=
previous_changes["file_file_size"].last
)
)
end
def step_or_result_or_repository_asset_value
# We must allow both step and result to be blank because of GUI
# (even though it's not really a "valid" asset)
@ -617,30 +524,4 @@ class Asset < ApplicationRecord
)
end
end
def cache
fetched_file = file.fetch
file_content = fetched_file.read
@file_content = encrypt(file_content)
@file_info = %Q[{"content_type" : "#{file.content_type}", "original_filename" : "#{file.original_filename}"}]
@file_info = encrypt(@file_info)
if !(file.content_type =~ /^image/).nil?
@preview_cached = "data:image/png;base64," + Base64.encode64(file_content)
end
end
def restore_cached(file_content, file_info)
decoded_data = decrypt(file_content)
decoded_data_info = decrypt(file_info)
decoded_data_info = JSON.parse decoded_data_info
data = StringIO.new(decoded_data)
data.class_eval do
attr_accessor :content_type, :original_filename
end
data.content_type = decoded_data_info['content_type']
data.original_filename = File.basename(decoded_data_info['original_filename'])
self.file = data
end
end

48
app/models/concerns/tiny_mce_images.rb
View file

@ -18,23 +18,17 @@ module TinyMceImages
description = TinyMceAsset.update_old_tinymce(description, self)
tiny_mce_assets.each do |tm_asset|
tmp_f = Tempfile.open(tm_asset.image_file_name, Rails.root.join('tmp'))
begin
tm_asset.image.copy_to_local_file(:large, tmp_f.path)
encoded_tm_asset = Base64.strict_encode64(tmp_f.read)
new_tm_asset_src = "data:image/jpg;base64,#{encoded_tm_asset}"
html_description = Nokogiri::HTML(description)
tm_asset_to_update = html_description.css(
"img[data-mce-token=\"#{Base62.encode(tm_asset.id)}\"]"
)[0]
next unless tm_asset_to_update
tm_asset_key = tm_asset.image.preview.key
encoded_tm_asset = Base64.strict_encode64(tm_asset.image.service.download(tm_asset_key))
new_tm_asset_src = "data:image/jpg;base64,#{encoded_tm_asset}"
html_description = Nokogiri::HTML(description)
tm_asset_to_update = html_description.css(
"img[data-mce-token=\"#{Base62.encode(tm_asset.id)}\"]"
)[0]
next unless tm_asset_to_update
tm_asset_to_update.attributes['src'].value = new_tm_asset_src
description = html_description.css('body').inner_html.to_s
ensure
tmp_f.close
tmp_f.unlink
end
tm_asset_to_update.attributes['src'].value = new_tm_asset_src
description = html_description.css('body').inner_html.to_s
end
description
end
@ -72,12 +66,15 @@ module TinyMceImages
cloned_img_ids = []
tiny_mce_assets.each do |tiny_img|
tiny_img_clone = TinyMceAsset.new(
image: tiny_img.image,
estimated_size: tiny_img.estimated_size,
object: target,
team: team
)
tiny_img_clone.save!
tiny_img_clone.transaction do
tiny_img_clone.save!
tiny_img_clone.image.attach(io: tiny_img.image.open, filename: tiny_img.image.filename.to_s)
end
target.tiny_mce_assets << tiny_img_clone
cloned_img_ids << [tiny_img.id, tiny_img_clone.id]
@ -86,7 +83,7 @@ module TinyMceImages
end
def copy_unknown_tiny_mce_images
asset_team_id = Team.find_by_object(self)
asset_team_id = Team.find_by_object(self).id
return unless asset_team_id
object_field = Extends::RICH_TEXT_FIELD_MAPPINGS[self.class.name]
@ -97,19 +94,26 @@ module TinyMceImages
if image['data-mce-token']
asset = TinyMceAsset.find_by_id(Base62.decode(image['data-mce-token']))
next if asset && asset.object == self
next if asset && asset.object == self && asset.team_id != asset_team_id
new_image = asset.image
new_image_filename = new_image.file_name
else
new_image = URI.parse(image['src'])
# We need implement size and type checks here
new_image = URI.parse(image['src']).open
new_image_filename = asset.class.generate_unique_secure_token + '.jpg'
end
new_asset = TinyMceAsset.create(
image: new_image,
object: self,
team_id: asset_team_id
)
new_asset.transaction do
new_asset.save!
new_asset.image.attach(io: new_image, filename: new_image_filename)
end
image['src'] = ''
image['class'] = 'img-responsive'
image['data-mce-token'] = Base62.encode(new_asset.id)

20
app/models/experiment.rb
View file

@ -28,10 +28,7 @@ class Experiment < ApplicationRecord
# Associations for old activity type
has_many :activities, inverse_of: :experiment
has_attached_file :workflowimg
validates_attachment :workflowimg,
content_type: { content_type: ['image/png'] },
if: :workflowimg_check
has_one_attached :workflowimg
auto_strip_attributes :name, :description, nullify: false
validates :name,
@ -220,13 +217,14 @@ class Experiment < ApplicationRecord
end
def generate_workflow_img
if workflowimg.present?
self.workflowimg = nil
save
end
workflowimg.purge if workflowimg.attached?
Experiments::GenerateWorkflowImageService.delay.call(experiment_id: id)
end
def workflowimg_exists?
workflowimg.service.exist?(workflowimg.blob.key)
end
# Get projects where user is either owner or user in the same team
# as this experiment
def projects_with_role_above_user(current_user)
@ -613,12 +611,6 @@ class Experiment < ApplicationRecord
true
end
def workflowimg_check
workflowimg_content_type
rescue
false
end
def log_activity(type_of, current_user, my_module)
Activities::CreateActivityService
.call(activity_type: type_of,

