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Merge branch 'master' into features/global-activities

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Miha Mencin 2019-03-25 14:35:24 +01:00 committed by GitHub
parent fd6e622b95 9fff93ab0e
commit 4a87216a3d
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73 changed files with 6028 additions and 3557 deletions
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41
.babelrc
View file

@ -1,35 +1,18 @@
{
"presets": [
[
"env",
{
"modules": false,
"targets": {
"browsers": ["last 2 versions", "ie 10"],
"uglify": true
},
"useBuiltIns": true
}
],
"react",
"es2015",
"flow"
["env", {
"modules": false,
"targets": {
"browsers": "> 1%",
"uglify": true
},
"useBuiltIns": true
}]
],
"plugins": [
"transform-flow-strip-types",
"transform-object-rest-spread",
"syntax-dynamic-import",
"transform-react-jsx-source",
[
"transform-class-properties",
{
"spec": true
}
]
],
"env": {
"test": {
"plugins": ["transform-es2015-modules-commonjs"]
}
}
"transform-object-rest-spread",
["transform-class-properties", { "spec": true }]
]
}

5
.postcssrc.yml
View file

@ -1,4 +1,3 @@
plugins:
postcss-smart-import: {}
precss: {}
autoprefixer: {}
postcss-import: {}
postcss-cssnext: {}

2
.rubocop.yml
View file

@ -363,7 +363,7 @@ Metrics/CyclomaticComplexity:
Enabled: false
Metrics/LineLength:
Max: 80
Max: 120
AllowHeredoc: true
AllowURI: true
URISchemes:

5
Gemfile
View file

@ -4,6 +4,8 @@ source 'http://rubygems.org'
ruby '2.4.5'
gem 'webpacker', '~> 3.5'
gem 'bootstrap-sass', '~> 3.3.7'
gem 'bootstrap_form'
gem 'devise', '~> 4.3.0'
@ -11,12 +13,11 @@ gem 'devise_invitable'
gem 'figaro'
gem 'pg', '~> 0.18'
gem 'pg_search' # PostgreSQL full text search
gem 'rails', '5.1.6'
gem 'rails', '~> 5.1.6.2'
gem 'recaptcha', require: 'recaptcha/rails'
gem 'sanitize', '~> 4.4'
gem 'sass-rails', '~> 5.0.6'
gem 'simple_token_authentication', '~> 1.15.1' # Token authentication for Devise
gem 'webpacker', '~> 2.0'
gem 'yomu'
# Gems for OAuth2 subsystem

78
Gemfile.lock
View file

@ -51,25 +51,25 @@ GIT
GEM
remote: http://rubygems.org/
specs:
actioncable (5.1.6)
actionpack (= 5.1.6)
actioncable (5.1.6.2)
actionpack (= 5.1.6.2)
nio4r (~> 2.0)
websocket-driver (~> 0.6.1)
actionmailer (5.1.6)
actionpack (= 5.1.6)
actionview (= 5.1.6)
activejob (= 5.1.6)
actionmailer (5.1.6.2)
actionpack (= 5.1.6.2)
actionview (= 5.1.6.2)
activejob (= 5.1.6.2)
mail (~> 2.5, >= 2.5.4)
rails-dom-testing (~> 2.0)
actionpack (5.1.6)
actionview (= 5.1.6)
activesupport (= 5.1.6)
actionpack (5.1.6.2)
actionview (= 5.1.6.2)
activesupport (= 5.1.6.2)
rack (~> 2.0)
rack-test (>= 0.6.3)
rails-dom-testing (~> 2.0)
rails-html-sanitizer (~> 1.0, >= 1.0.2)
actionview (5.1.6)
activesupport (= 5.1.6)
actionview (5.1.6.2)
activesupport (= 5.1.6.2)
builder (~> 3.1)
erubi (~> 1.4)
rails-dom-testing (~> 2.0)
@ -79,18 +79,18 @@ GEM
activemodel (>= 4.1, < 6)
case_transform (>= 0.2)
jsonapi-renderer (>= 0.1.1.beta1, < 0.3)
activejob (5.1.6)
activesupport (= 5.1.6)
activejob (5.1.6.2)
activesupport (= 5.1.6.2)
globalid (>= 0.3.6)
activemodel (5.1.6)
activesupport (= 5.1.6)
activerecord (5.1.6)
activemodel (= 5.1.6)
activesupport (= 5.1.6)
activemodel (5.1.6.2)
activesupport (= 5.1.6.2)
activerecord (5.1.6.2)
activemodel (= 5.1.6.2)
activesupport (= 5.1.6.2)
arel (~> 8.0)
activerecord-import (0.23.0)
activerecord (>= 3.2)
activesupport (5.1.6)
activesupport (5.1.6.2)
concurrent-ruby (~> 1.0, >= 1.0.2)
i18n (>= 0.7, < 2)
minitest (~> 5.1)
@ -300,7 +300,7 @@ GEM
logging (2.0.0)
little-plugger (~> 1.1)
multi_json (~> 1.10)
loofah (2.2.2)
loofah (2.2.3)
crass (~> 1.0.2)
nokogiri (>= 1.5.9)
mail (2.7.0)
@ -381,19 +381,21 @@ GEM
rack (2.0.6)
rack-attack (5.4.1)
rack (>= 1.0, < 3)
rack-proxy (0.6.5)
rack
rack-test (1.1.0)
rack (>= 1.0, < 3)
rails (5.1.6)
actioncable (= 5.1.6)
actionmailer (= 5.1.6)
actionpack (= 5.1.6)
actionview (= 5.1.6)
activejob (= 5.1.6)
activemodel (= 5.1.6)
activerecord (= 5.1.6)
activesupport (= 5.1.6)
rails (5.1.6.2)
actioncable (= 5.1.6.2)
actionmailer (= 5.1.6.2)
actionpack (= 5.1.6.2)
actionview (= 5.1.6.2)
activejob (= 5.1.6.2)
activemodel (= 5.1.6.2)
activerecord (= 5.1.6.2)
activesupport (= 5.1.6.2)
bundler (>= 1.3.0)
railties (= 5.1.6)
railties (= 5.1.6.2)
sprockets-rails (>= 2.0.0)
rails-controller-testing (1.0.2)
actionpack (~> 5.x, >= 5.0.1)
@ -411,14 +413,14 @@ GEM
rails (> 3.1)
rails_serve_static_assets (0.0.5)
rails_stdout_logging (0.0.5)
railties (5.1.6)
actionpack (= 5.1.6)
activesupport (= 5.1.6)
railties (5.1.6.2)
actionpack (= 5.1.6.2)
activesupport (= 5.1.6.2)
method_source
rake (>= 0.8.7)
thor (>= 0.18.1, < 2.0)
rainbow (3.0.0)
rake (12.3.1)
rake (12.3.2)
rb-fsevent (0.10.2)
rb-inotify (0.9.10)
ffi (>= 0.5.0, < 2)
@ -544,9 +546,9 @@ GEM
addressable (>= 2.3.6)
crack (>= 0.3.2)
hashdiff
webpacker (2.0)
webpacker (3.5.5)
activesupport (>= 4.2)
multi_json (~> 1.2)
rack-proxy (>= 0.6.1)
railties (>= 4.2)
websocket-driver (0.6.5)
websocket-extensions (>= 0.1.0)
@ -631,7 +633,7 @@ DEPENDENCIES
pry-rails
puma
rack-attack
rails (= 5.1.6)
rails (~> 5.1.6.2)
rails-controller-testing
rails_12factor
rails_autolink (~> 1.1, >= 1.1.6)
@ -662,7 +664,7 @@ DEPENDENCIES
uglifier (>= 1.3.0)
underscore-rails
webmock
webpacker (~> 2.0)
webpacker (~> 3.5)
whacamole
wicked_pdf (~> 1.1.0)
wkhtmltopdf-heroku

2
VERSION
View file

@ -1 +1 @@
1.15.3
1.15.8

36
app/assets/javascripts/experiments/dropdown_actions.js
View file

@ -119,27 +119,25 @@
});
}
$(document).on('turbolinks:load', function() {
// Bind modal to new-experiment action
initializeModal($('#new-experiment'), '#new-experiment-modal');
// Bind modal to new-experiment action
initializeModal($('#new-experiment'), '#new-experiment-modal');
// Bind modal to big-plus new experiment actions
initializeModal('.big-plus', '#new-experiment-modal');
// Bind modal to big-plus new experiment actions
initializeModal('.big-plus', '#new-experiment-modal');
// Bind modal to new-exp-title action
initializeModal('.new-exp-title', '#new-experiment-modal');
// Bind modal to new-exp-title action
initializeModal('.new-exp-title', '#new-experiment-modal');
// Bind modals to all clone-experiment actions
$.each($('.clone-experiment'), function() {
var id = $(this).closest('.experiment-panel').data('id');
initializeModal($(this), '#clone-experiment-modal-' + id);
});
// Bind modal to all actions listed on dropdown accesible from experiment
// panel
initializeDropdownActions();
// init
initEditNoDescription();
// Bind modals to all clone-experiment actions
$.each($('.clone-experiment'), function() {
var id = $(this).closest('.experiment-panel').data('id');
initializeModal($(this), '#clone-experiment-modal-' + id);
});
// Bind modal to all actions listed on dropdown accesible from experiment
// panel
initializeDropdownActions();
// init
initEditNoDescription();
})();

2
app/assets/javascripts/my_modules/protocols.js.erb
View file

@ -142,11 +142,13 @@ function initCopyToRepository() {
});
modal.modal("show");
submitBtn[0].disabled=false
})
.on("ajax:error", function() {} );
submitBtn.on("click", function() {
// Submit the embedded form
submitBtn[0].disabled=true
modalBody.find("form").submit();
});

