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Merge branch 'develop'

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This commit is contained in:
Oleksii Kriuchykhin 2023-09-20 11:14:56 +02:00
commit b7e2e227b5
77 changed files with 3077 additions and 199 deletions
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2
VERSION
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@ -1 +1 @@
1.28.1.3
1.28.2

10
app/assets/images/icon_small/sequence-editor.svg Normal file
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@ -0,0 +1,10 @@
<svg width="24" height="24" viewBox="0 0 24 24" fill="none" xmlns="http://www.w3.org/2000/svg">
<path d="M11.4923 3.51517C10.0704 3.60025 8.69275 4.04129 7.48581 4.79777C6.27887 5.55426 5.28139 6.60192 4.58502 7.84452C3.88865 9.08711 3.51572 10.4848 3.50049 11.9091C3.48526 13.3335 3.82822 14.7388 4.49786 15.996" stroke="#1D2939" stroke-linecap="round"/>
<path d="M11.5501 6.51843C10.6743 6.59031 9.8284 6.87102 9.08335 7.33704C8.3383 7.80307 7.71577 8.44084 7.26789 9.19694C6.82001 9.95304 6.55984 10.8055 6.50916 11.6828C6.45847 12.5601 6.61875 13.4368 6.97658 14.2395" stroke="#1D2939" stroke-linecap="round"/>
<path d="M10.7142 14.144C11.0835 14.3654 11.5036 14.4878 11.934 14.4991C12.3644 14.5105 12.7904 14.4105 13.1708 14.2089" stroke="#1D2939" stroke-linecap="round"/>
<path d="M11.5231 9.54591C11.0365 9.64048 10.5889 9.87759 10.2374 10.2271C9.88584 10.5766 9.64613 11.0227 9.54873 11.5088" stroke="#1D2939" stroke-linecap="round"/>
<path d="M16.4528 15.2284C17.2432 14.1382 17.6062 12.7958 17.473 11.4558" stroke="#1D2939" stroke-linecap="round"/>
<path d="M8.8669 16.5204C9.66189 17.0714 10.5881 17.403 11.5522 17.4817C12.5163 17.5605 13.4841 17.3836 14.358 16.9689" stroke="#1D2939" stroke-linecap="round"/>
<path d="M19.4459 7.90013C18.6397 6.43599 17.4197 5.24203 15.9386 4.46756" stroke="#1D2939" stroke-linecap="round"/>
<path d="M6.52764 18.5041C7.79803 19.573 9.35364 20.2464 11.0024 20.4413C12.6512 20.6361 14.3209 20.3439 15.8054 19.6006C17.29 18.8573 18.5244 17.6955 19.3562 16.2587C20.188 14.8219 20.5808 13.1729 20.4862 11.5154" stroke="#1D2939" stroke-linecap="round"/>
</svg>
Side by side

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Width:  |  Height:  |  Size: 1.6 KiB

2
app/assets/javascripts/i18n_bundle.js Normal file
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@ -0,0 +1,2 @@
//= require i18n.js
//= require i18n/translations

54
app/assets/javascripts/protocols/import_export/import.js
View file

@ -58,12 +58,41 @@ function importProtocolFromFile(
}
function getAssetBytes(folder, stepGuid, fileRef) {
var stepPath = stepGuid ? stepGuid + '/' : '';
var filePath = folder + stepPath + fileRef;
var assetBytes = zipFiles.files[cleanFilePath(filePath)].asBinary();
const stepPath = stepGuid ? stepGuid + '/' : '';
const filePath = folder + stepPath + fileRef;
const assetBytes = zipFiles.files[cleanFilePath(filePath)].asBinary();
return window.btoa(assetBytes);
}
function getAssetPreview(folder, stepGuid, fileRef, fileName, fileType) {
if ($.inArray(fileType, ['image/png', 'image/jpeg', 'image/gif', 'image/bmp']) > 0) {
return {
fileName: fileName,
fileType: fileType,
bytes: getAssetBytes(folder, stepGuid, fileRef)
};
} else {
const stepPath = stepGuid ? folder + stepGuid + '/' : folder;
let baseName;
baseName = fileRef.split('.');
baseName.pop();
baseName.join('.');
let previewFileRef = zipFiles.file(new RegExp(stepPath + 'previews/' + baseName));
if (previewFileRef.length > 0) {
const previewFileExt = previewFileRef[0].name.split('.').at(-1);
let previewFileName = fileName.split('.');
previewFileName.splice(-1, 1, previewFileExt);
previewFileName.join('.');
return {
fileName: previewFileName,
fileType: `image/${previewFileExt}`,
bytes: window.btoa(previewFileRef[0].asBinary())
};
}
}
return null;
}
/* Template functions */
function newPreviewElement(name, values) {
@ -82,14 +111,14 @@ function importProtocolFromFile(
}
function newAssetElement(folder, stepGuid, fileRef, fileName, fileType) {
var html = '<li class="col-xs-12">';
var assetBytes;
if ($.inArray(fileType, ['image/png', 'image/jpeg', 'image/gif', 'image/bmp']) > 0) {
assetBytes = getAssetBytes(folder, stepGuid, fileRef);
let html = '<li class="col-xs-12">';
let assetPreview = getAssetPreview(folder, stepGuid, fileRef, fileName, fileType);
html += '<img style="max-width:300px; max-height:300px;" src="data:' + fileType + ';base64,' + assetBytes + '" />';
if (assetPreview) {
html += '<img style="max-width:300px; max-height:300px;" src="data:' + assetPreview.fileType + ';base64,' + assetPreview.bytes + '" />';
html += '<br>';
}
html += '<span>' + fileName + '</span>';
html += '</li>';
return $.parseHTML(html);
@ -708,6 +737,7 @@ function importProtocolFromFile(
var assetId = $(this).attr('id');
var fileRef = $(this).attr('fileRef');
var fileName = $(this).children('fileName').text();
stepAssetJson.id = assetId;
stepAssetJson.fileName = fileName;
stepAssetJson.fileType = $(this).children('fileType').text();
@ -723,6 +753,14 @@ function importProtocolFromFile(
fileRef
);
stepAssetJson.preview_image = getAssetPreview(
protocolFolders[index],
stepGuid,
fileRef,
fileName,
null
);
stepAssetsJson.push(stepAssetJson);
});
stepJson.assets = stepAssetsJson;