46
app/models/protocol.rb
View file

@ -234,7 +234,7 @@ class Protocol < ApplicationRecord
end
# Deep-clone given array of assets
def self.deep_clone_assets(assets_to_clone, team)
def self.deep_clone_assets(assets_to_clone)
assets_to_clone.each do |src_id, dest_id|
src = Asset.find_by_id(src_id)
dest = Asset.find_by_id(dest_id)
@ -242,34 +242,7 @@ class Protocol < ApplicationRecord
next unless src.present? && dest.present?
# Clone file
dest.file = src.file
dest.save!
if dest.image?
dest.file.reprocess!(:large)
dest.file.reprocess!(:medium)
end
# Clone extracted text data if it exists
if (atd = src.asset_text_datum).present?
atd2 = AssetTextDatum.new(
data: atd.data,
asset: dest
)
atd2.save!
end
# Update estimated size of cloned asset
# (& file_present flag)
dest.update(
estimated_size: src.estimated_size,
file_present: true
)
# Update team's space taken
team.reload
team.take_space(dest.estimated_size)
team.save!
src.duplicate_file(dst)
end
end
@ -327,16 +300,8 @@ class Protocol < ApplicationRecord
# "Shallow" Copy assets
step.assets.each do |asset|
asset2 = Asset.new_empty(
asset.file_file_name,
asset.file_file_size
)
asset2.created_by = current_user
asset2.team = dest.team
asset2.last_modified_by = current_user
asset2.file_processing = true if asset.image?
asset2 = asset.dup
asset2.save!
step2.assets << asset2
assets_to_clone << [asset.id, asset2.id]
end
@ -357,10 +322,7 @@ class Protocol < ApplicationRecord
step.clone_tinymce_assets(step2, dest.team)
end
# Call clone helper
Protocol.delay(queue: :assets).deep_clone_assets(
assets_to_clone,
dest.team
)
Protocol.delay(queue: :assets).deep_clone_assets(assets_to_clone)
end
def in_repository_active?

7
app/models/repository_asset_value.rb
View file

@ -21,11 +21,11 @@ class RepositoryAssetValue < ApplicationRecord
SORTABLE_VALUE_INCLUDE = { repository_asset_value: :asset }.freeze
def formatted
asset.file_file_name
asset.file_name
end
def data
asset.file_file_name
asset.file_name
end
def data_changed?(_new_data)
@ -33,9 +33,8 @@ class RepositoryAssetValue < ApplicationRecord
end
def update_data!(new_data, user)
file = Paperclip.io_adapters.for(new_data[:file_data])
file.original_filename = new_data[:file_name]
asset.file = file
asset.file.attach(io: new_data[:file_data], filename: new_data[:file_name])
asset.last_modified_by = user
self.last_modified_by = user
asset.save! && save!

136
app/models/team.rb
View file

@ -71,124 +71,6 @@ class Team < ApplicationRecord
.where('full_name ILIKE ? OR email ILIKE ?', a_query, a_query)
end
# Imports samples into db
# -1 == sample_name,
# -2 == sample_type,
# -3 == sample_group
# TODO: use constants
def import_samples(sheet, mappings, user)
errors = false
nr_of_added = 0
total_nr = 0
header_skipped = false
# First let's query for all custom_fields we're refering to
custom_fields = []
sname_index = -1
stype_index = -1
sgroup_index = -1
mappings.each.with_index do |(_, v), i|
if v == '-1'
# Fill blank space, so our indices stay the same
custom_fields << nil
sname_index = i
elsif v == '-2'
custom_fields << nil
stype_index = i
elsif v == '-3'
custom_fields << nil
sgroup_index = i
else
cf = CustomField.find_by_id(v)
# Even if doesn't exist we add nil value in order not to destroy our
# indices
custom_fields << cf
end
end
rows = SpreadsheetParser.spreadsheet_enumerator(sheet)
# Now we can iterate through sample data and save stuff into db
rows.each do |row|
# Skip empty rows
next if row.empty?
unless header_skipped
header_skipped = true
next
end
total_nr += 1
row = SpreadsheetParser.parse_row(row, sheet)
sample = Sample.new(name: row[sname_index],
team: self,
user: user)
sample.transaction do
unless sample.valid?
errors = true
raise ActiveRecord::Rollback
end
row.each.with_index do |value, index|
next unless value.present?
if index == stype_index
stype = SampleType.where(team: self)
.where('name ILIKE ?', value.strip)
.take
unless stype
stype = SampleType.new(name: value.strip, team: self)
unless stype.save
errors = true
raise ActiveRecord::Rollback
end
end
sample.sample_type = stype
elsif index == sgroup_index
sgroup = SampleGroup.where(team: self)
.where('name ILIKE ?', value.strip)
.take
unless sgroup
sgroup = SampleGroup.new(name: value.strip, team: self)
unless sgroup.save
errors = true
raise ActiveRecord::Rollback
end
end
sample.sample_group = sgroup
elsif value && custom_fields[index]
# we're working with CustomField
scf = SampleCustomField.new(
sample: sample,
custom_field: custom_fields[index],
value: value
)
unless scf.valid?
errors = true
raise ActiveRecord::Rollback
end
sample.sample_custom_fields << scf
end
end
if Sample.import([sample],
recursive: true,
validate: false).failed_instances.any?
errors = true
raise ActiveRecord::Rollback
end
nr_of_added += 1
end
end
if errors
return { status: :error, nr_of_added: nr_of_added, total_nr: total_nr }
else
return { status: :ok, nr_of_added: nr_of_added, total_nr: total_nr }
end
end
def to_csv(samples, headers)
require "csv"
@ -335,14 +217,16 @@ class Team < ApplicationRecord
end
def self.find_by_object(obj)
case obj.class.name
when 'Protocol'
obj.team_id
when 'MyModule', 'Step'
obj.protocol.team_id
when 'ResultText'
obj.result.my_module.protocol.team_id
end
find(
case obj.class.name
when 'Protocol'
obj.team_id
when 'MyModule', 'Step'
obj.protocol.team_id
when 'ResultText'
obj.result.my_module.protocol.team_id
end
)
end
private

11
app/models/team_zip_export.rb
View file

@ -147,7 +147,7 @@ class TeamZipExport < ZipExport
.routes
.url_helpers
.zip_exports_download_export_all_path(self)}'>" \
"#{zip_file_file_name}</a>"
"#{zip_file_name}</a>"
)
UserNotification.create(notification: notification, user: user)
end
@ -197,11 +197,9 @@ class TeamZipExport < ZipExport
if type == :step
name = "#{directory}/" \
"#{append_file_suffix(asset.file_file_name,
"_#{i}_Step#{element.step.position_plus_one}")}"
"#{append_file_suffix(asset.file_name, "_#{i}_Step#{element.step.position_plus_one}")}"
elsif type == :result
name = "#{directory}/#{append_file_suffix(asset.file_file_name,
"_#{i}")}"
name = "#{directory}/#{append_file_suffix(asset.file_name, "_#{i}")}"
end
asset.file.copy_to_local_file(:original, name) if asset.file.exists?
asset_indexes[asset.id] = name
@ -254,8 +252,7 @@ class TeamZipExport < ZipExport
assets = {}
asset_counter = 0
handle_name_func = lambda do |asset|
file_name = append_file_suffix(asset.file_file_name,
"_#{asset_counter}").to_s
file_name = append_file_suffix(asset.file_name, "_#{asset_counter}").to_s
# Save pair for downloading it later
assets[asset] = "#{attach_path}/#{file_name}"