413
app/assets/javascripts/sitewide/file_preview.js Normal file
View file

@ -0,0 +1,413 @@
/* eslint no-underscore-dangle: ["error", { "allowAfterThis": true }]*/
/* eslint no-use-before-define: ["error", { "functions": false }]*/
/* global fabric tui animateSpinner setupAssetsLoading I18n*/
//= require assets
(function(global) {
'use strict';
global.initPreviewModal = function initPreviewModal() {
var name;
var url;
var downloadUrl;
$('.file-preview-link').off('click');
$('.file-preview-link').click(function(e) {
e.preventDefault();
name = $(this).find('p').text();
url = $(this).data('preview-url');
downloadUrl = $(this).attr('href');
openPreviewModal(name, url, downloadUrl);
});
};
// Adding rotation icon
function updateFabricControls() {
fabric.Object.prototype.drawBorders = function(ctx, styleOverride = {}) {
var wh = this._calculateCurrentDimensions();
var strokeWidth = 1 / this.borderScaleFactor;
var width = wh.x + strokeWidth;
var height = wh.y + strokeWidth;
var drawRotatingPoint = typeof styleOverride.hasRotatingPoint !== 'undefined'
? styleOverride.hasRotatingPoint : this.hasRotatingPoint;
var hasControls = typeof styleOverride.hasControls !== 'undefined'
? styleOverride.hasControls : this.hasControls;
var rotatingPointOffset = typeof styleOverride.rotatingPointOffset !== 'undefined'
? styleOverride.rotatingPointOffset : this.rotatingPointOffset;
var rotateHeight = -height / 2;
ctx.save();
ctx.strokeStyle = styleOverride.borderColor || this.borderColor;
this._setLineDash(ctx, styleOverride.borderDashArray || this.borderDashArray, null);
ctx.strokeRect(
-width / 2,
-height / 2,
width,
height
);
if (drawRotatingPoint && this.isControlVisible('mtr') && hasControls) {
ctx.beginPath();
ctx.moveTo(0, rotateHeight);
ctx.lineTo(0, rotateHeight - rotatingPointOffset + 10);
ctx.stroke();
}
ctx.restore();
return this;
};
fabric.Object.prototype.drawControls = function(ctx) {
var rotationImage = 'data:image/png;base64,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';
var rotate = new Image();
var rotateLeft;
var rotateTop;
var wh = this._calculateCurrentDimensions();
var width = wh.x;
var height = wh.y;
var scaleOffset = this.cornerSize;
var left = -(width + scaleOffset) / 2;
var top = -(height + scaleOffset) / 2;
var methodName = this.transparentCorners ? 'stroke' : 'fill';
if (!this.hasControls) {
return this;
}
ctx.save();
ctx.strokeStyle = this.cornerColor;
ctx.fillStyle = this.cornerColor;
if (!this.transparentCorners) {
ctx.strokeStyle = this.cornerStrokeColor;
}
this._setLineDash(ctx, this.cornerDashArray, null);
// top-left
this._drawControl(
'tl',
ctx,
methodName,
left,
top
);
// top-right
this._drawControl(
'tr',
ctx,
methodName,
left + width,
top
);
// bottom-left
this._drawControl(
'bl',
ctx,
methodName,
left,
top + height
);
// bottom-right
this._drawControl(
'br',
ctx,
methodName,
left + width,
top + height
);
if (!this.get('lockUniScaling')) {
// middle-top
this._drawControl(
'mt',
ctx,
methodName,
left + width / 2,
top
);
// middle-bottom
this._drawControl(
'mb',
ctx,
methodName,
left + width / 2,
top + height
);
// middle-right
this._drawControl(
'mr',
ctx,
methodName,
left + width,
top + height / 2
);
// middle-left
this._drawControl(
'ml',
ctx,
methodName,
left,
top + height / 2
);
}
// middle-top-rotate
if (this.hasRotatingPoint) {
rotate.src = rotationImage;
rotateLeft = left + width / 2 - 6;
rotateTop = top - this.rotatingPointOffset - 6;
ctx.drawImage(rotate, rotateLeft, rotateTop, 32, 32);
}
ctx.restore();
return this;
};
}
function initImageEditor(data) {
var imageEditor;
var blackTheme = {
'common.bi.image': '',
'common.bisize.width': '0',
'common.bisize.height': '0',
'common.backgroundImage': 'none',
'common.backgroundColor': '#1e1e1e',
'common.border': '0px',
// header
'header.backgroundImage': 'none',
'header.backgroundColor': 'transparent',
'header.border': '0px',
// load button
'loadButton.backgroundColor': '#fff',
'loadButton.border': '1px solid #ddd',
'loadButton.color': '#222',
'loadButton.fontFamily': '\'Noto Sans\', sans-serif',
'loadButton.fontSize': '12px',
// download button
'downloadButton.backgroundColor': '#fdba3b',
'downloadButton.border': '1px solid #fdba3b',
'downloadButton.color': '#fff',
'downloadButton.fontFamily': '\'Noto Sans\', sans-serif',
'downloadButton.fontSize': '12px',
// main icons
'menu.normalIcon.path': '/images/icon-d.svg',
'menu.normalIcon.name': 'icon-d',
'menu.activeIcon.path': '/images/icon-b.svg',
'menu.activeIcon.name': 'icon-b',
'menu.disabledIcon.path': '/images/icon-a.svg',
'menu.disabledIcon.name': 'icon-a',
'menu.hoverIcon.path': '/images/icon-c.svg',
'menu.hoverIcon.name': 'icon-c',
'menu.iconSize.width': '24px',
'menu.iconSize.height': '24px',
// submenu primary color
'submenu.backgroundColor': '#1e1e1e',
'submenu.partition.color': '#3c3c3c',
// submenu icons
'submenu.normalIcon.path': '/images/icon-d.svg',
'submenu.normalIcon.name': 'icon-d',
'submenu.activeIcon.path': '/images/icon-c.svg',
'submenu.activeIcon.name': 'icon-c',
'submenu.iconSize.width': '32px',
'submenu.iconSize.height': '32px',
// submenu labels
'submenu.normalLabel.color': '#8a8a8a',
'submenu.normalLabel.fontWeight': 'lighter',
'submenu.activeLabel.color': '#fff',
'submenu.activeLabel.fontWeight': 'lighter',
// checkbox style
'checkbox.border': '0px',
'checkbox.backgroundColor': '#fff',
// range style
'range.pointer.color': '#fff',
'range.bar.color': '#666',
'range.subbar.color': '#d1d1d1',
'range.disabledPointer.color': '#414141',
'range.disabledBar.color': '#282828',
'range.disabledSubbar.color': '#414141',
'range.value.color': '#fff',
'range.value.fontWeight': 'lighter',
'range.value.fontSize': '11px',
'range.value.border': '1px solid #353535',
'range.value.backgroundColor': '#151515',
'range.title.color': '#fff',
'range.title.fontWeight': 'lighter',
// colorpicker style
'colorpicker.button.border': '1px solid #1e1e1e',
'colorpicker.title.color': '#fff'
};
imageEditor = new tui.ImageEditor('#tui-image-editor', {
includeUI: {
loadImage: {
path: data['download-url'],
name: data.filename
},
theme: blackTheme,
initMenu: 'draw',
menuBarPosition: 'bottom'
},
cssMaxWidth: 700,
cssMaxHeight: 500,
selectionStyle: {
cornerSize: 20,
rotatingPointOffset: 70,
borderColor: '#333',
cornerColor: '#333',
cornerStyle: 'circle',
borderScaleFactor: 3
},
usageStatistics: false
});
$('#fileEditModal').find('.file-name').text('Editing: ' + data.filename);
$('#fileEditModal').modal('show');
$('.tui-image-editor-header').hide();
$('.file-save-link').off().click(function(ev) {
var dataUpload = new FormData();
ev.preventDefault();
ev.stopPropagation();
dataUpload.append('image', imageEditor.toDataURL());
animateSpinner(null, true);
$.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);
setupAssetsLoading();
}
}).done(function() {
animateSpinner(null, false);
imageEditor.destroy();
imageEditor = {};
$('#tui-image-editor').html('');
$('#fileEditModal').modal('hide');
});
});
window.onresize = function() {
imageEditor.ui.resizeEditor();
};
}
function openPreviewModal(name, url, downloadUrl) {
var modal = $('#filePreviewModal');
updateFabricControls();
$.ajax({
url: url,
type: 'GET',
dataType: 'json',
success: function(data) {
var link = modal.find('.file-download-link');
modal.find('.file-preview-container').empty();
modal.find('.file-wopi-controls').empty();
if (Object.prototype.hasOwnProperty.call(data, 'wopi-controls')) {
modal.find('.file-wopi-controls').html(data['wopi-controls']);
}
link.attr('href', downloadUrl);
link.attr('data-no-turbolink', true);
link.attr('data-status', 'asset-present');
if (data.type === 'image') {
if (data.processing) {
animateSpinner('.file-preview-container', true);
} else {
animateSpinner('.file-preview-container', false);
modal.find('.file-preview-container')
.append($('<img>')
.attr('src', data['large-preview-url'])
.attr('alt', name)
.click(function(ev) {
ev.stopPropagation();
}));
if (data.editable) {
modal.find('.file-edit-link').css('display', '');
modal.find('.file-edit-link').off().click(function(ev) {
ev.preventDefault();
ev.stopPropagation();
modal.modal('hide');
initImageEditor(data);
});
} else {
modal.find('.file-edit-link').css('display', 'none');
}
}
} else {
modal.find('.file-preview-container').html(data['preview-icon']);
}
if (data.processing) {
checkFileReady(url, modal);
}
modal.find('.file-name').text(name);
modal.find('.preview-close').click(function() {
modal.modal('hide');
});
modal.modal();
modal.find('a[disabled=disabled]').click(function(ev) {
ev.preventDefault();
});
$('.modal-backdrop').last().css('z-index', modal.css('z-index') - 1);
},
error: function() {
// TODO
}
});
}
function checkFileReady(url, modal) {
$.get(url, function(data) {
if (data.processing) {
$('.file-download-link')
.addClass('disabled-with-click-events')
.attr(
'title',
I18n.t('general.file.processing')
)
.click(function(ev) {
ev.preventDefault();
ev.stopPropagation();
});
setTimeout(function() {
checkFileReady(url, modal);
}, 10000);
} else {
if (data.type === 'image') {
modal.find('.file-preview-container').empty();
modal.find('.file-preview-container')
.append($('<img>')
.attr('src', data['large-preview-url'])
.attr('alt', data.filename)
.click(function(ev) {
ev.stopPropagation();
}));
modal.find('.file-name').text(data.filename);
modal.find('.modal-body').click(function() {
modal.modal('hide');
});
modal.modal();
$('.modal-backdrop').last().css('z-index', modal.css('z-index') - 1);
}
$('.file-download-link')
.removeClass('disabled-with-click-events')
.removeAttr('title')
.off();
}
});
}
}(window));

109
app/assets/javascripts/sitewide/file_preview.js.erb
View file

@ -1,109 +0,0 @@
(function(global) {
'use strict';
global.initPreviewModal = function initPreviewModal() {
var name;
var url;
var downloadUrl;
$('.file-preview-link').off('click');
$('.file-preview-link').click(function(e) {
e.preventDefault();
name = $(this).find('p').text();
url = $(this).data('preview-url');
downloadUrl = $(this).attr('href');
openPreviewModal(name, url, downloadUrl);
});
}
function openPreviewModal(name, url, downloadUrl) {
var modal = $('#filePreviewModal');
$.ajax({
url: url,
type: 'GET',
dataType: 'json',
success: function(data) {
modal.find('.file-preview-container').empty();
modal.find('.file-wopi-controls').empty();
if (data.hasOwnProperty('wopi-controls')) {
modal.find('.file-wopi-controls').html(data['wopi-controls']);
}
var link = modal.find('.file-download-link');
link.attr('href', downloadUrl);
link.attr('data-no-turbolink', true);
link.attr('data-status', 'asset-present');
if (data['type'] === 'image') {
if(data['processing']) {
animateSpinner('.file-preview-container', true);
} else {
animateSpinner('.file-preview-container', false);
modal.find('.file-preview-container')
.append($('<img>')
.attr('src', data['large-preview-url'])
.attr('alt', name)
.click(function(ev) {
ev.stopPropagation();
})
);
}
} else {
modal.find('.file-preview-container').html(data['preview-icon']);
}
if(data['processing']) {
checkFileReady(url, modal);
}
modal.find('.file-name').text(name);
modal.find('.preview-close').click(function() {
modal.modal('hide');
});
modal.modal();
modal.find('a[disabled=disabled]').click(function(ev){
ev.preventDefault();
});
$('.modal-backdrop').last().css('z-index', modal.css('z-index') - 1);
},
error: function(ev) {
// TODO
}
});
}
function checkFileReady(url, modal) {
$.get(url, function(data) {
if(data['processing']) {
$('.file-download-link')
.addClass('disabled-with-click-events')
.attr('title',
'<%= I18n.t('general.file.processing')%>')
.click(function(ev) {
ev.preventDefault();
ev.stopPropagation();
});
setTimeout(function() {
checkFileReady(url, modal);
}, 10000);
} else {
if(data['type'] === 'image') {
modal.find('.file-preview-container').empty();
modal.find('.file-preview-container')
.append($('<img>')
.attr('src', data['large-preview-url'])
.attr('alt', data['filename'])
.click(function(ev) {
ev.stopPropagation();
})
);
modal.find('.file-name').text(data['filename']);
modal.find('.modal-body').click(function() {
modal.modal('hide');
});
modal.modal();
$('.modal-backdrop').last().css('z-index', modal.css('z-index') - 1);
}
$('.file-download-link')
.removeClass('disabled-with-click-events')
.removeAttr('title')
.off();
}
})
}
})(window);