2
app/assets/javascripts/sitewide/active_storage_previews.js
View file

@ -17,6 +17,8 @@ var ActiveStoragePreviews = (function() {
if (img.retryCount >= RETRY_COUNT) return;
$(img).css('opacity', 0);
if (!$(img).parent().hasClass('processing')) $(img).parent().addClass('processing');
setTimeout(() => {

35
app/assets/javascripts/sitewide/iframe_modal.js Normal file
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@ -0,0 +1,35 @@
/* global iFrameModal */
// General-purpose iframe modal. For closing the modal, you need will to take care of triggering
// the 'hide' event on the modal itself, example from inside the iframe:
// parent.document.getElementById('iFrameModal').dispatchEvent(new Event('hide'));
$(document).on('turbolinks:load', function() {
window.iFrameModal = document.getElementById('iFrameModal');
let iFrameModalFrame = document.getElementById('iFrameModalFrame');
// Block from running when accessing page without defined iframe modal
// (sign in, reset password, accept invitation, 2fa)
if (!iFrameModalFrame || !iFrameModal) return;
window.showIFrameModal = (url) => {
iFrameModalFrame.setAttribute('src', url);
iFrameModal.classList.remove('hidden');
iFrameModal.dispatchEvent(new Event('shown'));
};
iFrameModal.addEventListener('hide', () => {
iFrameModal.classList.add('hidden');
iFrameModalFrame.removeAttribute('src');
iFrameModal.dispatchEvent(new Event('hidden'));
});
iFrameModal.addEventListener('shown', () => {
document.body.classList.add('overflow-hidden');
document.body.classList.remove('overflow-auto');
});
iFrameModal.addEventListener('hidden', () => {
document.body.classList.remove('overflow-hidden');
document.body.classList.add('overflow-auto');
});
});

6
app/assets/javascripts/sitewide/marvinjs_editor.js
View file

@ -303,6 +303,12 @@ $(document).on('click', '.marvinjs-edit-button', function() {
});
});
$(document).on('click', '.gene-sequence-edit-button', function() {
var editButton = $(this);
$('#filePreviewModal').modal('hide');
window.showIFrameModal(editButton.data('sequence-edit-url'));
});
$(document).on('turbolinks:load', function() {
MarvinJsEditor = MarvinJsEditorApi();
if (MarvinJsEditor.enabled()) {

2
app/assets/stylesheets/reports.scss
View file

@ -67,6 +67,8 @@ label {
* Global fix for handsontable
*/
.hot-table-container {
display: flex;
overflow: auto;
.ht_master .wtHolder {
height: auto !important;
width: auto !important;

2
app/assets/stylesheets/reports_print.scss
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@ -29,6 +29,8 @@ div.print-report {
}
.hot-table-container {
display: flex;
overflow: auto;
.ht_master .wtHolder {
overflow: hidden !important;

12
app/assets/stylesheets/shared/assets.scss
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@ -445,3 +445,15 @@
padding: 4px 8px;
white-space: nowrap;
}
.sn-file-ove {
height: 1.5rem;
width: 1.5rem;
&::before {
content: url("icon_small/sequence-editor.svg");
display: inline-block;
margin: auto;
width: 100%;
}
}

15
app/assets/stylesheets/shared/file_preview.scss
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@ -26,11 +26,22 @@
.file-preview-container {
align-items: center;
background-color: var(--sn-color-white);
display: flex;
height: 100%;
height: calc(100% - 4rem);
justify-content: center;
margin: 2rem;
text-align: center;
width: 100%;
width: calc(100% - 4rem);
.asset-image {
background-color: var(--sn-white);
}
.gene-sequence-asset {
height: 500px;
width: 500px;
}
&.processing {
background-image: url("/images/medium/loading_white.svg");

10
app/assets/stylesheets/shared_styles/elements/input_fields.scss
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@ -15,7 +15,7 @@
.sci-input-field {
@include font-button;
animation-timing-function: $timing-function-sharp;
border: $border-secondary;
border: 1px solid var(--sn-light-grey);
border-radius: $border-radius-default !important;
box-shadow: none;
height: 36px;
@ -24,12 +24,18 @@
transition: .3s;
width: 100%;
&:hover {
border: 1px solid var(--sn-science-blue-hover);
}
&:focus {
border: $border-focus;
}
&:disabled {
background: transparent;
background-color: var(--sn-super-light-grey);
color: var(--sn-light-grey);
border: 1px solid var(--sn-light-grey);
}
&::placeholder {