3
app/models/temp_file.rb
View file

@ -3,8 +3,7 @@
class TempFile < ApplicationRecord
validates :session_id, presence: true
has_attached_file :file
do_not_validate_attachment_file_type :file
has_one_attached :file
class << self
def destroy_obsolete(temp_file_id)

127
app/models/tiny_mce_asset.rb
View file

@ -4,7 +4,7 @@ class TinyMceAsset < ApplicationRecord
extend ProtocolsExporter
attr_accessor :reference
before_create :set_reference, optional: true
after_create :update_estimated_size, :self_destruct
after_create :calculate_estimated_size, :self_destruct
after_destroy :release_team_space
belongs_to :team, inverse_of: :tiny_mce_assets, optional: true
@ -22,20 +22,23 @@ class TinyMceAsset < ApplicationRecord
belongs_to :object, polymorphic: true,
optional: true,
inverse_of: :tiny_mce_assets
has_attached_file :image,
styles: { large: [Constants::LARGE_PIC_FORMAT, :jpg] },
convert_options: { large: '-quality 100 -strip' }
validates_attachment_content_type :image,
content_type: %r{^image/#{ Regexp.union(
Constants::WHITELISTED_IMAGE_TYPES
) }}
validates_attachment :image,
presence: true,
size: {
less_than: Rails.configuration.x\
.file_max_size_mb.megabytes
}
has_one_attached :image
# has_attached_file :image,
# styles: { large: [Constants::LARGE_PIC_FORMAT, :jpg] },
# convert_options: { large: '-quality 100 -strip' }
# validates_attachment_content_type :image,
# content_type: %r{^image/#{ Regexp.union(
# Constants::WHITELISTED_IMAGE_TYPES
# ) }}
# validates_attachment :image,
# presence: true,
# size: {
# less_than: Rails.configuration.x\
# .file_max_size_mb.megabytes
# }
validates :estimated_size, presence: true
def source
@ -67,13 +70,10 @@ class TinyMceAsset < ApplicationRecord
tm_assets = description.css('img[data-mce-token]')
tm_assets.each do |tm_asset|
asset_id = tm_asset.attr('data-mce-token')
new_asset_url = find_by_id(Base62.decode(asset_id))
next unless new_asset_url
assets_source = new_asset_url.source
if assets_source
tm_asset.set_attribute('data-source-id', assets_source.id)
tm_asset.set_attribute('data-source-type', assets_source.class.name)
new_asset = obj.tiny_mce_assets.find_by_id(Base62.decode(asset_id))
if new_asset
tm_asset.attributes['src'].value = Rails.application.routes.url_helpers.url_for(new_asset.image)
tm_asset['class'] = 'img-responsive'
end
tm_asset.attributes['src'].value = new_asset_url.url
tm_asset['class'] = 'img-responsive'
@ -81,47 +81,51 @@ class TinyMceAsset < ApplicationRecord
description.css('body').inner_html.to_s
end
def presigned_url(style = :large,
download: false,
timeout: Constants::URL_LONG_EXPIRE_TIME)
if stored_on_s3?
download_arg = ('attachment; filename=' + CGI.escape(image_file_name) if download)
def file_name
return '' unless image.attached?
signer = Aws::S3::Presigner.new(client: S3_BUCKET.client)
signer.presigned_url(:get_object,
bucket: S3_BUCKET.name,
key: image.path(style)[1..-1],
expires_in: timeout,
response_content_disposition: download_arg)
end
image.blob&.filename&.to_s
end
def stored_on_s3?
image.options[:storage].to_sym == :s3
def file_size
return 0 unless image.attached?
image.blob&.byte_size
end
def url(style = :large, timeout: Constants::URL_LONG_EXPIRE_TIME)
if image.is_stored_on_s3?
presigned_url(style, timeout: timeout)
else
image.url(style)
end
def content_type
image&.blob&.content_type
end
def open
if image.is_stored_on_s3?
Kernel.open(presigned_url, 'rb')
else
File.open(image.path, 'rb')
end
def file_size
image&.blob&.byte_size
end
def preview
image.variant(resize: Constants::LARGE_PIC_FORMAT)
end
def self.delete_unsaved_image(id)
asset = find_by_id(id)
asset.destroy if asset && !asset.saved
end
def self.update_estimated_size(id)
asset = find_by_id(id)
return unless asset&.image&.attached?
def self.update_old_tinymce(description, obj = nil, import = false)
size = asset.image.blob.byte_size
return if size.blank?
e_size = size * Constants::ASSET_ESTIMATED_SIZE_FACTOR
asset.update(estimated_size: e_size)
Rails.logger.info "Asset #{id}: Estimated size successfully calculated"
# update team space taken
asset.team.take_space(e_size)
asset.team.save
end
def self.update_old_tinymce(description, obj = nil)
return description unless description
description.scan(/\[~tiny_mce_id:(\w+)\]/).flatten.each do |token|
@ -148,12 +152,9 @@ class TinyMceAsset < ApplicationRecord
if exists?
order(:id).each do |tiny_mce_asset|
asset_guid = get_guid(tiny_mce_asset.id)
asset_file_name =
"rte-#{asset_guid.to_s +
File.extname(tiny_mce_asset.image_file_name).to_s}"
asset_file_name = "rte-#{asset_guid.to_s + File.extname(tiny_mce_asset.image.filename.to_s)}"
ostream.put_next_entry("#{dir}/#{asset_file_name}")
input_file = tiny_mce_asset.open
ostream.print(input_file.read)
ostream.print(tiny_mce_asset.image.download)
input_file.close
end
end
@ -176,12 +177,17 @@ class TinyMceAsset < ApplicationRecord
return false unless team_id
tiny_img_clone = TinyMceAsset.new(
image: image,
estimated_size: estimated_size,
object: obj,
team_id: team_id
)
tiny_img_clone.save!
tiny_img_clone.transaction do
tiny_img_clone.save!
tiny_img_clone.image.attach(io: image.download, filename: image.filename.to_s)
end
return false unless tiny_img_clone.persisted?
obj.tiny_mce_assets << tiny_img_clone
# Prepare array of image to update
@ -202,15 +208,8 @@ class TinyMceAsset < ApplicationRecord
TinyMceAsset.delay(queue: :assets, run_at: 1.days.from_now).delete_unsaved_image(id)
end
def update_estimated_size
return if image_file_size.blank?
es = image_file_size * Constants::ASSET_ESTIMATED_SIZE_FACTOR
update(estimated_size: es)
Rails.logger.info "Asset #{id}: Estimated size successfully calculated"
# update team space taken
team.take_space(es)
team.save
def calculate_estimated_size
TinyMceAsset.delay(queue: :assets, run_at: 5.minutes.from_now).update_estimated_size(id)
end
def release_team_space