5
app/assets/javascripts/users/settings/teams/invite_users_modal.js
View file

@ -158,8 +158,12 @@
});
});
}).on('shown.bs.modal', function() {
var script = document.createElement('script');
tagsInput.tagsinput('focus');
recaptchaErrorMsgDiv.addClass('hidden');
script.type = 'text/javascript';
script.src = 'https://www.google.com/recaptcha/api.js?hl=en';
$(script).insertAfter('#recaptcha-service');
// Remove 'data-invited="true"' status
modal.removeAttr('data-invited');
}).on('hide.bs.modal', function() {
@ -171,6 +175,7 @@
teamSelectorDropdown2.addClass('disabled');
animateSpinner(modalDialog, false);
recaptchaErrorMsgDiv.addClass('hidden');
$('#recaptcha-service').next().remove();
// Unbind event listeners
teamSelectorCheckbox.off('change');

10
app/assets/stylesheets/system_notifications.scss
View file

@ -13,16 +13,6 @@
position: relative;
width: 100%;
&[data-unread="0"] {
.body-block {
.title {
font-weight: normal;
}
}
}
&:hover {
background: $color-concrete;
color: $color-emperor;

64
app/assets/stylesheets/themes/scinote.scss
View file

@ -176,7 +176,7 @@ mark,.mark {
color: $color-emperor;
}
.circle {
.circle-icon {
@extend .badge;
background-color: $brand-primary;
border-radius: 1em;
@ -1518,6 +1518,68 @@ table.dataTable {
float: right;
margin-right: 20px;
}
.file-edit-link {
color: $color-white;
display: inline-block;
float: right;
margin-right: 20px;
}
}
// Image edit modal
.modal-file-edit {
background: transparent;
font-size: $font-size-large;
padding: 0 !important;
.preview-close {
background: transparent;
border: 0;
color: $color-white;
display: inline-block;
float: right;
}
.modal-dialog {
height: 100%;
margin: 0;
padding: 0;
width: auto;
}
.modal-content {
background: transparent;
border: 0;
-webkit-box-shadow: none;
box-shadow: none;
color: $color-white;
height: 100%;
width: auto;
}
.modal-header {
background: $color-black;
border: 0;
height: 60px;
text-align: center;
.file-name {
float: left;
}
}
.modal-body {
height: calc(100% - 60px);
padding: 0;
}
.file-save-link {
color: $color-white;
display: inline-block;
float: right;
margin-right: 20px;
}
}
// Disable textarea resizing throughout application

62
app/controllers/assets_controller.rb
View file

@ -44,12 +44,14 @@ class AssetsController < ApplicationController
def file_preview
response_json = {
'id' => @asset.id,
'type' => (@asset.is_image? ? 'image' : 'file'),
'filename' => truncate(@asset.file_file_name,
length:
Constants::FILENAME_TRUNCATION_LENGTH),
'download-url' => download_asset_path(@asset)
'download-url' => download_asset_path(@asset, timestamp: Time.now.to_i),
'editable' => @asset.editable?(current_user)
}
if @asset.is_image?
@ -78,20 +80,7 @@ class AssetsController < ApplicationController
elsif @assoc.class == RepositoryCell
can_manage_repository_rows?(@repository.team)
end
file_ext = @asset.file_file_name.split('.').last
if Constants::WOPI_EDITABLE_FORMATS.include?(file_ext)
edit_supported = true
title = ''
else
edit_supported = false
title = if Constants::FILE_TEXT_FORMATS.include?(file_ext)
I18n.t('assets.wopi_supported_text_formats_title')
elsif Constants::FILE_TABLE_FORMATS.include?(file_ext)
I18n.t('assets.wopi_supported_table_formats_title')
else
I18n.t('assets.wopi_supported_presentation_formats_title')
end
end
edit_supported, title = wopi_file_edit_button_status
response_json['wopi-controls'] = render_to_string(
partial: 'shared/file_wopi_controlls.html.erb',
locals: {
@ -109,6 +98,25 @@ class AssetsController < ApplicationController
end
end
# 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
if Constants::WOPI_EDITABLE_FORMATS.include?(file_ext)
edit_supported = true
title = ''
else
edit_supported = false
title = if Constants::FILE_TEXT_FORMATS.include?(file_ext)
I18n.t('assets.wopi_supported_text_formats_title')
elsif Constants::FILE_TABLE_FORMATS.include?(file_ext)
I18n.t('assets.wopi_supported_table_formats_title')
else
I18n.t('assets.wopi_supported_presentation_formats_title')
end
end
return edit_supported, title
end
def download
if !@asset.file_present
render_404 and return
@ -143,6 +151,30 @@ class AssetsController < ApplicationController
render layout: false
end
def update_image
@asset = Asset.find(params[:id])
return render_403 unless can_read_team?(@asset.team)
image_file = Paperclip.io_adapters.for(params[:image])
image_format = image_file.content_type.split('/')[1]
image_file.original_filename = @asset.file_file_name.ext(image_format)
@asset.file = image_file
@asset.save!
# Post process file here
@asset.post_process_file(@asset.team)
respond_to do |format|
format.json do
render json: {
html: render_to_string(
partial: 'shared/asset_link',
locals: { asset: @asset, display_image_tag: true },
formats: :html
)
}
end
end
end
private
def load_vars

17
app/controllers/users/sessions_controller.rb
View file

@ -11,9 +11,20 @@ class Users::SessionsController < Devise::SessionsController
end
# POST /resource/sign_in
# def create
# super
# end
def create
super
# Schedule templates creation for user
TemplatesService.new.schedule_creation_for_user(current_user)
# Schedule demo project creation for user
current_user.created_teams.each do |team|
FirstTimeDataGenerator.delay(
queue: :new_demo_project,
priority: 10
).seed_demo_data_with_id(current_user.id, team.id)
end
end
# DELETE /resource/sign_out
# def destroy

6
app/helpers/repository_datatable_helper.rb
View file

@ -53,9 +53,9 @@ module RepositoryDatatableHelper
def assigned_row(record, assigned_rows)
if assigned_rows&.include?(record)
"<span class='circle'>&nbsp;</span>"
"<span class='circle-icon'>&nbsp;</span>"
else
"<span class='circle disabled'>&nbsp;</span>"
"<span class='circle-icon disabled'>&nbsp;</span>"
end
end
@ -80,4 +80,4 @@ module RepositoryDatatableHelper
col.slice(:visible, :searchable)
end.to_json
end
end
end

7
app/javascript/packs/tui_image_editor.js Normal file
View file

@ -0,0 +1,7 @@
global.tui = {};
global.tui.usageStatistics = false;
require('tui-code-snippet');
require('tui-color-picker');
global.tui.ImageEditor = require('tui-image-editor');

2
app/javascript/packs/tui_image_editor_styles.scss Normal file
View file

@ -0,0 +1,2 @@
@import "~tui-color-picker/dist/tui-color-picker";
@import "~tui-image-editor/dist/tui-image-editor";

15
app/models/asset.rb
View file

@ -10,8 +10,10 @@ class Asset < ApplicationRecord
# Paperclip validation
has_attached_file :file,
styles: { large: [Constants::LARGE_PIC_FORMAT, :jpg],
medium: [Constants::MEDIUM_PIC_FORMAT, :jpg] },
styles: {
large: [Constants::LARGE_PIC_FORMAT, :jpg],
medium: [Constants::MEDIUM_PIC_FORMAT, :jpg]
},
convert_options: {
medium: '-quality 70 -strip',
all: '-background "#d2d2d2" -flatten +matte'
@ -463,6 +465,15 @@ class Asset < ApplicationRecord
save
end
def editable?(user)
objects = %w(step result)
my_module = send(objects.find { |object| send(object) }).my_module
Canaid::PermissionsHolder.instance.eval(:manage_experiment, user, my_module.experiment) &&
!locked? &&
%r{^image/#{Regexp.union(Constants::WHITELISTED_IMAGE_TYPES_EDITABLE)}} ===
file.content_type
end
protected
# Checks if attachments is an image (in post processing imagemagick will

2
app/models/team.rb
View file

@ -317,7 +317,7 @@ class Team < ApplicationRecord
def generate_template_project
return if without_templates
TemplatesService.new.update_team(self)
TemplatesService.new.delay(queue: :templates).update_team(self)
end
include FirstTimeDataGenerator

17
app/models/team_zip_export.rb
View file

@ -129,22 +129,10 @@ class TeamZipExport < ZipExport
)
file = FileUtils.touch("#{project_path}/#{html_name}").first
File.open(file, 'wb') { |f| f.write(project_report_pdf) }
# Add Handsontable and dependent JS files (mimick frontend formula
# processing).
required_js = %w(handsontable.full.min.js lodash.js numeral.js numeric.js
md5.js jstat.js formula.js parser.js ruleJS.js
handsontable.formula.js big.min.js)
required_js.each do |filename|
filepath = File.join(Rails.root,
"vendor/assets/javascripts/#{filename}/")
dest_folder = "#{project_path}/"
FileUtils.cp(filepath, dest_folder)
end
end
ensure
# Change current dir outside tmp_dir, since tmp_dir will be deleted
Dir.chdir(File.join(Rails.root, 'tmp'))
Dir.chdir(Rails.root)
end
def generate_notification(user)
@ -152,6 +140,7 @@ class TeamZipExport < ZipExport
type_of: :deliver,
title: I18n.t('zip_export.notification_title'),
message: "<a data-id='#{id}' " \
"data-turbolinks='false' " \
"href='#{Rails.application
.routes
.url_helpers

3
app/models/user.rb
View file

@ -488,7 +488,8 @@ class User < ApplicationRecord
# This method must be overwriten for addons that will be installed
def show_login_system_notification?
user_system_notifications.show_on_login.present?
user_system_notifications.show_on_login.present? &&
(ENV['ENABLE_TUTORIAL'] != 'true' || settings['tutorial_completed'])
end
# json friendly attributes

1
app/models/user_project.rb
View file

@ -13,6 +13,7 @@ class UserProject < ApplicationRecord
belongs_to :project, inverse_of: :user_projects, touch: true, optional: true
before_destroy :destroy_associations
validates_uniqueness_of :user_id, scope: :project_id
def role_str
I18n.t("user_projects.enums.role.#{role.to_s}")