4
app/assets/stylesheets/sn_icon_font.css Normal file
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@ -0,0 +1,4 @@
/*
*= require sn-icon-font
*= require sn-inter-font
*/

10
app/assets/stylesheets/tailwind/inputs.css
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@ -29,6 +29,16 @@
box-shadow: none;
}
.sci-input-container-v2 input:hover {
border-color: var(--sn-science-blue-hover);
}
.sci-input-container-v2 input:disabled {
background-color: var(--sn-super-light-grey);
color: var(--sn-light-grey);
border: 1px solid var(--sn-light-grey);
}
.sci-input-container-v2 .sn-icon {
@apply m-2;
color: var(--sn-black)

174
app/controllers/gene_sequence_assets_controller.rb Normal file
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@ -0,0 +1,174 @@
# frozen_string_literal: true
class GeneSequenceAssetsController < ApplicationController
include ActiveStorage::SetCurrent
skip_before_action :verify_authenticity_token
before_action :check_open_vector_service_enabled, except: %i(new edit)
before_action :load_vars, except: %i(new create)
before_action :load_create_vars, only: %i(new create)
before_action :check_read_permission
before_action :check_manage_permission, only: %i(new update create)
def new
render :edit, layout: false
end
def edit
@file_url = rails_representation_url(@asset.file)
@file_name = @asset.render_file_name
log_activity('sequence_asset_edit_started')
render :edit, layout: false
end
def create
save_asset!
log_activity('sequence_asset_added')
head :ok
end
def update
save_asset!
log_activity('sequence_asset_edit_finished')
head :ok
end
def destroy
log_activity('sequence_asset_deleted')
head :ok
end
private
def save_asset!
ActiveRecord::Base.transaction do
ensure_asset!
@asset.file.purge
@asset.preview_image.purge
@asset.file.attach(
io: StringIO.new(params[:sequence_data].to_json),
filename: "#{params[:sequence_name]}.json"
)
@asset.preview_image.attach(
io: StringIO.new(Base64.decode64(params[:base64_image].split(',').last)),
filename: "#{params[:sequence_name]}.png"
)
file = @asset.file
file.blob.metadata['asset_type'] = 'gene_sequence'
file.blob.metadata['name'] = params[:sequence_name]
file.save!
@asset.view_mode ||= @parent.assets_view_mode
@asset.save!
end
end
def ensure_asset!
return if @asset
return unless @parent
@asset = @parent.assets.create!(last_modified_by: current_user, team: current_team)
end
def load_vars
@ove_enabled = OpenVectorEditorService.enabled?
@asset = current_team.assets.find_by(id: params[:id])
return render_404 unless @asset
@parent ||= @asset.step
@parent ||= @asset.result
case @parent
when Step
@protocol = @parent.protocol
when Result
@my_module = @parent.my_module
end
end
def load_create_vars
@ove_enabled = OpenVectorEditorService.enabled?
@parent = case params[:parent_type]
when 'Step'
Step.find_by(id: params[:parent_id])
when 'Result'
Result.find_by(id: params[:parent_id])
end
case @parent
when Step
@protocol = @parent.protocol
when Result
@result = @parent
end
end
def check_read_permission
case @parent
when Step
return render_403 unless can_read_protocol_in_module?(@protocol) ||
can_read_protocol_in_repository?(@protocol)
when Result
return render_403 unless can_read_my_module?(@my_module)
else
render_403
end
end
def check_manage_permission
render_403 unless asset_managable?
end
def check_open_vector_service_enabled
render_403 unless OpenVectorEditorService.enabled?
end
helper_method :asset_managable?
def asset_managable?
case @parent
when Step
can_manage_step?(@parent)
when Result
can_manage_my_module?(@parent)
else
false
end
end
def log_activity(type_of, project = nil, message_items = {})
return unless @parent.is_a?(Step)
my_module = @parent.my_module
default_items = {
protocol: @parent.protocol.id,
step: @parent.id,
asset_name: { id: @asset.id, value_for: 'file_name' },
step_position: { id: @parent.id, value_for: 'position_plus_one' }
}
if my_module
project = my_module.project
default_items[:my_module] = my_module.id
type_of = "task_#{type_of}".to_sym
else
type_of = "protocol_#{type_of}".to_sym
end
message_items = default_items.merge(message_items)
Activities::CreateActivityService.call(
activity_type: type_of,
owner: current_user,
team: @parent.protocol.team,
subject: @parent.protocol,
message_items: message_items,
project: project
)
end
end

8
app/controllers/global_activities_controller.rb
View file

@ -65,13 +65,17 @@ class GlobalActivitiesController < ApplicationController
end
def team_filter
render json: current_user.teams.ordered.global_activity_filter(activity_filters, params[:query])
teams = current_user.teams.ordered.global_activity_filter(activity_filters, params[:query])
render json: teams.select(:id, :name)
.map { |i| { value: i[:id], label: escape_input(i[:name]) } }
end
def user_filter
filter = activity_filters
filter = { subjects: { MyModule: [params[:my_module_id].to_i] } } if params[:my_module_id]
render json: current_user.global_activity_filter(filter, params[:query])
users = current_user.global_activity_filter(filter, params[:query])
render json: users.select(:full_name, :id)
.map { |i| { label: escape_input(i[:full_name]), value: i[:id] } }
end
def project_filter