66
app/models/user.rb
View file

@ -15,14 +15,17 @@ class User < ApplicationRecord
:timeoutable, :omniauthable,
omniauth_providers: Extends::OMNIAUTH_PROVIDERS,
stretches: Constants::PASSWORD_STRETCH_FACTOR
has_attached_file :avatar,
styles: {
medium: Constants::MEDIUM_PIC_FORMAT,
thumb: Constants::THUMB_PIC_FORMAT,
icon: Constants::ICON_PIC_FORMAT,
icon_small: Constants::ICON_SMALL_PIC_FORMAT
},
default_url: Constants::DEFAULT_AVATAR_URL
has_one_attached :avatar
# has_attached_file :avatar,
# styles: {
# medium: Constants::MEDIUM_PIC_FORMAT,
# thumb: Constants::THUMB_PIC_FORMAT,
# icon: Constants::ICON_PIC_FORMAT,
# icon_small: Constants::ICON_SMALL_PIC_FORMAT
# },
# default_url: Constants::DEFAULT_AVATAR_URL
auto_strip_attributes :full_name, :initials, nullify: false
validates :full_name,
@ -35,10 +38,10 @@ class User < ApplicationRecord
presence: true,
length: { maximum: Constants::EMAIL_MAX_LENGTH }
validates_attachment :avatar,
:content_type => { :content_type => ["image/jpeg", "image/png"] },
size: { less_than: Constants::AVATAR_MAX_SIZE_MB.megabyte,
message: I18n.t('client_api.user.avatar_too_big') }
# validates_attachment :avatar,
# :content_type => { :content_type => ["image/jpeg", "image/png"] },
# size: { less_than: Constants::AVATAR_MAX_SIZE_MB.megabyte,
# message: I18n.t('client_api.user.avatar_too_big') }
validate :time_zone_check
store_accessor :settings, :time_zone, :notifications_settings
@ -226,11 +229,6 @@ class User < ApplicationRecord
foreign_key: :resource_owner_id,
dependent: :delete_all
# If other errors besides parameter "avatar" exist,
# they will propagate to "avatar" also, so remove them
# and put all other (more specific ones) in it
after_validation :filter_paperclip_errors
before_destroy :destroy_notifications
def name
@ -249,6 +247,26 @@ class User < ApplicationRecord
@avatar_remote_url = url_value
end
def avatar_variant(style)
format = case style.to_sym
when :medium
Constants::MEDIUM_PIC_FORMAT
when :thumb
Constants::THUMB_PIC_FORMAT
when :icon
Constants::ICON_PIC_FORMAT
when :icon_small
Constants::ICON_SMALL_PIC_FORMAT
else
Constants::ICON_SMALL_PIC_FORMAT
end
avatar.variant(resize: format)
end
def avatar_url(style)
Rails.application.routes.url_helpers.url_for(avatar_variant(style))
end
def date_format
settings[:date_format] || Constants::DEFAULT_DATE_FORMAT
end
@ -311,20 +329,6 @@ class User < ApplicationRecord
self.avatar_file_size = size.to_i
end
def filter_paperclip_errors
if errors.key? :avatar
errors.delete(:avatar)
messages = []
errors.each do |attribute|
errors.full_messages_for(attribute).each do |message|
messages << message.split(' ').drop(1).join(' ')
end
end
errors.clear
errors.add(:avatar, messages.join(','))
end
end
# Whether user is active (= confirmed) or not
def active?
confirmed_at.present?