1
app/models/user_team.rb
View file

@ -14,6 +14,7 @@ class UserTeam < ApplicationRecord
before_destroy :destroy_associations
after_create :create_samples_table_state
validates_uniqueness_of :user_id, scope: :team_id
def role_str
I18n.t("user_teams.enums.role.#{role}")

1
app/models/zip_export.rb
View file

@ -90,6 +90,7 @@ class ZipExport < ApplicationRecord
type_of: :deliver,
title: I18n.t('zip_export.notification_title'),
message: "<a data-id='#{id}' " \
"data-turbolinks='false' " \
"href='#{Rails.application
.routes
.url_helpers

1
app/services/experiments/move_to_project_service.rb
View file

@ -82,6 +82,7 @@ module Experiments
message_items: { experiment: @exp.id,
project_new: @project.id,
project_original: @original_project.id })
end
end
end

1
app/services/projects_overview_service.rb
View file

@ -72,6 +72,7 @@ class ProjectsOverviewService
.joins('LEFT OUTER JOIN user_projects ON '\
'user_projects.project_id = projects.id')
.left_outer_joins(:user_my_modules)
.where('projects.id': @team.projects)
.where('user_my_modules.user_id = :user_id '\
'OR (user_projects.role = 0 '\
'AND user_projects.user_id = :user_id)', user_id: @user.id)

27
app/services/templates_service.rb
View file

@ -32,13 +32,16 @@ class TemplatesService
return unless owner.present?
updated = false
exp_tmplt_dir_prefix = "#{@base_dir}/experiment_"
existing = tmpl_project.experiments.where.not(uuid: nil).pluck(:uuid)
@experiment_templates.except(*existing).each_value do |id|
importer_service = TeamImporter.new
importer_service.import_experiment_template_from_dir(
exp_tmplt_dir_prefix + id.to_s, tmpl_project.id, owner.id
)
updated = true
# Create lock in case another worker starts to update same team
tmpl_project.with_lock do
existing = tmpl_project.experiments.where.not(uuid: nil).pluck(:uuid)
@experiment_templates.except(*existing).each_value do |id|
importer_service = TeamImporter.new
importer_service.import_experiment_template_from_dir(
exp_tmplt_dir_prefix + id.to_s, tmpl_project.id, owner.id
)
updated = true
end
end
updated
end
@ -52,4 +55,14 @@ class TemplatesService
end
[updated_counter, processed_counter]
end
def schedule_creation_for_user(user)
user.teams.each do |team|
next if team.projects.where(template: true).any?
TemplatesService.new.delay(
queue: :templates
).update_team(team)
end
end
end

28
app/utilities/delayed_uploader_demo.rb
View file

@ -19,7 +19,8 @@ module DelayedUploaderDemo
current_team:,
result_name:,
created_at: Time.now,
file_name:
file_name:,
comment: nil
)
temp_asset = get_asset(current_user, current_team, file_name)
temp_result = Result.new(
@ -32,6 +33,10 @@ module DelayedUploaderDemo
temp_result.save
temp_asset.save
# Generate comment if it exists
generate_result_comment(temp_result, current_user, comment) if comment
temp_asset.post_process_file(my_module.experiment.project.team)
end
@ -42,4 +47,25 @@ module DelayedUploaderDemo
step.assets << temp_asset
temp_asset.post_process_file(step.my_module.experiment.project.team)
end
def self.generate_result_comment(result, user, message, created_at = nil)
created_at ||= result.created_at
ResultComment.create(
user: user,
message: message,
created_at: created_at,
result: result
)
Activity.new(
type_of: :add_comment_to_result,
user: user,
project: result.my_module.experiment.project,
my_module: result.my_module,
created_at: created_at,
updated_at: created_at,
message: I18n.t('activities.add_comment_to_result',
user: user.full_name,
result: result.name)
).sneaky_save
end
end