6
app/controllers/protocols_controller.rb
View file

@ -697,6 +697,12 @@ class ProtocolsController < ApplicationController
asset_file_name = asset_guid.to_s + File.extname(asset.file_name).to_s
ostream.put_next_entry("#{step_dir}/#{asset_file_name}")
ostream.print(asset.file.download)
next unless asset.preview_image.attached?
asset_preview_image_name = asset_guid.to_s + File.extname(asset.preview_image_file_name).to_s
ostream.put_next_entry("#{step_dir}/previews/#{asset_preview_image_name}")
ostream.print(asset.preview_image.download)
end
end
ostream = step.tiny_mce_assets.save_to_eln(ostream, step_dir)

2
app/helpers/file_icons_helper.rb
View file

@ -40,6 +40,8 @@ module FileIconsHelper
image_link = 'icon_small/pptx_file.svg'
elsif asset.file.attached? && asset.file.metadata['asset_type'] == 'marvinjs'
image_link = 'icon_small/marvinjs_file.svg'
elsif asset.file.attached? && asset.file.metadata['asset_type'] == 'gene_sequence'
image_link = 'icon_small/sequence-editor.svg'
end
# Now check for custom mappings or possible overrides

2
app/javascript/packs/open_vector_editor.js Normal file
View file

@ -0,0 +1,2 @@
import '@teselagen/ove';
import '@teselagen/ove/style.css';

11
app/javascript/packs/vue/open_vector_editor.js Normal file
View file

@ -0,0 +1,11 @@
import TurbolinksAdapter from 'vue-turbolinks';
import Vue from 'vue/dist/vue.esm';
import OpenVectorEditor from '../../vue/ove/OpenVectorEditor.vue';
Vue.use(TurbolinksAdapter);
Vue.prototype.i18n = window.I18n;
new Vue({
el: '#open-vector-editor',
components: { OpenVectorEditor }
});

154
app/javascript/vue/ove/OpenVectorEditor.vue Normal file
View file

@ -0,0 +1,154 @@
<template>
<div class="ove-wrapper flex flex-col h-screen">
<div class="ove-header flex justify-between h-14 px-4 py-2">
<span class="file-name flex items-center ml-3 w-56">
<div class="sci-input-container-v2 w-full">
<input v-model="sequenceName"
class="sci-input-field"
type="text"
:disabled="readOnly"
:placeholder="i18n.t('open_vector_editor.sequence_name_placeholder')"/>
</div>
</span>
<div v-if="oveWarning" class="flex items-center">
<i class="mr-1 text-brand-warning sn-icon sn-icon-alert-warning"></i>
<p v-html="oveWarning" class="mb-0"></p>
</div>
<div class="ove-buttons text-sn-blue">
<button :style="{ pointerEvents: 'all' }" @click="saveAndClose" class="btn btn-light font-sans" :disabled="this.readOnly">
<i class="sn-icon sn-icon-save"></i>
{{ i18n.t('SaveClose') }}
</button>
<button @click="closeModal" class="preview-close btn btn-light icon-btn">
<i class="sn-icon sn-icon-close"></i>
</button>
</div>
</div>
<div ref="container" class="ove-container w-full h-full">
</div>
</div>
</template>
<script>
import axios from 'axios';
import { blobToBase64 } from '../shared/blobToBase64.js'
export default {
name: 'OpenVectorEditor',
props: {
fileUrl: { type: String },
fileName: { type: String },
updateUrl: { type: String },
canEditFile: { type: String },
oveWarning: { type: String }
},
data() {
return {
editor: null,
sequenceName: null,
closeAfterSave: false,
readOnly: this.canEditFile !== 'true'
}
},
mounted() {
let editorConfig = {
onSave: this.saveFile,
generatePng: true,
showMenuBar: true,
alwaysAllowSave: true,
menuFilter: this.menuFilter,
beforeReadOnlyChange: this.readOnlyHandler,
ToolBarProps: {
toolList: [
'saveTool',
'downloadTool',
{ name: 'importTool', tooltip: I18n.t('open_vector_editor.editor.tooltips.importTool'), disabled: this.readOnly },
'undoTool',
'redoTool',
'cutsiteTool',
'featureTool',
'partTool',
'oligoTool',
'orfTool',
// Hide allignment tool
// 'alignmentTool',
'editTool',
'findTool',
'visibilityTool'
]
}
}
if (this.readOnly) {
editorConfig = {
...editorConfig,
showReadOnly: false,
ToolBarProps: {
toolList: []
}
}
}
this.editor = window.createVectorEditor(this.$refs.container, editorConfig);
this.sequenceName = this.fileName;
if (this.fileUrl) {
this.loadFile();
} else {
this.editor.updateEditor(
{
sequenceData: { circular: true, name: this.sequenceName },
readOnly: this.readOnly
}
);
}
},
methods: {
loadFile() {
fetch(this.fileUrl).then((response) => response.json()).then(
(json) => this.editor.updateEditor(
{ sequenceData: json, readOnly: this.readOnly }
)
);
},
saveAndClose() {
this.closeAfterSave = true;
document.querySelector('[data-test=saveTool]').click()
},
saveFile(opts, sequenceDataToSave, editorState, onSuccessCallback) {
if (this.readOnly) return;
blobToBase64(opts.pngFile).then((base64image) => {
(this.fileUrl ? axios.patch : axios.post)(
this.updateUrl,
{
sequence_data: sequenceDataToSave,
sequence_name: this.sequenceName || this.i18n.t('open_vector_editor.default_sequence_name'),
base64_image: base64image
}
).then(() => {
parent.document.getElementById('iFrameModal').dispatchEvent(new Event('sequenceSaved'));
if (this.closeAfterSave) this.closeModal();
});
});
},
closeModal() {
if (parent !== window) {
parent.document.getElementById('iFrameModal').dispatchEvent(new Event('hide'));
}
},
menuFilter(menus) {
return menus.map(menu => {
if(menu.text !== 'Help') return menu;
const menuOverride = {
...menu,
submenu: menu.submenu.filter(item => item.cmd !== 'versionNumber')
}
return menuOverride;
});
},
readOnlyHandler(val) { this.readOnly = val; return true }
}
}
</script>