86
app/models/zip_export.rb
View file

@ -22,71 +22,51 @@ class ZipExport < ApplicationRecord
belongs_to :user, optional: true
# Override path only for S3
if ENV['PAPERCLIP_STORAGE'] == 's3'
s3_path =
if ENV['S3_SUBFOLDER']
"/#{ENV['S3_SUBFOLDER']}/zip_exports/:attachment/"\
":id_partition/:hash/:style/:filename"
else
'/zip_exports/:attachment/:id_partition/:hash/:style/:filename'
end
# if ENV['PAPERCLIP_STORAGE'] == 's3'
# s3_path =
# if ENV['S3_SUBFOLDER']
# "/#{ENV['S3_SUBFOLDER']}/zip_exports/:attachment/"\
# ":id_partition/:hash/:style/:filename"
# else
# '/zip_exports/:attachment/:id_partition/:hash/:style/:filename'
# end
#
# has_attached_file :zip_file, path: s3_path
# else
# has_attached_file :zip_file
# end
has_attached_file :zip_file, path: s3_path
else
has_attached_file :zip_file
end
has_one_attached :zip_file
validates_attachment :zip_file,
content_type: { content_type: 'application/zip' }
# validates_attachment :zip_file,
# content_type: { content_type: 'application/zip' }
after_create :self_destruct
# When using S3 file upload, we can limit file accessibility with url signing
def presigned_url(style = :original,
download: false,
timeout: Constants::URL_SHORT_EXPIRE_TIME)
if stored_on_s3?
if download
download_arg = 'attachment; filename=' + URI.escape(zip_file_file_name)
else
download_arg = nil
end
signer = Aws::S3::Presigner.new(client: S3_BUCKET.client)
signer.presigned_url(:get_object,
bucket: S3_BUCKET.name,
key: zip_file.path(style)[1..-1],
expires_in: timeout,
response_content_disposition: download_arg)
end
end
def stored_on_s3?
zip_file.options[:storage].to_sym == :s3
end
def self.delete_expired_export(id)
export = find_by_id(id)
export.destroy if export
export&.destroy
end
def zip_file_name
return '' unless file.attached?
zip_file.blob&.filename&.to_s
end
def generate_exportable_zip(user, data, type, options = {})
I18n.backend.date_format =
user.settings[:date_format] || Constants::DEFAULT_DATE_FORMAT
zip_input_dir = FileUtils.mkdir_p(
File.join(Rails.root, "tmp/temp_zip_#{Time.now.to_i}")
).first
zip_dir = FileUtils.mkdir_p(File.join(Rails.root, 'tmp/zip-ready')).first
zip_file = File.new(
File.join(zip_dir, "export_#{Time.now.strftime('%F %H-%M-%S_UTC')}.zip"),
'w+'
)
I18n.backend.date_format = user.settings[:date_format] || Constants::DEFAULT_DATE_FORMAT
zip_input_dir = FileUtils.mkdir_p(File.join(Rails.root, "tmp/temp_zip_#{Time.now.to_i}")).first
tmp_zip_dir = FileUtils.mkdir_p(File.join(Rails.root, 'tmp/zip-ready')).first
tmp_zip_name = "export_#{Time.now.strftime('%F %H-%M-%S_UTC')}.zip"
tmp_zip_file = File.new(File.join(tmp_zip_dir, tmp_zip_name), 'w+')
fill_content(zip_input_dir, data, type, options)
zip!(zip_input_dir, zip_file)
self.zip_file = File.open(zip_file)
zip!(zip_input_dir, tmp_zip_file)
zip_file.attach(io: File.open(tmp_zip_file), filename: tmp_zip_name)
generate_notification(user) if save
ensure
FileUtils.rm_rf([zip_input_dir, zip_file], secure: true)
FileUtils.rm_rf([zip_input_dir, tmp_zip_file], secure: true)
end
handle_asynchronously :generate_exportable_zip
@ -122,7 +102,7 @@ class ZipExport < ApplicationRecord
.routes
.url_helpers
.zip_exports_download_path(self)}'>" \
"#{zip_file_file_name}</a>"
"#{zip_file_name}</a>"
)
UserNotification.create(notification: notification, user: user)
end

8
app/serializers/api/v1/repository_asset_value_serializer.rb
View file

@ -10,20 +10,18 @@ module Api
end
def file_name
object.asset&.file_file_name
object.asset&.file_name
end
def file_size
object.asset&.file_file_size
object.asset&.file_size
end
def url
if !object.asset&.file&.exists?
nil
elsif object.asset&.file&.is_stored_on_s3?
object.asset.presigned_url(download: true)
else
object.asset.file.url
rails_blob_path(object.asset.file, disposition: 'attachment')
end
end
end

8
app/serializers/api/v1/result_asset_serializer.rb
View file

@ -11,20 +11,18 @@ module Api
end
def file_name
object.asset&.file_file_name
object.asset&.file_name
end
def file_size
object.asset&.file_file_size
object.asset&.file_size
end
def url
if !object.asset&.file&.exists?
nil
elsif object.asset&.file&.is_stored_on_s3?
object.asset.presigned_url(download: true)
else
object.asset.file.url
rails_blob_path(object.asset.file, disposition: 'attachment')
end
end
end

4
app/services/experiments/generate_workflow_image_service.rb
View file

@ -76,9 +76,9 @@ module Experiments
def save_file
file = Tempfile.open(%w(wimg .png), Rails.root.join('tmp'))
@graph.output(png: file.path)
@exp.workflowimg = file
@exp.workflowimg.attach(io: file, filename: File.basename(file.path))
file.close
@exp.save
file.unlink
@exp.touch(:workflowimg_updated_at)
end
end

2
app/services/experiments/move_to_project_service.rb
View file

@ -29,8 +29,6 @@ module Experiments
end
raise ActiveRecord::Rollback unless @exp.save
# To pass the ExperimentsController#updated_img check
@exp.update(workflowimg_updated_at: @exp.updated_at)
end
@errors.merge!(@exp.errors.to_hash) unless @exp.valid?

27
app/services/repository_actions/duplicate_cell.rb
View file

@ -43,7 +43,7 @@ module RepositoryActions
def duplicate_repository_asset_value
old_value = @cell.value
new_asset = create_new_asset(old_value.asset)
new_asset = old_value.asset.duplicate
RepositoryAssetValue.create(
old_value.attributes.merge(
id: nil, asset: new_asset, created_by: @user, last_modified_by: @user,
@ -67,30 +67,5 @@ module RepositoryActions
)
)
end
# reuses the same code we have in copy protocols action
def create_new_asset(old_asset)
new_asset = Asset.new_empty(
old_asset.file_file_name,
old_asset.file_file_size
)
new_asset.created_by = old_asset.created_by
new_asset.team = @team
new_asset.last_modified_by = @user
new_asset.file_processing = true if old_asset.image?
new_asset.file = old_asset.file
new_asset.save
return unless new_asset.valid?
if new_asset.image?
new_asset.file.reprocess!(:large)
new_asset.file.reprocess!(:medium)
end
new_asset.post_process_file(new_asset.team)
new_asset
end
end
end