272
app/utilities/first_time_data_generator.rb
View file

@ -1,6 +1,9 @@
module FirstTimeDataGenerator
# Default inventory repository
REPO_SAMPLES_NAME = 'Samples'.freeze
# Create data for demo for new users
def seed_demo_data(user, team)
def seed_demo_data(user, team, asset_queue = :demo)
@user = user
# If private private team does not exist,
@ -8,28 +11,80 @@ module FirstTimeDataGenerator
# Do nothing
return unless team
# create custom repository samples
repository = Repository.create(
name: 'Samples',
# Skip this team if user already has a demo project
return if team.projects.where(demo: true).any?
name = '[NEW] Demo project by SciNote'
exp_name = 'Polymerase chain reaction'
# If there is an existing demo project, archive and rename it
if team.projects.where(name: name).present?
# TODO: check if we still need this code
# old = team.projects.where(name: 'Demo project - qPCR')[0]
# old.archive! user
i = 1
while team.projects.where(
name: name = "#{name} (#{i})"
).present?
i += 1
end
end
project = Project.create(
visibility: 0,
name: name,
due_date: nil,
team: team,
created_by: user
created_by: user,
created_at: generate_random_time(1.week.ago),
last_modified_by: user,
archived: false,
template: false,
demo: true
)
# check if samples repo already exist, then create custom repository samples
repository = Repository.where(team: team).where(name: REPO_SAMPLES_NAME)
repository =
if repository.blank?
if team.repositories.count < Rails.configuration.x.repositories_limit
Repository.create(
name: REPO_SAMPLES_NAME,
team: team,
created_by: user
)
else
# User first repo just as a placeholder, this call will fail anyhow
Repository.create(
name: team.repositories.first.name,
team: team,
created_by: user
)
end
else
repository.first
end
# create list value column for sample types
repository_column_sample_types = RepositoryColumn.create(
repository: repository,
created_by: user,
data_type: :RepositoryListValue,
name: 'Sample Types'
)
repo_columns = []
['Sample Types', 'Sample Groups'].each do |repo_name|
repo_column = repository.repository_columns.where(name: repo_name)
# create list value column for sample groups
repository_column_sample_groups = RepositoryColumn.create(
repository: repository,
created_by: user,
data_type: :RepositoryListValue,
name: 'Sample Groups'
)
repo_columns <<
if repo_column.blank?
RepositoryColumn.create(
repository: repository,
created_by: user,
data_type: :RepositoryListValue,
name: repo_name
)
else
repo_column.first
end
end
# Maintain old names
repository_column_sample_types, repository_column_sample_groups =
repo_columns
# create few list items for sample types
repository_items_sample_types = []
@ -41,7 +96,15 @@ module FirstTimeDataGenerator
repository_column: repository_column_sample_types,
repository: repository
)
repository_items_sample_types << item
# Check if it already exists
if item.persisted?
repository_items_sample_types << item
else
repository_items_sample_types << repository_column_sample_types
.repository_list_items
.where(data: name).first
end
end
# create few list items for sample groups
@ -54,7 +117,15 @@ module FirstTimeDataGenerator
repository_column: repository_column_sample_groups,
repository: repository
)
repository_items_sample_groups << item
# Check if it already exists
if item.persisted?
repository_items_sample_groups << item
else
repository_items_sample_groups << repository_column_sample_groups
.repository_list_items
.where(data: name).first
end
end
repository_rows_to_assign = []
@ -152,32 +223,6 @@ module FirstTimeDataGenerator
)
end
name = 'Demo project'
exp_name = 'qPCR Experiment Version 01'
# If there is an existing demo project, archive and rename it
if team.projects.where(name: name).present?
# TODO: check if we still need this code
# old = team.projects.where(name: 'Demo project - qPCR')[0]
# old.archive! user
i = 1
while team.projects.where(
name: name = "#{name} (#{i})"
).present?
i += 1
end
end
project = Project.create(
visibility: 0,
name: name,
due_date: nil,
team: team,
created_by: user,
created_at: generate_random_time(1.week.ago),
last_modified_by: user,
archived: false
)
experiment_description =
'Polymerase chain reaction (PCR) monitors the amplification of DNA ' \
'in real time (qPCR cyclers constantly scan qPCR plates). It is, in ' \
@ -498,19 +543,22 @@ module FirstTimeDataGenerator
'Collection of potatoes'
]
second_rep_item = smart_annotate_rep_item(repository_rows_to_assign.second)
third_rep_item = smart_annotate_rep_item(repository_rows_to_assign.third)
fifth_rep_item = smart_annotate_rep_item(repository_rows_to_assign.fifth)
module_step_descriptions = [
'<html>
<body>
<p>50% of samples should be mock inoculated
<span class=\"atwho-inserted\"contenteditable=\"false\"
data-atwho-at-query=\"#\">[#' + sample_name + '3~rep_item~3]</span>
data-atwho-at-query=\"#\">[#' + third_rep_item + ']</span>
<span class=\"atwho-inserted\" contenteditable=\"false\"
data-atwho-at-query=\"#\">[#' + sample_name + '5~rep_item~5]</span>
data-atwho-at-query=\"#\">[#' + fifth_rep_item + ']</span>
while other 50% with PVY NTN virus
<span class=\"atwho-inserted\" contenteditable=\"false\"
data-atwho-at-query=\"#\">[#' + sample_name + '3~rep_item~3]</span>
data-atwho-at-query=\"#\">[#' + third_rep_item + ']</span>
<span class=\"atwho-inserted\" contenteditable=\"false\"
data-atwho-at-query=\"#\">[#' + sample_name + '5~rep_item~5]</span>.
data-atwho-at-query=\"#\">[#' + fifth_rep_item + ']</span>.
</p>
</body>
</html>',
@ -524,6 +572,9 @@ module FirstTimeDataGenerator
module_step_names,
module_step_descriptions)
# Delete repository items, if we went over the limit
repository_rows_to_assign.map(&:destroy) unless repository.id
# Add table to existig step
step = my_modules[1].protocol.steps.where('position = 0').take
Table.create(
@ -533,19 +584,18 @@ module FirstTimeDataGenerator
contents: tab_content['module2']['samples_table']
)
# Add file to existig step
DelayedUploaderDemo.delay(queue: :demo).add_step_asset(
DelayedUploaderDemo.delay(queue: asset_queue).add_step_asset(
step: my_modules[1].protocol.steps.where('position = 0').take,
current_user: user,
current_team: team,
file_name: 'PVY-inoculated_plant_symptoms.JPG'
)
# Add comment to step 1
user_annotation = '[@' + user.name + '~' + user.id.to_s + ']'
user_annotation = user.name
generate_step_comment(
step,
user,
user_annotation + ' I have used different sample [#' + sample_name +
'2~rep_item~2]'
"#{user_annotation} I have used different sample [##{second_rep_item}]"
)
# Add comment to step 3
step = my_modules[1].protocol.steps.where('position = 2').take
@ -555,7 +605,7 @@ module FirstTimeDataGenerator
user_annotation + ' Please complete this by Monday.'
)
# Results
DelayedUploaderDemo.delay(queue: :demo).generate_result_asset(
DelayedUploaderDemo.delay(queue: asset_queue).generate_result_asset(
my_module: my_modules[1],
current_user: user,
current_team: team,
@ -564,7 +614,7 @@ module FirstTimeDataGenerator
file_name: 'mock-inoculated-plant.JPG'
)
DelayedUploaderDemo.delay(queue: :demo).generate_result_asset(
DelayedUploaderDemo.delay(queue: asset_queue).generate_result_asset(
my_module: my_modules[1],
current_user: user,
current_team: team,
@ -651,11 +701,12 @@ module FirstTimeDataGenerator
user: user
)
qpcr_id = MyModule.where(name: 'qPCR').last.id.base62_encode
generate_result_comment(
DelayedUploaderDemo.generate_result_comment(
temp_result,
user,
user_annotation + ' Please check if results match results in ' \
'[#qPCR~tsk~' + qpcr_id + ']'
'[#qPCR~tsk~' + qpcr_id + ']',
generate_random_time(temp_result.created_at, 1.days)
)
temp_result.table = Table.new(
created_by: user,
@ -665,13 +716,14 @@ module FirstTimeDataGenerator
temp_result.save
# Second result
DelayedUploaderDemo.delay(queue: :demo).generate_result_asset(
DelayedUploaderDemo.delay(queue: asset_queue).generate_result_asset(
my_module: my_modules[2],
current_user: user,
current_team: team,
result_name: 'Agarose gel electrophoresis of totRNA samples',
created_at: generate_random_time(my_modules[2].created_at, 3.days),
file_name: 'totRNA_gel.jpg'
file_name: 'totRNA_gel.jpg',
comment: user_annotation + ' Could you check if this is okay?'
)
# ----------------- Module 4 ------------------
@ -762,7 +814,7 @@ module FirstTimeDataGenerator
generate_module_steps(my_modules[3], module_step_names, module_step_descriptions)
# Add file to existig step 1
DelayedUploaderDemo.delay(queue: :demo).add_step_asset(
DelayedUploaderDemo.delay(queue: asset_queue).add_step_asset(
step: my_modules[3].protocol.steps.where('position = 0').take,
current_user: user,
current_team: team,
@ -793,8 +845,8 @@ module FirstTimeDataGenerator
'If desired, more than 30 mg tissue can be disrupted and homogenized ' \
'at the start of the procedure (increase the volume of Buffer RLT ' \
'proportionately). Use a portion of the homogenate corresponding to no ' \
'more than 30 mg tissue for RNA purification, and store the rest at –80',
'°C. Buffer RLT may form a precipitate upon storage. If necessary, ' \
'more than 30 mg tissue for RNA purification, and store the rest at –80°C.',
'Buffer RLT may form a precipitate upon storage. If necessary, ' \
'redissolve by warming, and then place at room temperature (15–25°C).',
'Buffer RLT and Buffer RW1 contain a guanidine salt and are therefore ' \
'not compatible with disinfecting reagents containing bleach. See page ' \
@ -804,8 +856,8 @@ module FirstTimeDataGenerator
'Perform all centrifugation steps at 20–25°C in a standard ' \
'microcentrifuge. Ensure that the centrifuge does not cool below 20°C.'
]
module_checklist_items.each do |item|
checklist.checklist_items << ChecklistItem.new(text: item)
module_checklist_items.each_with_index do |item, ind|
checklist.checklist_items << ChecklistItem.new(text: item, position: ind)
end
checklist.save
@ -829,8 +881,8 @@ module FirstTimeDataGenerator
'If performing optional on-column DNase digestion, prepare DNase I ' \
'stock solution as described in Appendix D (page 67).'
]
module_checklist_items.each do |item|
checklist.checklist_items << ChecklistItem.new(text: item)
module_checklist_items.each_with_index do |item, ind|
checklist.checklist_items << ChecklistItem.new(text: item, position: ind)
end
checklist.save
@ -855,13 +907,13 @@ module FirstTimeDataGenerator
'genomic DNA contamination”, page 21), follow steps D1–D4 (page 67) ' \
'after performing this step.'
]
module_checklist_items.each do |item|
checklist.checklist_items << ChecklistItem.new(text: item)
module_checklist_items.each_with_index do |item, ind|
checklist.checklist_items << ChecklistItem.new(text: item, position: ind)
end
checklist.save
# Results
DelayedUploaderDemo.delay(queue: :demo).generate_result_asset(
DelayedUploaderDemo.delay(queue: asset_queue).generate_result_asset(
my_module: my_modules[3],
current_user: user,
current_team: team,
@ -914,8 +966,8 @@ module FirstTimeDataGenerator
step: step
)
module_checklist_items.each do |item|
checklist.checklist_items << ChecklistItem.new(text: item)
module_checklist_items.each_with_index do |item, ind|
checklist.checklist_items << ChecklistItem.new(text: item, position: ind)
end
checklist.save
@ -977,41 +1029,41 @@ module FirstTimeDataGenerator
'Clean surfaces with 70% ethanol or RNA remover',
'Turn on the UV light'
]
module_checklist_items.each do |item|
checklist.checklist_items << ChecklistItem.new(text: item)
module_checklist_items.each_with_index do |item, ind|
checklist.checklist_items << ChecklistItem.new(text: item, position: ind)
end
checklist.save
# Add file to existig steps
DelayedUploaderDemo.delay(queue: :demo).add_step_asset(
DelayedUploaderDemo.delay(queue: asset_queue).add_step_asset(
step: my_modules[5].protocol.steps.where('position = 0').take,
current_user: user,
current_team: team,
file_name: 'Mixes_Templats.xlsx'
)
DelayedUploaderDemo.delay(queue: :demo).add_step_asset(
DelayedUploaderDemo.delay(queue: asset_queue).add_step_asset(
step: my_modules[5].protocol.steps.where('position = 1').take,
current_user: user,
current_team: team,
file_name: 'qPCR_template.jpg'
)
DelayedUploaderDemo.delay(queue: :demo).add_step_asset(
DelayedUploaderDemo.delay(queue: asset_queue).add_step_asset(
step: my_modules[5].protocol.steps.where('position = 1').take,
current_user: user,
current_team: team,
file_name: '96plate.docx'
)
DelayedUploaderDemo.delay(queue: :demo).add_step_asset(
DelayedUploaderDemo.delay(queue: asset_queue).add_step_asset(
step: my_modules[5].protocol.steps.where('position = 2').take,
current_user: user,
current_team: team,
file_name: 'cycling_conditions.JPG'
)
DelayedUploaderDemo.delay(queue: :demo).add_step_asset(
DelayedUploaderDemo.delay(queue: asset_queue).add_step_asset(
step: my_modules[5].protocol.steps.where('position = 2').take,
current_user: user,
current_team: team,
@ -1039,7 +1091,7 @@ module FirstTimeDataGenerator
temp_result.save
# Results
DelayedUploaderDemo.delay(queue: :demo).generate_result_asset(
DelayedUploaderDemo.delay(queue: asset_queue).generate_result_asset(
my_module: my_modules[5],
current_user: user,
current_team: team,
@ -1048,7 +1100,7 @@ module FirstTimeDataGenerator
file_name: '1505745387970-1058053257.jpg'
)
DelayedUploaderDemo.delay(queue: :demo).generate_result_asset(
DelayedUploaderDemo.delay(queue: asset_queue).generate_result_asset(
my_module: my_modules[5],
current_user: user,
current_team: team,
@ -1057,7 +1109,7 @@ module FirstTimeDataGenerator
file_name: 'chromatogram.png'
)
DelayedUploaderDemo.delay(queue: :demo).generate_result_asset(
DelayedUploaderDemo.delay(queue: asset_queue).generate_result_asset(
my_module: my_modules[5],
current_user: user,
current_team: team,
@ -1066,16 +1118,20 @@ module FirstTimeDataGenerator
file_name: 'curves.JPG'
)
DelayedUploaderDemo.delay(queue: :demo).generate_result_asset(
DelayedUploaderDemo.delay(queue: asset_queue).generate_result_asset(
my_module: my_modules[5],
current_user: user,
current_team: team,
result_name: 'Bacteria plates YPGA',
created_at: generate_random_time(my_modules[5].created_at, 2.days),
file_name: 'Bacterial_colonies.jpg'
file_name: 'Bacterial_colonies.jpg',
comment: user_annotation + ' please check the results again. ' \
'<span class=\"atwho-inserted\" contenteditable=\"false\"' \
'data-atwho-at-query=\"#\">[#' + fifth_rep_item + ']</span>' \
' seems to be acting strange?'
)
DelayedUploaderDemo.delay(queue: :demo).generate_result_asset(
DelayedUploaderDemo.delay(queue: asset_queue).generate_result_asset(
my_module: my_modules[5],
current_user: user,
current_team: team,
@ -1226,21 +1282,21 @@ module FirstTimeDataGenerator
module_step_descriptions)
# Add file to existig steps
DelayedUploaderDemo.delay(queue: :demo).add_step_asset(
DelayedUploaderDemo.delay(queue: asset_queue).add_step_asset(
step: my_modules[6].protocol.steps.where('position = 0').take,
current_user: user,
current_team: team,
file_name: 'Native_SDS-PAGE_for_complex_analysis.jpg'
)
DelayedUploaderDemo.delay(queue: :demo).add_step_asset(
DelayedUploaderDemo.delay(queue: asset_queue).add_step_asset(
step: my_modules[6].protocol.steps.where('position = 4').take,
current_user: user,
current_team: team,
file_name: 'Native-PAGE-Nature_protocols.pdf'
)
DelayedUploaderDemo.delay(queue: :demo).add_step_asset(
DelayedUploaderDemo.delay(queue: asset_queue).add_step_asset(
step: my_modules[6].protocol.steps.where('position = 5').take,
current_user: user,
current_team: team,
@ -1258,8 +1314,8 @@ module FirstTimeDataGenerator
'Check stock of reagents & order new stock if needed',
'Use gloves at all times'
]
module_checklist_items.each do |item|
checklist.checklist_items << ChecklistItem.new(text: item)
module_checklist_items.each_with_index do |item, ind|
checklist.checklist_items << ChecklistItem.new(text: item, position: ind)
end
checklist.save
@ -1291,14 +1347,14 @@ module FirstTimeDataGenerator
module_step_descriptions)
# Add file to existig step
DelayedUploaderDemo.delay(queue: :demo).add_step_asset(
DelayedUploaderDemo.delay(queue: asset_queue).add_step_asset(
step: my_modules[7].protocol.steps.where('position = 0').take,
current_user: user,
current_team: team,
file_name: 'ddCq-quantification_diagnostics-template.xls'
)
DelayedUploaderDemo.delay(queue: :demo).add_step_asset(
DelayedUploaderDemo.delay(queue: asset_queue).add_step_asset(
step: my_modules[7].protocol.steps.where('position = 0').take,
current_user: user,
current_team: team,
@ -1314,7 +1370,7 @@ module FirstTimeDataGenerator
)
# Add result
DelayedUploaderDemo.delay(queue: :demo).generate_result_asset(
DelayedUploaderDemo.delay(queue: asset_queue).generate_result_asset(
my_module: my_modules[7],
current_user: user,
current_team: team,
@ -1323,7 +1379,7 @@ module FirstTimeDataGenerator
file_name: 'ddCq-quantification_diagnostics-results.xls'
)
DelayedUploaderDemo.delay(queue: :demo).generate_result_asset(
DelayedUploaderDemo.delay(queue: asset_queue).generate_result_asset(
my_module: my_modules[7],
current_user: user,
current_team: team,
@ -1332,7 +1388,7 @@ module FirstTimeDataGenerator
file_name: 'dilution_curve-efficiency.JPG'
)
DelayedUploaderDemo.delay(queue: :demo).generate_result_asset(
DelayedUploaderDemo.delay(queue: asset_queue).generate_result_asset(
my_module: my_modules[7],
current_user: user,
current_team: team,
@ -1345,6 +1401,23 @@ module FirstTimeDataGenerator
experiment.delay.generate_workflow_img
end
# Used for delayed jobs
def self.seed_demo_data_with_id(user_id, team_id)
extend self
user = User.find(user_id)
team = Team.find(team_id)
unless user || team
Rails.logger.warning("Could not retrieve user or team in " \
"seed_demo_data_with_id. " \
"User #{user_id} was mapped to #{user.inspect}." \
"Team #{team_id} was mapped to #{team.inspect}.")
return
end
seed_demo_data(user, team, :new_demo_project)
end
# WARNING: This only works on PostgreSQL
def pluck_random(scope)
scope.order('RANDOM()').first
@ -1385,9 +1458,9 @@ module FirstTimeDataGenerator
if rand < 0.3
polite_comment = 'This looks well.'
elsif rand < 0.4
polite_comment = 'Seems satisfactory.'
polite_comment = 'Great job!'
elsif rand < 0.4
polite_comment = 'Try a bit harder next time.'
polite_comment = 'Thanks for getting this done.'
end
if polite_comment
commented_on = generate_random_time(completed_on)
@ -1422,6 +1495,7 @@ module FirstTimeDataGenerator
)
end
def generate_result_comment(result, user, message, created_at = nil)
created_at ||= generate_random_time(result.created_at, 1.days)
ResultComment.create(
@ -1441,4 +1515,8 @@ module FirstTimeDataGenerator
step: step
)
end
def smart_annotate_rep_item(item)
"#{item.name}~rep_item~#{Base62.encode(item.id)}"
end
end