22
app/javascript/vue/protocol/attachments.vue
View file

@ -1,5 +1,5 @@
<template>
<div class="step-attachments">
<div class="step-attachments" v-if="attachments && attachments.length">
<div class="attachments-actions">
<div class="title">
<h3>{{ i18n.t('protocols.steps.files', {count: attachments.length}) }}</h3>
@ -27,6 +27,12 @@
{{ i18n.t('protocols.steps.attachments.menu.office_file') }}
</a>
</li>
<li v-if="step.attributes.open_vector_editor_context.new_sequence_asset_url">
<a @click="openOVEditor" class="open-vector-editor-button" tabindex="0" @keyup.enter="openOVEditor">
<img :src="step.attributes.open_vector_editor_context.icon"/>
{{ i18n.t('open_vector_editor.new_sequence_file') }}
</a>
</li>
<li v-if="step.attributes.marvinjs_enabled">
<a
class="new-marvinjs-upload-button"
@ -36,7 +42,7 @@
:data-sketch-container="`.attachments[data-step-id=${step.id}]`"
>
<span class="new-marvinjs-upload-icon">
<img :src="step.attributes.marvinjs_context.icon">
<i class="sn-icon sn-icon-marvinjs"></i>
</span>
{{ i18n.t('protocols.steps.attachments.menu.chemical_drawing') }}
</a>
@ -68,8 +74,9 @@
</div>
</div>
<div class="attachments">
<template v-for="(attachment, index) in attachmentsOrdered">
<template >
<component
v-for="(attachment, index) in attachmentsOrdered"
:is="attachment_view_mode(attachmentsOrdered[index])"
:key="attachment.id"
:attachment="attachment"
@ -150,6 +157,7 @@
}
},
mounted() {
this.initOVE(this);
this.initMarvinJS();
$(this.$refs.actionsDropdownButton).on('shown.bs.dropdown hidden.bs.dropdown', this.handleDropdownPosition);
},
@ -174,6 +182,11 @@
deleteAttachment(id) {
this.$emit('attachment:deleted', id)
},
initOVE(component) {
$(window.iFrameModal).on('sequenceSaved', function() {
component.$emit('attachment:uploaded');
});
},
initMarvinJS() {
// legacy logic from app/assets/javascripts/sitewide/marvinjs_editor.js
MarvinJsEditor.initNewButton(
@ -190,6 +203,9 @@
}
});
},
openOVEditor() {
window.showIFrameModal(this.step.attributes.open_vector_editor_context.new_sequence_asset_url);
},
handleDropdownPosition() {
this.$refs.actionsDropdownButton.classList.toggle("dropup", !this.isInViewport(this.$refs.actionsDropdown));
},

24
app/javascript/vue/protocol/step.vue
View file

@ -140,8 +140,8 @@
<div class="collapse in" :id="'stepBody' + step.id">
<div class="step-elements">
<div class="step-timestamp">{{ i18n.t('protocols.steps.timestamp', {date: step.attributes.created_at, user: step.attributes.created_by}) }}</div>
<template v-for="(element, index) in orderedElements">
<component
v-for="(element, index) in orderedElements"
:is="elements[index].attributes.orderable_type"
:key="index"
:element.sync="elements[index]"
@ -154,17 +154,16 @@
@reorder="openReorderModal"
@component:insert="insertElement"
/>
</template>
<Attachments v-if="attachments.length"
:step="step"
:attachments="attachments"
:attachmentsReady="attachmentsReady"
@attachments:openFileModal="showFileModal = true"
@attachment:deleted="attachmentDeleted"
@attachment:uploaded="loadAttachments"
@attachments:order="changeAttachmentsOrder"
@attachments:viewMode="changeAttachmentsViewMode"
@attachment:viewMode="updateAttachmentViewMode"/>
<Attachments
:step="step"
:attachments="attachments"
:attachmentsReady="attachmentsReady"
@attachments:openFileModal="showFileModal = true"
@attachment:deleted="attachmentDeleted"
@attachment:uploaded="loadAttachments"
@attachments:order="changeAttachmentsOrder"
@attachments:viewMode="changeAttachmentsViewMode"
@attachment:viewMode="updateAttachmentViewMode"/>
</div>
</div>
<deleteStepModal v-if="confirmingDelete" @confirm="deleteStep" @cancel="closeDeleteModal"/>
@ -308,7 +307,6 @@
$.get(this.urls.attachments_url, (result) => {
this.attachments = result.data
if (this.attachments.findIndex((e) => e.attributes.attached === false) >= 0) {
setTimeout(() => {
this.loadAttachments()