47
app/services/repository_datatable_service.rb
View file

@ -163,4 +163,51 @@ class RepositoryDatatableService
def sort_null_direction(val)
val == 'ASC' ? 'LAST' : 'FIRST'
end
def filter_by_asset_value(records, id, dir)
records.joins(
"LEFT OUTER JOIN (SELECT repository_cells.repository_row_id,
active_storage_blobs.filename AS value
FROM repository_cells
INNER JOIN repository_asset_values
ON repository_asset_values.id = repository_cells.value_id
INNER JOIN assets
ON repository_asset_values.asset_id = assets.id
INNER JOIN active_storage_attachments
ON active_storage_attachments.record_id = assets.id
AND active_storage_attachments.record_type = 'Asset'
AND active_storage_attachments.name = 'file'
INNER JOIN active_storage_blobs
ON active_storage_blobs.id = active_storage_attachments.blob_id
WHERE repository_cells.repository_column_id = #{id}) AS values
ON values.repository_row_id = repository_rows.id"
).order("values.value #{dir}")
end
def filter_by_text_value(records, id, dir)
records.joins(
"LEFT OUTER JOIN (SELECT repository_cells.repository_row_id,
repository_text_values.data AS value
FROM repository_cells
INNER JOIN repository_text_values
ON repository_text_values.id = repository_cells.value_id
WHERE repository_cells.repository_column_id = #{id}) AS values
ON values.repository_row_id = repository_rows.id"
).order("values.value #{dir}")
end
def filter_by_list_value(records, id, dir)
records.joins(
"LEFT OUTER JOIN (SELECT repository_cells.repository_row_id,
repository_list_items.data AS value
FROM repository_cells
INNER JOIN repository_list_values
ON repository_list_values.id = repository_cells.value_id
INNER JOIN repository_list_items
ON repository_list_values.repository_list_item_id =
repository_list_items.id
WHERE repository_cells.repository_column_id = #{id}) AS values
ON values.repository_row_id = repository_rows.id"
).order("values.value #{dir}")
end
end

5
app/services/spreadsheet_parser.rb
View file

@ -4,11 +4,6 @@ class SpreadsheetParser
filename = file.original_filename
file_path = file.path
if file.class == Paperclip::Attachment && file.is_stored_on_s3?
fa = file.fetch
file_path = fa.path
end
case File.extname(filename)
when '.csv'
Roo::CSV.new(file_path, extension: :csv)

6
app/services/team_importer.rb
View file

@ -340,8 +340,8 @@ class TeamImporter
tiny_mce_asset.object_id = mappings[tiny_mce_asset.object_id]
end
tiny_mce_asset.team = team
tiny_mce_asset.image = tiny_mce_file
tiny_mce_asset.save!
tiny_mce_asset.image.attach(io: tiny_mce_file, filename: tiny_mce_file.basename)
@mce_asset_counter += 1
if tiny_mce_asset.object_id.present?
object = tiny_mce_asset.object
@ -794,7 +794,7 @@ class TeamImporter
def create_asset(asset_json, team, user_id = nil)
asset = Asset.new(asset_json)
File.open(
"#{@import_dir}/assets/#{asset.id}/#{asset.file_file_name}"
"#{@import_dir}/assets/#{asset.id}/#{asset.file_name}"
) do |file|
orig_asset_id = asset.id
asset.id = nil
@ -802,9 +802,9 @@ class TeamImporter
asset.last_modified_by_id =
user_id || find_user(asset.last_modified_by_id)
asset.team = team
asset.file = file
asset.in_template = true if @is_template
asset.save!
asset.file.attach(io: file, filename: file.basename)
asset.post_process_file(team)
@asset_mappings[orig_asset_id] = asset.id
@asset_counter += 1

13
app/utilities/protocols_exporter.rb
View file

@ -51,12 +51,11 @@ module ProtocolsExporter
next unless img
img_guid = get_guid(img.id)
asset_file_name = "rte-#{img_guid}" \
"#{File.extname(img.image_file_name)}"
asset_file_name = "rte-#{img_guid}#{File.extname(img.file_name)}"
asset_xml = "<tinyMceAsset tokenId=\"#{match[1]}\" id=\"#{img.id}\" guid=\"#{img_guid}\" " \
"fileRef=\"#{asset_file_name}\">\n"
asset_xml << "<fileName>#{img.image_file_name}</fileName>\n"
asset_xml << "<fileType>#{img.image_content_type}</fileType>\n"
asset_xml << "<fileName>#{img.file_name}</fileName>\n"
asset_xml << "<fileType>#{img.content_type}</fileType>\n"
asset_xml << "</tinyMceAsset>\n"
tiny_assets_xml << asset_xml
end
@ -100,11 +99,11 @@ module ProtocolsExporter
step.assets.order(:id).each do |asset|
asset_guid = get_guid(asset.id)
asset_file_name = "#{asset_guid}" \
"#{File.extname(asset.file_file_name)}"
"#{File.extname(asset.file_name)}"
asset_xml = "<asset id=\"#{asset.id}\" guid=\"#{asset_guid}\" " \
"fileRef=\"#{asset_file_name}\">\n"
asset_xml << "<fileName>#{asset.file_file_name}</fileName>\n"
asset_xml << "<fileType>#{asset.file_content_type}</fileType>\n"
asset_xml << "<fileName>#{asset.file_name}</fileName>\n"
asset_xml << "<fileType>#{asset.content_type}</fileType>\n"
asset_xml << "</asset>\n"
step_xml << asset_xml
end

13
app/utilities/protocols_importer.rb
View file

@ -111,9 +111,7 @@ module ProtocolsImporter
)
# Decode the file bytes
asset.file = StringIO.new(Base64.decode64(asset_json['bytes']))
asset.file_file_name = asset_json['fileName']
asset.file_content_type = asset_json['fileType']
asset.file.attach(io: StringIO.new(Base64.decode64(asset_json['bytes'])), filename: asset_json['fileName'])
asset.save!
asset_ids << asset.id
@ -152,12 +150,11 @@ module ProtocolsImporter
team_id: team.id,
saved: true
)
# Decode the file bytes
tiny_mce_img.image = StringIO.new(
Base64.decode64(tiny_mce_img_json['bytes'])
)
tiny_mce_img.image_content_type = tiny_mce_img_json['fileType']
tiny_mce_img.save!
# Decode the file bytes
tiny_mce_img.image.attach(io: StringIO.new(Base64.decode64(tiny_mce_img_json['bytes'])),
filename: tiny_mce_img_json['fileName'])
if description.gsub!("data-mce-token=\"#{tiny_mce_img_json['tokenId']}\"",
"data-mce-token=\"#{Base62.encode(tiny_mce_img.id)}\"")
else

4
app/utilities/wopi_util.rb
View file

@ -83,7 +83,7 @@ module WopiUtil
default_step_items =
{ step: @asset.step.id,
step_position: { id: @asset.step.id, value_for: 'position_plus_one' },
asset_name: { id: @asset.id, value_for: 'file_file_name' },
asset_name: { id: @asset.id, value_for: 'file_name' },
action: action }
if @protocol.in_module?
project = @protocol.my_module.experiment.project
@ -113,7 +113,7 @@ module WopiUtil
project: @my_module.experiment.project,
message_items: {
result: @asset.result.id,
asset_name: { id: @asset.id, value_for: 'file_file_name' },
asset_name: { id: @asset.id, value_for: 'file_name' },
action: action
})
end