5
app/views/layouts/application.html.erb
View file

@ -17,6 +17,10 @@
<% if content_for?(:head) %>
<%= yield(:head) %>
<% end %>
<%= javascript_pack_tag 'tui_image_editor' %>
<%= stylesheet_pack_tag 'tui_image_editor_styles' %>
</head>
<body
class="<%= yield :body_class %>"
@ -39,6 +43,7 @@
<!-- About us modal -->
<%= render "shared/about_modal" %>
<%= render "shared/file_preview_modal.html.erb" %>
<%= render "shared/file_edit_modal.html.erb" %>
<%= render "shared/navigation" %>
<% if user_signed_in? && flash[:system_notification_modal] && current_user.show_login_system_notification? %>

23
app/views/shared/_file_edit_modal.html.erb Normal file
View file

@ -0,0 +1,23 @@
<div id="fileEditModal"
class="modal modal-file-edit"
role="dialog"
aria-labelledby="fileEditModal"
aria-hidden="true"
data-backdrop="static"
data-keyboard="false">
<div class="modal-dialog">
<div class="modal-content">
<div class="modal-header">
<button type="button" class="preview-close" data-dismiss="modal"><span class="fas fa-times"></span></button>
<span class="file-name"></span>
<a class="file-save-link" href='#'>
<p><span class="fas fa-save"></span> <%= t('SaveClose')%></p>
</a>
</div>
<div class="modal-body">
<div id="tui-image-editor">
</div>
</div>
</div>
</div>
</div>

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

@ -12,9 +12,12 @@
<button type="button" class="preview-close" data-dismiss="modal"><span class="fas fa-times"></span></button>
<span class="file-name"></span>
<span class="file-wopi-controls"></span>
<a class="file-download-link" href='#'>
<a class="file-download-link" href="#" data-turbolinks="false">
<p><span class="fas fa-download"></span> <%= t('Download')%></p>
</a>
<a class="file-edit-link" style="display:none" href='#'>
<p><span class="fas fa-pencil-alt"></span> <%= t('Edit')%></p>
</a>
</div>
<div class="modal-body">
<div class="file-preview-container">

1
app/views/shared/_invite_users_modal.html.erb
View file

@ -103,7 +103,6 @@ invite_to_team = type.in?(%w(invite_to_team invite_to_team_with_role))
<div id="recaptcha-service" class="g-recaptcha"
data-callback="recaptchaCallback"
data-sitekey=<%= ENV['RECAPTCHA_SITE_KEY'] %>></div>
<script type="text/javascript" src="https://www.google.com/recaptcha/api.js?hl=en"></script>
<input type="hidden" id="recaptcha-invite-modal" value="">
<div class="form-group has-error hidden" id="recaptcha-error-msg" >
<span class="has-error help-block"></span>

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

@ -22,7 +22,7 @@
<a href="#"
id="system-notifications-dropdown"
class="dropdown-toggle"
title="System notifications"
title="<%= t('system_notifications.navbar.tooltip') %>"
data-toggle="dropdown"
role="button"
aria-haspopup="true"

27
app/views/team_zip_exports/report.html.erb
View file

@ -11,19 +11,20 @@
.html_safe %>
</style>
<script src="handsontable.full.min.js"></script>
<!-- Libraries for formulas -->
<script src="lodash.js"></script>
<script src="numeral.js"></script>
<script src="numeric.js"></script>
<script src="md5.js"></script>
<script src="jstat.js"></script>
<script src="formula.js"></script>
<script src="parser.js"></script>
<script src="ruleJS.js"></script>
<script src="handsontable.formula.js"></script>
<script src="big.min.js"></script>
<!-- Libraries for tables and formulas -->
<% ['handsontable.full.min.js', 'lodash.js', 'numeral.js', 'numeric.js',
'md5.js', 'jstat.js', 'formula.js', 'parser.js', 'ruleJS.js',
'handsontable.formula.js', 'big.min.js' ].each do |js_asset| %>
<script type="text/javascript">
<%= Rails.application
.assets_manifest
.find_sources(js_asset)
.first
.to_s
.force_encoding(Encoding::UTF_8)
.html_safe %>
</script>
<% end %>
<!-- Init Handsontables -->
<script>

33
bin/webpack
View file

@ -1,28 +1,15 @@
#!/usr/bin/env ruby
$stdout.sync = true
require "shellwords"
require "yaml"
ENV["RAILS_ENV"] ||= ENV["RACK_ENV"] || "development"
ENV["NODE_ENV"] ||= "development"
ENV["RAILS_ENV"] ||= "development"
RAILS_ENV = ENV["RAILS_ENV"]
require "pathname"
ENV["BUNDLE_GEMFILE"] ||= File.expand_path("../../Gemfile",
Pathname.new(__FILE__).realpath)
ENV["NODE_ENV"] ||= RAILS_ENV
NODE_ENV = ENV["NODE_ENV"]
require "rubygems"
require "bundler/setup"
APP_PATH = File.expand_path("../", __dir__)
NODE_MODULES_PATH = File.join(APP_PATH, "node_modules")
WEBPACK_CONFIG = File.join(APP_PATH, "config/webpack/#{NODE_ENV}.js")
unless File.exist?(WEBPACK_CONFIG)
puts "Webpack configuration not found."
puts "Please run bundle exec rails webpacker:install to install webpacker"
exit!
end
newenv = { "NODE_PATH" => NODE_MODULES_PATH.shellescape }
cmdline = ["yarn", "run", "webpack", "--", "--config", WEBPACK_CONFIG] + ARGV
Dir.chdir(APP_PATH) do
exec newenv, *cmdline
end
require "webpacker"
require "webpacker/webpack_runner"
Webpacker::WebpackRunner.run(ARGV)

48
bin/webpack-dev-server
View file

@ -1,43 +1,15 @@
#!/usr/bin/env ruby
$stdout.sync = true
require "shellwords"
require "yaml"
ENV["RAILS_ENV"] ||= ENV["RACK_ENV"] || "development"
ENV["NODE_ENV"] ||= "development"
ENV["RAILS_ENV"] ||= "development"
RAILS_ENV = ENV["RAILS_ENV"]
require "pathname"
ENV["BUNDLE_GEMFILE"] ||= File.expand_path("../../Gemfile",
Pathname.new(__FILE__).realpath)
ENV["NODE_ENV"] ||= RAILS_ENV
NODE_ENV = ENV["NODE_ENV"]
require "rubygems"
require "bundler/setup"
APP_PATH = File.expand_path("../", __dir__)
CONFIG_FILE = File.join(APP_PATH, "config/webpacker.yml")
NODE_MODULES_PATH = File.join(APP_PATH, "node_modules")
WEBPACK_CONFIG = File.join(APP_PATH, "config/webpack/development.js")
def args(key)
index = ARGV.index(key)
index ? ARGV[index + 1] : nil
end
begin
dev_server = YAML.load_file(CONFIG_FILE)["development"]["dev_server"]
DEV_SERVER_HOST = "http#{"s" if args('--https') || dev_server["https"]}://#{args('--host') || dev_server["host"]}:#{args('--port') || dev_server["port"]}"
rescue Errno::ENOENT, NoMethodError
puts "Webpack dev_server configuration not found in #{CONFIG_FILE}."
puts "Please run bundle exec rails webpacker:install to install webpacker"
exit!
end
newenv = {
"NODE_PATH" => NODE_MODULES_PATH.shellescape,
"ASSET_HOST" => DEV_SERVER_HOST.shellescape
}.freeze
cmdline = ["yarn", "run", "webpack-dev-server", "--", "--progress", "--color", "--config", WEBPACK_CONFIG] + ARGV
Dir.chdir(APP_PATH) do
exec newenv, *cmdline
end
require "webpacker"
require "webpacker/dev_server_runner"
Webpacker::DevServerRunner.run(ARGV)

3
config/environments/development.rb
View file

@ -1,4 +1,7 @@
Rails.application.configure do
# Verifies that versions and hashed value of the package contents in the project's package.json
config.webpacker.check_yarn_integrity = true
# Settings specified here will take precedence over those in config/application.rb.
# In the development environment your application's code is reloaded on

3
config/environments/production.rb
View file

@ -1,4 +1,7 @@
Rails.application.configure do
# Verifies that versions and hashed value of the package contents in the project's package.json
config.webpacker.check_yarn_integrity = false
# Settings specified here will take precedence over those in config/application.rb.
# Code is not reloaded between requests.

6
config/initializers/backtrace_silencers.rb
View file

@ -3,5 +3,11 @@
# You can add backtrace silencers for libraries that you're using but don't wish to see in your backtraces.
# Rails.backtrace_cleaner.add_silencer { |line| line =~ /my_noisy_library/ }
# Silence the WOPI method override to prevent "trapping" of stack/backtrace
# See https://stackoverflow.com/questions/29498145
Rails.backtrace_cleaner.add_silencer do |line|
line =~ %r{app/middlewares/wopi_method_override}
end
# You can also remove all the silencers if you're trying to debug a problem that might stem from framework code.
# Rails.backtrace_cleaner.remove_silencers!