11
app/javascript/vue/protocol/step_attachments/context_menu.vue
View file

@ -20,6 +20,12 @@
{{ attachment.attributes.wopi_context.button_text }}
</a>
</li>
<li v-if="attachment.attributes.asset_type == 'gene_sequence' && attachment.attributes.urls.open_vector_editor_edit">
<a class="ove-edit-button" @click="openOVEditor(attachment.attributes.urls.open_vector_editor_edit)">
<span class="sn-icon sn-icon-sequence-editor"></span>
{{ i18n.t('open_vector_editor.edit_sequence') }}
</a>
</li>
<li v-if="attachment.attributes.asset_type == 'marvinjs' && attachment.attributes.urls.marvin_js_start_edit">
<a class="marvinjs-edit-button"
:data-sketch-id="attachment.id"
@ -28,7 +34,7 @@
:data-sketch-name="attachment.attributes.metadata.name"
:data-sketch-description="attachment.attributes.metadata.description"
>
<img :src="attachment.attributes.urls.marvin_js_icon"/>
<span class="sn-icon sn-icon-marvinjs"></span>
{{ i18n.t('assets.file_preview.edit_in_marvinjs') }}
</a>
</li>
@ -129,6 +135,9 @@
deleteAttachment() {
this.deleteModal = false
this.$emit('attachment:delete')
},
openOVEditor(url) {
window.showIFrameModal(url);
}
}
}

14
app/javascript/vue/protocol/step_attachments/file_modal.vue
View file

@ -34,7 +34,7 @@
{{ i18n.t("protocols.steps.attachments.file_modal.drag_zone_notification", {position: step.attributes.position + 1}) }}
</div>
</div>
<div class="divider" v-if="step.attributes.marvinjs_enabled || step.attributes.wopi_enabled">
<div class="divider" v-if="step.attributes.marvinjs_enabled || step.attributes.wopi_enabled || step.attributes.open_vector_editor_context.new_sequence_asset_url">
{{ i18n.t("protocols.steps.attachments.file_modal.or") }}
</div>
<div class="integrations-container">
@ -44,6 +44,12 @@
{{ i18n.t('assets.create_wopi_file.button_text') }}
</a>
</div>
<div class="integration-block" v-if="step.attributes.open_vector_editor_context.new_sequence_asset_url">
<a @click="openOVEditor" class="open-vector-editor-button btn btn-light">
<img :src="step.attributes.open_vector_editor_context.icon"/>
{{ i18n.t('open_vector_editor.new_sequence') }}
</a>
</div>
<div class="integration-block marvinjs" v-if="step.attributes.marvinjs_enabled">
<a
class="new-marvinjs-upload-button btn btn-light"
@ -57,7 +63,7 @@
<span class="new-marvinjs-upload-icon">
<img :src="step.attributes.marvinjs_context.icon"/>
</span>
{{ i18n.t('marvinjs.new_button') }}
{{ i18n.t('marvinjs.new_li_button') }}
</a>
</div>
</div>
@ -148,6 +154,10 @@
HelperModule.flashAlertMsg(this.i18n.t('errors.general'), 'danger');
}
});
},
openOVEditor() {
$(this.$refs.modal).modal('hide');
window.showIFrameModal(this.step.attributes.open_vector_editor_context.new_sequence_asset_url);
}
}
}

1
app/javascript/vue/protocol/step_attachments/list.vue
View file

@ -2,6 +2,7 @@
<div class="list-attachment-container asset"
:data-asset-id="attachment.id"
>
<div v-html="attachment.attributes.icon"></div>
<i class="fas asset-icon" :class="attachment.attributes.icon"></i>
<a :href="attachment.attributes.urls.blob"
class="file-preview-link file-name"

8
app/javascript/vue/protocol/step_attachments/thumbnail.vue
View file

@ -10,13 +10,15 @@
:data-gallery-view-id="stepId"
:data-preview-url="attachment.attributes.urls.preview"
>
<div class="attachment-preview" :class= "attachment.attributes.asset_type">
<img v-if="attachment.attributes.medium_preview !== null"
<div v-if="attachment.attributes.medium_preview" class="attachment-preview" :class= "attachment.attributes.asset_type">
<img
:src="attachment.attributes.medium_preview"
@error="ActiveStoragePreviews.reCheckPreview"
@load="ActiveStoragePreviews.showPreview"
style='opacity: 0' />
<i v-else class="fas" :class="attachment.attributes.icon"></i>
</div>
<div v-else class="attachment-preview flex">
<span class="fa fa-paperclip m-auto text-4xl"></span>
</div>
<div class="attachment-label"
data-toggle="tooltip"

1
app/javascript/vue/protocol/step_elements/table.vue
View file

@ -237,6 +237,7 @@
setTimeout(this.updateTable, 100) // delay makes cancel button work
}
});
this.$nextTick(this.tableObject.render);
}
}
}