2
app/views/assets/edit.erb
View file

@ -6,7 +6,7 @@
<!-- Enable IE Standards mode -->
<meta http-equiv="x-ua-compatible" content="ie=edge">
<title><%= t('assets.head_title.edit', file_name: @asset.file_file_name) %></title>
<title><%= t('assets.head_title.edit', file_name: @asset.file_name) %></title>
<meta name="description" content="">
<meta name="viewport"
content="width=device-width, initial-scale=1, maximum-scale=1, minimum-scale=1, user-scalable=no">

2
app/views/assets/view.erb
View file

@ -6,7 +6,7 @@
<!-- Enable IE Standards mode -->
<meta http-equiv="x-ua-compatible" content="ie=edge">
<title><%= t('assets.head_title.view', file_name: @asset.file_file_name) %></title>
<title><%= t('assets.head_title.view', file_name: @asset.file_name) %></title>
<meta name="description" content="">
<meta name="viewport"
content="width=device-width, initial-scale=1, maximum-scale=1, minimum-scale=1, user-scalable=no">

5
app/views/projects/show/_workflow_img.html.erb
View file

@ -1,4 +1 @@
<%= image_tag(@experiment.workflowimg.expiring_url(
Constants::URL_SHORT_EXPIRE_TIME
),
class: 'img-responsive center-block') %>
<%= image_tag url_for(@experiment.workflowimg), class: 'img-responsive center-block' %>

2
app/views/reports/elements/_my_module_result_asset_element.html.erb
View file

@ -24,7 +24,7 @@
</a>
<% else %>
<em><%=t "projects.reports.elements.result_asset.file_name",
file: truncate(asset.file_file_name,
file: truncate(asset.file_name,
length: Constants::FILENAME_TRUNCATION_LENGTH) %></em>
<% end %>
</div>

4
app/views/reports/elements/_step_asset_element.html.erb
View file

@ -2,7 +2,7 @@
<% is_image = asset.image? %>
<% timestamp = asset.created_at %>
<% icon_class = 'fas ' + (is_image ? 'fa-image' : 'fa-file') %>
<div class="report-element report-step-attachment-element report-step-asset-element" data-ts="<%= timestamp.to_i %>" data-type="step_asset" data-id='{ "asset_id": <%= asset.id %> }' data-scroll-id="<%= asset.id %>" data-name="<%=t "projects.reports.elements.step_asset.sidebar_name", file: asset.file_file_name %>" data-icon-class="<%= icon_class %>">
<div class="report-element report-step-attachment-element report-step-asset-element" data-ts="<%= timestamp.to_i %>" data-type="step_asset" data-id='{ "asset_id": <%= asset.id %> }' data-scroll-id="<%= asset.id %>" data-name="<%=t "projects.reports.elements.step_asset.sidebar_name", file: asset.file_name %>" data-icon-class="<%= icon_class %>">
<div class="report-element-header">
<div class="row">
<div class="pull-left attachment-icon">
@ -16,7 +16,7 @@
</a>
<% else %>
<em><%=t 'projects.reports.elements.step_asset.file_name',
file: truncate(asset.file_file_name,
file: truncate(asset.file_name,
length: Constants::FILENAME_TRUNCATION_LENGTH) %></em>
<% end %>
</div>

2
app/views/result_assets/_edit.html.erb
View file

@ -5,7 +5,7 @@
<span><strong><%=t "result_assets.edit.uploaded_asset" %></strong></span>
<p style="margin: 10px;">
<%= file_extension_icon(ff.object) %>
<%= ff.object.file_file_name %>
<%= ff.object.file_name %>
</p>
<%= ff.file_field :file %>
<% end %>

2
app/views/search/results/partials/_asset_text.html.erb
View file

@ -1,6 +1,6 @@
<% query ||= nil %>
<% asset_read_allowed = false %>
<% text = query.present? ? highlight(asset.file_file_name, query.strip.split(/\s+/)) : asset.file_file_name %>
<% text = query.present? ? highlight(asset.file_name, query.strip.split(/\s+/)) : asset.file_name %>
<% if asset.step %>
<% protocol = asset.step.protocol %>

16
app/views/shared/_asset_link.html.erb
View file

@ -2,19 +2,15 @@
class: 'file-preview-link',
id: "modal_link#{asset.id}",
data: { no_turbolink: true, id: true, status: 'asset-present', 'preview-url': asset_file_preview_path(asset) } do %>
<% if asset.image? && display_image_tag %>
<% if display_image_tag && asset.previewable? %>
<%= image_tag asset.medium_preview %>
<% end %>
<% if display_image_tag %>
<p>
<%= truncate(asset.file_file_name,
length: Constants::FILENAME_TRUNCATION_LENGTH) %>
<%= truncate(asset.file_name, length: Constants::FILENAME_TRUNCATION_LENGTH) %>
</p>
<% else %>
<span>
<%= truncate(asset.file_file_name,
length: Constants::FILENAME_TRUNCATION_LENGTH) %>
</span>
<% else %>
<span>
<%= truncate(asset.file_name, length: Constants::FILENAME_TRUNCATION_LENGTH) %>
</span>
<% end %>
<% end %>

2
app/views/shared/_file_preview_icon.html.erb
View file

@ -1,5 +1,5 @@
<div>
<% if asset.file.previewable_document? %>
<% if asset.previewable? %>
<%= image_tag(asset.large_preview) %>
<% else %>
<i class="fas fa-10x <%= file_fa_icon_class(asset) %>"></i>

2
app/views/steps/attachments/_placeholder.html.erb
View file

@ -22,5 +22,5 @@
<% end %>
<% end %>
</div>
<% end %>
<% end %>
</div>

1
app/views/users/registrations/edit.html.erb
View file

@ -239,4 +239,3 @@
<%= stylesheet_pack_tag 'custom/croppie_styles' %>
<%= javascript_include_tag("canvas-to-blob.min") %>
<%= javascript_include_tag "users/registrations/edit" %>