12
config/initializers/constants.rb
View file

@ -219,15 +219,19 @@ class Constants
'gif', 'jpeg', 'pjpeg', 'png', 'x-png', 'svg+xml', 'bmp', 'tiff'
].freeze
WHITELISTED_IMAGE_TYPES_EDITABLE = %w(
gif jpeg pjpeg png
).freeze
WHITELISTED_TAGS = %w(
a b strong i em li ul ol h1 del ins h2 h3 h4 h5 h6 br sub sup p code hr div
span u s blockquote pre col colgroup table thead tbody th tr td
).freeze
WHITELISTED_ATTRIBUTES = %w(
href src width height alt cite datetime title class name xml:lang abbr style
target data-*
).freeze
WHITELISTED_ATTRIBUTES = [
'href', 'src', 'width', 'height', 'alt', 'cite', 'datetime', 'title',
'class', 'name', 'xml:lang', 'abbr', 'style', 'target', :data
].freeze
WHITELISTED_CSS_ATTRIBUTES = {
allow_comments: false,

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 += [:password]
Rails.application.config.filter_parameters += %i(password image)

1
config/initializers/paperclip.rb
View file

@ -1,3 +1,4 @@
Paperclip::DataUriAdapter.register
if ENV['PAPERCLIP_HASH_SECRET'].nil?
puts "WARNING! Environment variable PAPERCLIP_HASH_SECRET must be set."

5
config/locales/en.yml
View file

@ -1292,6 +1292,8 @@ en:
create:
success_flash: "Successfully added sample group <strong>%{sample_group}</strong> to team <strong>%{team}</strong>."
system_notifications:
navbar:
tooltip: 'What’s new notifications'
emails:
subject: "You've received a What's new notification"
intro_paragraph: "Hi %{user_name}, you've received What's new notification in SciNote:"
@ -2010,6 +2012,9 @@ en:
Asset: "File"
Assets: "Files"
Download: "Download"
Edit: "Edit"
Save: "Save"
SaveClose: "Save & Close"
Module: "Task"
Modules: "Tasks"
Project: "Project"

2
config/routes.rb
View file

@ -572,6 +572,8 @@ Rails.application.routes.draw do
get 'files/:id/preview', to: 'assets#preview', as: 'preview_asset'
get 'files/:id/view', to: 'assets#view', as: 'view_asset'
get 'files/:id/edit', to: 'assets#edit', as: 'edit_asset'
post 'files/:id/update_image', to: 'assets#update_image',
as: 'update_asset_image'
devise_scope :user do
get 'avatar/:id/:style' => 'users/registrations#avatar', as: 'avatar'

35
config/webpack/configuration.js
View file

@ -1,35 +0,0 @@
// Common configuration for webpacker loaded from config/webpacker.yml
const { join, resolve } = require('path')
const { env } = require('process')
const { safeLoad } = require('js-yaml')
const { readFileSync } = require('fs')
const configPath = resolve('config', 'webpacker.yml')
const loadersDir = join(__dirname, 'loaders')
const settings = safeLoad(readFileSync(configPath), 'utf8')[env.NODE_ENV]
function removeOuterSlashes(string) {
return string.replace(/^\/*/, '').replace(/\/*$/, '')
}
function formatPublicPath(host = '', path = '') {
let formattedHost = removeOuterSlashes(host)
if (formattedHost && !/^http/i.test(formattedHost)) {
formattedHost = `//${formattedHost}`
}
const formattedPath = removeOuterSlashes(path)
return `${formattedHost}/${formattedPath}/`
}
const output = {
path: resolve('public', settings.public_output_path),
publicPath: formatPublicPath(env.ASSET_HOST, settings.public_output_path)
}
module.exports = {
settings,
env,
loadersDir,
output
}

33
config/webpack/development.js
View file

@ -1,32 +1,5 @@
// Note: You must restart bin/webpack-dev-server for changes to take effect
process.env.NODE_ENV = process.env.NODE_ENV || 'development'
const merge = require('webpack-merge')
const sharedConfig = require('./shared.js')
const { settings, output } = require('./configuration.js')
const environment = require('./environment')
module.exports = merge(sharedConfig, {
devtool: 'cheap-eval-source-map',
stats: {
errorDetails: true
},
output: {
pathinfo: true
},
devServer: {
clientLogLevel: 'none',
https: settings.dev_server.https,
host: settings.dev_server.host,
port: settings.dev_server.port,
contentBase: output.path,
publicPath: output.publicPath,
compress: true,
headers: { 'Access-Control-Allow-Origin': '*' },
historyApiFallback: true,
watchOptions: {
ignored: /node_modules/
}
}
})
module.exports = environment.toWebpackConfig()

3
config/webpack/environment.js Normal file
View file

@ -0,0 +1,3 @@
const { environment } = require('@rails/webpacker')
module.exports = environment

12
config/webpack/loaders/assets.js
View file

@ -1,12 +0,0 @@
const { env, publicPath } = require('../configuration.js')
module.exports = {
test: /\.(jpg|jpeg|png|gif|svg|eot|ttf|woff|woff2)$/i,
use: [{
loader: 'file-loader',
options: {
publicPath,
name: env.NODE_ENV === 'production' ? '[name]-[hash].[ext]' : '[name].[ext]'
}
}]
}

5
config/webpack/loaders/babel.js
View file

@ -1,5 +0,0 @@
module.exports = {
test: /\.js(\.erb)?$/,
exclude: /node_modules/,
loader: 'babel-loader'
}

4
config/webpack/loaders/coffee.js
View file

@ -1,4 +0,0 @@
module.exports = {
test: /\.coffee(\.erb)?$/,
loader: 'coffee-loader'
}

9
config/webpack/loaders/erb.js
View file

@ -1,9 +0,0 @@
module.exports = {
test: /\.erb$/,
enforce: 'pre',
exclude: /node_modules/,
loader: 'rails-erb-loader',
options: {
runner: 'bin/rails runner'
}
}

5
config/webpack/loaders/react.js vendored
View file

@ -1,5 +0,0 @@
module.exports = {
test: /\.(js|jsx)?(\.erb)?$/,
exclude: /node_modules/,
loader: 'babel-loader'
}

15
config/webpack/loaders/sass.js
View file

@ -1,15 +0,0 @@
const ExtractTextPlugin = require('extract-text-webpack-plugin')
const { env } = require('../configuration.js')
module.exports = {
test: /\.(scss|sass|css)$/i,
use: ExtractTextPlugin.extract({
fallback: 'style-loader',
use: [
{ loader: 'css-loader', options: { minimize: env.NODE_ENV === 'production' } },
{ loader: 'postcss-loader', options: { sourceMap: true } },
'resolve-url-loader',
{ loader: 'sass-loader', options: { sourceMap: true } }
]
})
}

36
config/webpack/production.js
View file

@ -1,35 +1,5 @@
// Note: You must restart bin/webpack-dev-server for changes to take effect
process.env.NODE_ENV = process.env.NODE_ENV || 'production'
/* eslint global-require: 0 */
const environment = require('./environment')
const webpack = require('webpack')
const merge = require('webpack-merge')
const CompressionPlugin = require('compression-webpack-plugin')
const sharedConfig = require('./shared.js')
module.exports = merge(sharedConfig, {
output: { filename: '[name]-[chunkhash].js' },
devtool: 'source-map',
stats: 'normal',
plugins: [
new webpack.optimize.UglifyJsPlugin({
minimize: true,
sourceMap: true,
compress: {
warnings: false
},
output: {
comments: false
}
}),
new CompressionPlugin({
asset: '[path].gz[query]',
algorithm: 'gzip',
test: /\.(js|css|html|json|ico|svg|eot|otf|ttf)$/
})
]
})
module.exports = environment.toWebpackConfig()

58
config/webpack/shared.js
View file

@ -1,58 +0,0 @@
// Note: You must restart bin/webpack-dev-server for changes to take effect
/* eslint global-require: 0 */
/* eslint import/no-dynamic-require: 0 */
const webpack = require('webpack')
const { basename, dirname, join, relative, resolve } = require('path')
const { sync } = require('glob')
const ExtractTextPlugin = require('extract-text-webpack-plugin')
const ManifestPlugin = require('webpack-manifest-plugin')
const extname = require('path-complete-extname')
const { env, settings, output, loadersDir } = require('./configuration.js')
const extensionGlob = `**/*{${settings.extensions.join(',')}}*`
const entryPath = join(settings.source_path, settings.source_entry_path)
const packPaths = sync(join(entryPath, extensionGlob))
module.exports = {
entry: packPaths.reduce(
(map, entry) => {
const localMap = map
const namespace = relative(join(entryPath), dirname(entry))
localMap[join(namespace, basename(entry, extname(entry)))] = resolve(entry)
return localMap
}, {}
),
output: {
filename: '[name].js',
path: output.path,
publicPath: output.publicPath
},
module: {
rules: sync(join(loadersDir, '*.js')).map(loader => require(loader))
},
plugins: [
new webpack.EnvironmentPlugin(JSON.parse(JSON.stringify(env))),
new ExtractTextPlugin(env.NODE_ENV === 'production' ? '[name]-[hash].css' : '[name].css'),
new ManifestPlugin({
publicPath: output.publicPath,
writeToFileEmit: true
})
],
resolve: {
extensions: settings.extensions,
modules: [
resolve(settings.source_path),
'node_modules'
]
},
resolveLoader: {
modules: ['node_modules']
}
}

7
config/webpack/test.js
View file

@ -1,6 +1,5 @@
// Note: You must restart bin/webpack-dev-server for changes to take effect
process.env.NODE_ENV = process.env.NODE_ENV || 'development'
const merge = require('webpack-merge')
const sharedConfig = require('./shared.js')
const environment = require('./environment')
module.exports = merge(sharedConfig, {})
module.exports = environment.toWebpackConfig()

44
config/webpacker.yml
View file

@ -4,17 +4,23 @@ default: &default
source_path: app/javascript
source_entry_path: packs
public_output_path: packs
cache_path: tmp/cache/webpacker
# Additional paths webpack should lookup modules
# ['app/assets', 'engine/foo/app/assets']
resolved_paths: []
# Reload manifest.json on all requests so we reload latest compiled packs
cache_manifest: false
extensions:
- .coffee
- .erb
- .js
- .jsx
- .ts
- .vue
- .sass
- .scss
- .css
- .module.sass
- .module.scss
- .module.css
- .png
- .svg
- .gif
@ -23,16 +29,40 @@ default: &default
development:
<<: *default
compile: true
# Reference: https://webpack.js.org/configuration/dev-server/
dev_server:
host: 0.0.0.0
port: 8080
https: false
host: 0.0.0.0
port: 3035
public: 0.0.0.0:3035
hmr: false
# Inline should be set to true if using HMR
inline: true
overlay: true
compress: true
disable_host_check: true
use_local_ip: false
quiet: false
headers:
'Access-Control-Allow-Origin': '*'
watch_options:
ignored: /node_modules/
test:
<<: *default
compile: true
# Compile test packs to a separate directory
public_output_path: packs-test
production:
<<: *default
# Production depends on precompilation of packs prior to booting for performance.
compile: false
# Cache manifest.json for performance
cache_manifest: true

16
db/migrate/20190227125306_add_unique_index_on_user_teams.rb Normal file
View file

@ -0,0 +1,16 @@
# frozen_string_literal: true
class AddUniqueIndexOnUserTeams < ActiveRecord::Migration[5.1]
def up
# firstly delete the duplicates
execute 'WITH uniq AS
(SELECT DISTINCT ON (user_id, team_id) * FROM user_teams)
DELETE FROM user_teams WHERE user_teams.id NOT IN
(SELECT id FROM uniq)'
add_index :user_teams, %i(user_id team_id), unique: true
end
def down
remove_index :user_teams, column: %i(user_id team_id)
end
end