4
app/javascript/vue/protocol_import/file_import_modal.vue
View file

@ -9,10 +9,6 @@
<div class="modal-body text-xs" v-html="i18n.t(`protocols.import_modal.${state}.body_html`, { url: protocolUrl })">
</div>
<div class="modal-footer">
<button type="button"
class="btn btn-default"
data-dismiss="modal">{{ i18n.t('protocols.import_modal.cancel') }}</button>
<button v-if="state === 'confirm'" type="button"
class="btn btn-primary"
@click.stop.prevent="confirm">{{ i18n.t('protocols.import_modal.import') }}</button>

9
app/javascript/vue/shared/blobToBase64.js Normal file
View file

@ -0,0 +1,9 @@
export function blobToBase64(blob) {
const reader = new FileReader();
reader.readAsDataURL(blob);
return new Promise(resolve => {
reader.onloadend = () => {
resolve(reader.result);
};
});
}

32
app/models/asset.rb
View file

@ -17,6 +17,7 @@ class Asset < ApplicationRecord
# ActiveStorage configuration
has_one_attached :file
has_one_attached :file_pdf_preview
has_one_attached :preview_image
# Asset validation
# This could cause some problems if you create empty asset and want to
@ -165,17 +166,21 @@ class Asset < ApplicationRecord
end
def previewable?
return false unless file.attached?
return false unless preview_image.attached? || file.attached?
previewable_document?(blob) || previewable_image?
end
def preview_attachment
preview_image.attached? ? preview_image : file
end
def medium_preview
file.representation(resize_to_limit: Constants::MEDIUM_PIC_FORMAT)
preview_attachment.representation(resize_to_limit: Constants::MEDIUM_PIC_FORMAT)
end
def large_preview
file.representation(resize_to_limit: Constants::LARGE_PIC_FORMAT)
preview_attachment.representation(resize_to_limit: Constants::LARGE_PIC_FORMAT)
end
def file_name
@ -184,6 +189,12 @@ class Asset < ApplicationRecord
file.blob&.filename&.sanitized
end
def preview_image_file_name
return '' unless preview_image.attached?
preview_image.blob&.filename&.sanitized
end
def render_file_name
if file.attached? && file.metadata['asset_type']
file.metadata['name']
@ -221,6 +232,18 @@ class Asset < ApplicationRecord
to_blob = ActiveStorage::Blob.create_and_upload!(io: tmp_file, filename: blob.filename, metadata: blob.metadata)
to_asset.file.attach(to_blob)
end
if preview_image.attached?
preview_image.blob.open do |tmp_preview_image|
to_blob = ActiveStorage::Blob.create_and_upload!(
io: tmp_preview_image,
filename: blob.filename,
metadata: blob.metadata
)
to_asset.preview_image.attach(to_blob)
end
end
to_asset.post_process_file(to_asset.team)
end
@ -449,7 +472,8 @@ class Asset < ApplicationRecord
end
def previewable_image?
file.blob&.content_type =~ %r{^image/#{Regexp.union(Constants::WHITELISTED_IMAGE_TYPES)}}
preview_image.attached? ||
file.blob&.content_type =~ %r{^image/#{Regexp.union(Constants::WHITELISTED_IMAGE_TYPES)}}
end
def step_or_result_or_repository_asset_value

47
app/models/concerns/team_by_subject_model.rb
View file

@ -1,47 +0,0 @@
# frozen_string_literal: true
module TeamBySubjectModel
extend ActiveSupport::Concern
class_methods do
def team_by_subject(subjects)
teams = []
valid_subjects = Extends::ACTIVITY_SUBJECT_CHILDREN
# Check all activity subject
valid_subjects.each do |subject, _children|
subject = subject.to_s.camelize.to_sym
next unless subjects[subject]
parent_array = [subject.to_s.underscore]
find_parent = true
# Trying to build parent array
while find_parent
possible_parent = valid_subjects.find { |_sub, ch| ((ch || []).include? parent_array[-1].pluralize.to_sym) }
possible_parent = { Project: nil } if parent_array[-1] == 'experiment'
if possible_parent
parent_array.push(possible_parent.flatten[0].to_s.underscore)
else
find_parent = false
end
end
# Remove initial object from parent array
parent_array.shift
subjects[subject].each do |child|
child_subject = subject.to_s.constantize.find_by_id(child)
next unless child_subject
# Call all parent subjects
parent_array.each do |parent|
temp_child_subject = child_subject.public_send(parent)
# Some fix for protocols in repository
break unless temp_child_subject
child_subject = temp_child_subject
end
teams.push(child_subject.team_id)
end
end
teams.uniq
end
end
end

1
app/models/repository_row.rb
View file

@ -11,6 +11,7 @@ class RepositoryRow < ApplicationRecord
include PrefixedIdModel
belongs_to :repository, class_name: 'RepositoryBase'
delegate :team, to: :repository
belongs_to :parent, class_name: 'RepositoryRow', optional: true
belongs_to :created_by, foreign_key: :created_by_id, class_name: 'User'
belongs_to :last_modified_by, foreign_key: :last_modified_by_id, class_name: 'User'

1
app/models/result.rb
View file

@ -14,6 +14,7 @@ class Result < ApplicationRecord
belongs_to :archived_by, foreign_key: 'archived_by_id', class_name: 'User', optional: true
belongs_to :restored_by, foreign_key: 'restored_by_id', class_name: 'User', optional: true
belongs_to :my_module, inverse_of: :results
delegate :team, to: :my_module
has_one :result_asset, inverse_of: :result, dependent: :destroy
has_one :asset, through: :result_asset
has_one :result_table, inverse_of: :result, dependent: :destroy