4
config/environments/production.rb
View file

@ -48,7 +48,7 @@ Rails.application.configure do
# Compress JavaScripts and CSS.
config.assets.js_compressor = :uglifier
config.assets.js_compressor = Uglifier.new(harmony: true)
# config.assets.css_compressor = :sass
# Do not fallback to assets pipeline if a precompiled asset is missed.
@ -71,6 +71,8 @@ Rails.application.configure do
# Force all access to the app over SSL, use Strict-Transport-Security, and use secure cookies.
config.force_ssl = ENV['RAILS_FORCE_SSL'].present?
config.ssl_options = { redirect: { exclude: ->(request) { request.path =~ %r{api\/health} } } }
# Use the lowest log level to ensure availability of diagnostic information
# when problems arise.
config.log_level = :debug

1
config/initializers/assets.rb
View file

@ -76,7 +76,6 @@ Rails.application.config.assets.precompile += %w(canvas-to-blob.min.js)
Rails.application.config.assets.precompile += %w(Sortable.min.js)
Rails.application.config.assets.precompile += %w(reports_pdf.css)
Rails.application.config.assets.precompile += %w(jszip.min.js)
Rails.application.config.assets.precompile += %w(assets.js)
Rails.application.config.assets.precompile += %w(comments.js)
Rails.application.config.assets.precompile += %w(projects/show.js)
Rails.application.config.assets.precompile += %w(notifications.js)

6
config/initializers/constants.rb
View file

@ -93,9 +93,9 @@ class Constants
# Picture size formats
LARGE_PIC_FORMAT = '800x600>'.freeze
MEDIUM_PIC_FORMAT = '300x300>'.freeze
THUMB_PIC_FORMAT = '100x100#'.freeze
ICON_PIC_FORMAT = '40x40#'.freeze
ICON_SMALL_PIC_FORMAT = '30x30#'.freeze
THUMB_PIC_FORMAT = '100x100'.freeze
ICON_PIC_FORMAT = '40x40'.freeze
ICON_SMALL_PIC_FORMAT = '30x30'.freeze
# Hands-on-table number of starting columns and rows
HANDSONTABLE_INIT_COLS_CNT = 5

4
config/initializers/extends.rb
View file

@ -55,12 +55,12 @@ class Extends
# are only supported
REPOSITORY_EXTRA_SEARCH_ATTR = ['repository_text_values.data',
'repository_list_items.data',
'assets.file_file_name']
'active_storage_blobs.filename']
# Array of includes used in search query for repository rows
REPOSITORY_SEARCH_INCLUDES = [:repository_text_value,
repository_list_value: :repository_list_item,
repository_asset_value: :asset]
repository_asset_value: { asset: { file_attachment: :blob } }]
# List of implemented core API versions
API_VERSIONS = ['v1']

2
config/initializers/filter_parameter_logging.rb
View file

@ -1,4 +1,4 @@
# Be sure to restart your server when you modify this file.
# Configure sensitive parameters which will be filtered from the log file.
Rails.application.config.filter_parameters += %i(password image)
Rails.application.config.filter_parameters += [:password, :image, /^avatar$/]

1
config/locales/en.yml
View file

@ -1265,7 +1265,6 @@ en:
scinote_columns_html: "<em>SciNote</em> columns:"
file_columns: "Imported columns:"
example_value: "Imported file content:"
import_samples: "Import samples"
do_not_include_column: "Do not include this column"
errors:
invalid_file: "The file you provided is invalid. Make sure the file is encoded using %{encoding}."

6
config/routes.rb
View file

@ -192,8 +192,6 @@ Rails.application.routes.draw do
# end
member do
post 'parse_sheet', defaults: { format: 'json' }
# post 'import_samples'
# post 'export_samples'
post 'export_repository', to: 'repositories#export_repository'
post 'export_projects'
get 'export_projects_modal'
@ -582,7 +580,10 @@ Rails.application.routes.draw do
# We cannot use 'resources :assets' because assets is a reserved route
# in Rails (assets pipeline) and causes funky behavior
<<<<<<< HEAD
get 'files/:id/present', to: 'assets#file_present', as: 'file_present_asset'
=======
>>>>>>> activestorage_migration
get 'files/:id/preview',
to: 'assets#file_preview',
as: 'asset_file_preview'
@ -599,7 +600,6 @@ Rails.application.routes.draw do
devise_scope :user do
get 'avatar/:id/:style' => 'users/registrations#avatar', as: 'avatar'
post 'avatar_signature' => 'users/registrations#signature'
get 'users/auth_token_sign_in' => 'users/sessions#auth_token_create'
get 'users/sign_up_provider' => 'users/registrations#new_with_provider'
post 'users/complete_sign_up_provider' =>

4
db/migrate/20190613134100_convert_to_active_storage.rb
View file

@ -99,8 +99,8 @@ class ConvertToActiveStorage < ActiveRecord::Migration[5.2]
if ENV['PAPERCLIP_STORAGE'] == 's3'
interpolate(':class/:attachment/:id_partition/:hash/original/:filename', instance, attachment)
else
key = SecureRandom.uuid
File.join('storage', key.first(2), key.first(4).last(2))
instance.class.generate_unique_secure_token
# File.join('storage', key.first(2), key.first(4).last(2))
end
end

2
docker-compose.production.yml
View file

@ -37,7 +37,9 @@ services:
- RAILS_ENV=production
volumes:
- scinote_production_files:/usr/src/app/public/system
- scinote_production_storage:/usr/src/app/storage
volumes:
scinote_production_postgres:
scinote_production_files:
scinote_production_storage:

2
docker-compose.yml
View file

@ -29,6 +29,7 @@ services:
- .:/usr/src/app
- scinote_development_bundler:/usr/local/bundle/
- scinote_development_files:/usr/src/app/public/system
- scinote_development_storage:/usr/src/app/storage
webpack:
build:
@ -54,3 +55,4 @@ volumes:
scinote_development_postgres:
scinote_development_bundler:
scinote_development_files:
scinote_development_storage:

1
spec/services/templates_service_spec.rb
View file

@ -88,7 +88,6 @@ describe TemplatesService do
.to eq(tmpl_step.step_comments.size)
end
end
Asset.all.each(&:paperclip_delete)
FileUtils.remove_dir(tmplts_dir)
end
end