16
db/migrate/20190227125352_add_unique_index_on_user_projects.rb Normal file
View file

@ -0,0 +1,16 @@
# frozen_string_literal: true
class AddUniqueIndexOnUserProjects < ActiveRecord::Migration[5.1]
def up
# firstly delete the duplicates
execute 'WITH uniq AS
(SELECT DISTINCT ON (user_id, project_id) * FROM user_projects)
DELETE FROM user_projects WHERE user_projects.id NOT IN
(SELECT id FROM uniq)'
add_index :user_projects, %i(user_id project_id), unique: true
end
def down
remove_index :user_projects, columns: %i(user_id project_id)
end
end

6
db/migrate/20190304153544_add_demo_flag_to_project.rb Normal file
View file

@ -0,0 +1,6 @@
# frozen_string_literal: true
class AddDemoFlagToProject < ActiveRecord::Migration[5.1]
def change
add_column :projects, :demo, :boolean, null: false, default: false
end
end

5
db/schema.rb
View file

@ -10,7 +10,7 @@
#
# It's strongly recommended that you check this file into your version control system.
ActiveRecord::Schema.define(version: 20190227110801) do
ActiveRecord::Schema.define(version: 20190304153544) do
# These are extensions that must be enabled in order to support this database
enable_extension "plpgsql"
@ -305,6 +305,7 @@ ActiveRecord::Schema.define(version: 20190227110801) do
t.datetime "restored_on"
t.string "experiments_order"
t.boolean "template"
t.boolean "demo", default: false, null: false
t.index "trim_html_tags((name)::text) gin_trgm_ops", name: "index_projects_on_name", using: :gin
t.index ["archived_by_id"], name: "index_projects_on_archived_by_id"
t.index ["created_by_id"], name: "index_projects_on_created_by_id"
@ -803,6 +804,7 @@ ActiveRecord::Schema.define(version: 20190227110801) do
t.bigint "assigned_by_id"
t.index ["assigned_by_id"], name: "index_user_projects_on_assigned_by_id"
t.index ["project_id"], name: "index_user_projects_on_project_id"
t.index ["user_id", "project_id"], name: "index_user_projects_on_user_id_and_project_id", unique: true
t.index ["user_id"], name: "index_user_projects_on_user_id"
end
@ -828,6 +830,7 @@ ActiveRecord::Schema.define(version: 20190227110801) do
t.bigint "assigned_by_id"
t.index ["assigned_by_id"], name: "index_user_teams_on_assigned_by_id"
t.index ["team_id"], name: "index_user_teams_on_team_id"
t.index ["user_id", "team_id"], name: "index_user_teams_on_user_id_and_team_id", unique: true
t.index ["user_id"], name: "index_user_teams_on_user_id"
end

5
docker-compose.yml
View file

@ -24,6 +24,7 @@ services:
bundle exec rails s -b 0.0.0.0"
environment:
- RAILS_ENV=development
- WEBPACKER_DEV_SERVER_HOST=webpack
volumes:
- .:/usr/src/app
- scinote_development_bundler:/usr/local/bundle/
@ -38,13 +39,15 @@ services:
stdin_open: true
tty: true
ports:
- "8080:8080"
- "3035:3035"
command: >
bash -c "./bin/webpack-dev-server"
environment:
- RAILS_ENV=development
volumes:
- .:/usr/src/app
- scinote_development_bundler:/usr/local/bundle/
- scinote_development_files:/usr/src/app/public/system
volumes:
scinote_development_postgres:

46
lib/tasks/data.rake
View file

@ -131,23 +131,53 @@ namespace :data do
end
desc 'Update all templates projects'
task update_all_templates: :environment do
task :update_all_templates,
%i(slice_size) => [:environment] do |_, args|
args.with_defaults(slice_size: 800)
Rails.logger.info('Templates, syncing all templates projects')
updated, total = TemplatesService.new.update_all_templates
Rails.logger.info(
"Templates, total number of updated projects: #{updated} out of #{total}}"
)
Team.all.order(updated_at: :desc)
.each_slice(args[:slice_size].to_i).with_index do |teams, i|
Rails.logger.info("Processing slice with index #{i}. " \
"First team: #{teams.first.id}, " \
"Last team: #{teams.last.id}.")
teams.each do |team|
TemplatesService.new.delay(
run_at: i.hours.from_now,
queue: :templates,
priority: 5
).update_team(team)
end
end
end
desc 'Create demo project on existing users'
task create_demo_project_on_existing_users: :environment do
task :create_demo_project_on_existing_users,
%i(slice_size) => [:environment] do |_, args|
args.with_defaults(slice_size: 800)
require "#{Rails.root}/app/utilities/first_time_data_generator"
include FirstTimeDataGenerator
Rails.logger.info('Creating demo project on existing users')
User.find_each do |user|
seed_demo_data(user, user.teams.first)
Team.all.order(updated_at: :desc)
.each_slice(args[:slice_size]).with_index do |teams, i|
Rails.logger.info("Processing slice with index #{i}. " \
"First team: #{teams.first.id}, " \
"Last team: #{teams.last.id}.")
teams.each do |team|
owner_ut = team.user_teams.where(role: 2).first
next unless owner_ut
FirstTimeDataGenerator.delay(
run_at: i.hours.from_now,
queue: :new_demo_project,
priority: 10
).seed_demo_data_with_id(owner_ut.user.id, team.id)
end
end
end
end

74
lib/tasks/rename_duplicates_protocols.rake Normal file
View file

@ -0,0 +1,74 @@
# frozen_string_literal: true
# rubocop:disable Metrics/BlockLength
namespace :protocols do
desc 'Rename dupluicates protocols '
task rename_duplicates_team_protocols: :environment do
# checking for public protocols
public_protocols = Protocol.select(:name, :team_id)
.where.not(name: nil).where(protocol_type: 3)
.group(:name, :team_id, :protocol_type)
.having('COUNT(*) > 1')
public_protocols.each do |dup_name|
protocols_to_update = Protocol.where(
name: dup_name.name,
team_id: dup_name.team_id,
protocol_type: 3
).order(created_at: :asc)
protocols_to_update.each_with_index do |protocol, index|
next if index.zero?
protocol.update(name: "#{protocol.name} (#{index})")
end
end
# checking for private protocols
private_protocols = Protocol.select(:name, :team_id, :added_by_id)
.where.not(name: nil).where(protocol_type: 2)
.group(
:name,
:team_id,
:protocol_type,
:added_by_id
)
.having('COUNT(*) > 1')
private_protocols.each do |dup_name|
protocols_to_update = Protocol.where(
name: dup_name.name,
team_id: dup_name.team_id,
protocol_type: 2,
added_by_id: dup_name.added_by_id
).order(created_at: :asc)
protocols_to_update.each_with_index do |protocol, index|
next if index.zero?
protocol.update(name: "#{protocol.name} (#{index})")
end
end
# checking for archived protocols
archived_protocols = Protocol.select(:name, :team_id, :added_by_id)
.where.not(name: nil).where(protocol_type: 4)
.group(
:name,
:team_id,
:protocol_type,
:added_by_id
)
.having('COUNT(*) > 1')
archived_protocols.each do |dup_name|
protocols_to_update = Protocol.where(
name: dup_name.name,
team_id: dup_name.team_id,
protocol_type: 4,
added_by_id: dup_name.added_by_id
).order(created_at: :asc)
protocols_to_update.each_with_index do |protocol, index|
next if index.zero?
protocol.update(name: "#{protocol.name} (#{index})")
end
end
end
end
# rubocop:enable Metrics/BlockLength

6823
package-lock.json generated
View file

File diff suppressed because it is too large Load diff

7
package.json
View file

@ -42,6 +42,7 @@
"webpack-dev-server": "^2.11.2"
},
"dependencies": {
"@rails/webpacker": "^3.5.5",
"autoprefixer": "^7.2.6",
"axios": "^0.16.2",
"babel-core": "^6.26.3",
@ -59,6 +60,7 @@
"compression-webpack-plugin": "^1.1.11",
"css-loader": "^0.28.11",
"extract-text-webpack-plugin": "^3.0.2",
"fabric": "1.6.7",
"file-loader": "^0.11.2",
"glob": "^7.1.2",
"immutability-helper": "^2.7.1",
@ -67,6 +69,7 @@
"lodash": "^4.17.10",
"moment": "^2.22.2",
"moment-timezone": "^0.5.21",
"node-gyp": "^3.8.0",
"node-sass": "^4.9.2",
"path-complete-extname": "^0.1.0",
"postcss-loader": "^2.1.6",
@ -93,10 +96,14 @@
"redux": "^3.7.2",
"redux-thunk": "^2.3.0",
"resolve-url-loader": "^2.3.0",
"safe-umd-webpack-plugin": "^4.0.0",
"sass-loader": "^6.0.7",
"shortid": "^2.2.12",
"style-loader": "^0.18.2",
"styled-components": "^2.4.1",
"tui-code-snippet": "^1.5.0",
"tui-color-picker": "^2.2.0",
"tui-image-editor": "git://github.com/biosistemika/tui.image-editor",
"webpack": "^3.12.0",
"webpack-manifest-plugin": "^1.3.2",
"webpack-merge": "^4.1.3"

235
public/images/icon-a.svg Normal file
View file

@ -0,0 +1,235 @@
<?xml version="1.0" encoding="UTF-8"?><!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd"><svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink"><defs>
<circle id="a" cx="16" cy="16" r="16"/>
</defs><symbol id="icon-a-ic-apply" viewBox="0 0 24 24">
<g fill="none" fill-rule="evenodd">
<path d="M0 0h24v24H0z"/>
<path stroke="#434343" d="M4 12.011l5 5L20.011 6"/>
</g>
</symbol><symbol id="icon-a-ic-cancel" viewBox="0 0 24 24">
<g fill="none" fill-rule="evenodd">
<path d="M0 0h24v24H0z"/>
<path stroke="#434343" d="M6 6l12 12M18 6L6 18"/>
</g>
</symbol><symbol id="icon-a-ic-color-transparent-w" viewBox="0 0 32 32">
<g fill="none" fill-rule="evenodd">
<g>
<use fill="#FFF" xlink:href="#a"/>
<circle cx="16" cy="16" r="15.5" stroke="#D5D5D5"/>
</g>
<path stroke="#FF4040" stroke-width="1.5" d="M27 5L5 27"/>
</g>
</symbol><symbol id="icon-a-ic-crop" viewBox="0 0 24 24">
<g fill="none" fill-rule="evenodd">
<path d="M0 0h24v24H0z"/>
<path fill="#434343" d="M4 0h1v20a1 1 0 0 1-1-1V0zM20 17h-1V5h1v12zm0 2v5h-1v-5h1z"/>
<path fill="#434343" d="M5 19h19v1H5zM4.762 4v1H0V4h4.762zM7 4h12a1 1 0 0 1 1 1H7V4z"/>
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spec/services/client_api/user_team_service_spec.rb
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@ -68,7 +68,6 @@ describe ClientApi::UserTeamService do
describe '#update_role!' do
it 'should raise ClientApi::CustomUserTeamError if no role is set' do
create :user_team, team: team_one, user: user_one
ut_service = ClientApi::UserTeamService.new(
user: user_one,
team_id: team_one.id,