8
app/models/settings.rb
View file

@ -1,14 +1,18 @@
# frozen_string_literal: true
class Settings < ApplicationRecord
attr_accessor :merged_values
before_validation -> { self.values = merged_values || values }
def self.instance
first || new
end
def values
merged_values = super
self.merged_values ||= super
self.class.instance_methods(false).grep(/^load_values_from_[A-Z0-9_]*/).each do |method|
merged_values = merged_values.merge(public_send(method))
self.merged_values = self.merged_values.merge(public_send(method))
end
merged_values
end

1
app/models/step.rb
View file

@ -32,6 +32,7 @@ class Step < ApplicationRecord
belongs_to :user, inverse_of: :steps
belongs_to :last_modified_by, foreign_key: 'last_modified_by_id', class_name: 'User', optional: true
belongs_to :protocol, inverse_of: :steps
delegate :team, to: :protocol
has_many :step_orderable_elements, inverse_of: :step, dependent: :destroy
has_many :checklists, inverse_of: :step, dependent: :destroy
has_many :step_comments, foreign_key: :associated_id, dependent: :destroy

19
app/models/team.rb
View file

@ -5,7 +5,6 @@ class Team < ApplicationRecord
include ViewableModel
include Assignable
include PermissionCheckableModel
include TeamBySubjectModel
include TinyMceImages
# Not really MVC-compliant, but we just use it for logger
@ -169,14 +168,26 @@ class Team < ApplicationRecord
ProtocolKeyword.where(team: self).pluck(:name)
end
def self.by_activity_subjects(subjects)
team_ids = []
valid_subjects = subjects.select { |k| Extends::SEARCHABLE_ACTIVITY_SUBJECT_TYPES.include?(k.to_s) }
valid_subjects.each do |subject_name, subject_id|
subject = subject_name.to_s.constantize.find_by(id: subject_id)
next if subject.blank?
team_ids << subject.team.id
end
where(id: team_ids.uniq)
end
def self.global_activity_filter(filters, search_query)
query = where('name ILIKE ?', "%#{search_query}%")
query = where_attributes_like(:name, search_query)
if filters[:users]
user_teams = User.where(id: filters[:users]).joins(:teams).group(:team_id).select(:team_id)
query = query.where(id: user_teams)
end
query = query.where(id: team_by_subject(filters[:subjects])) if filters[:subjects]
query.select(:id, :name).map { |i| { value: i[:id], label: ApplicationController.helpers.escape_input(i[:name]) } }
query = query.by_activity_subjects(filters[:subjects]) if filters[:subjects].present?
query
end
def self.search_by_object(obj)

9
app/models/user.rb
View file

@ -4,7 +4,6 @@ class User < ApplicationRecord
include SearchableModel
include SettingsModel
include VariablesModel
include TeamBySubjectModel
include InputSanitizeHelper
include ActiveStorageConcerns
@ -581,13 +580,11 @@ class User < ApplicationRecord
end
def global_activity_filter(filters, search_query)
query_teams = teams.pluck(:id)
query_teams &= filters[:teams].map(&:to_i) if filters[:teams]
query_teams &= User.team_by_subject(filters[:subjects]) if filters[:subjects]
query_teams = teams
query_teams = query_teams.where(id: filters[:teams].map(&:to_i)) if filters[:teams].present?
query_teams = query_teams.by_activity_subjects(filters[:subjects]) if filters[:subjects].present?
User.where(id: UserAssignment.where(assignable_id: query_teams, assignable_type: 'Team').select(:user_id))
.search(false, search_query)
.select(:full_name, :id)
.map { |i| { label: escape_input(i[:full_name]), value: i[:id] } }
end
def file_name

5
app/serializers/asset_serializer.rb
View file

@ -14,11 +14,11 @@ class AssetSerializer < ActiveModel::Serializer
:updated_at, :metadata, :image_editable, :image_context, :pdf, :attached
def icon
file_fa_icon_class(object)
file_extension_icon_html(object)
end
def file_name
escape_input(object.render_file_name)
object.render_file_name
end
def updated_at
@ -127,6 +127,7 @@ class AssetSerializer < ActiveModel::Serializer
delete: asset_destroy_path(object)
)
end
urls[:open_vector_editor_edit] = edit_gene_sequence_asset_path(object.id) if can_manage_asset?(user, object)
urls[:wopi_action] = object.get_action_url(user, 'embedview') if wopi && can_manage_asset?(user, object)
urls[:blob] = rails_blob_path(object.file, disposition: 'attachment') if object.file.attached?

12
app/serializers/step_serializer.rb
View file

@ -9,7 +9,8 @@ class StepSerializer < ActiveModel::Serializer
attributes :name, :position, :completed, :attachments_manageble, :urls, :assets_view_mode,
:marvinjs_enabled, :marvinjs_context, :created_by, :created_at, :assets_order,
:wopi_enabled, :wopi_context, :comments_count, :unseen_comments, :storage_limit
:wopi_enabled, :wopi_context, :comments_count, :unseen_comments, :storage_limit,
:open_vector_editor_context
def marvinjs_enabled
MarvinJsService.enabled?
@ -24,6 +25,15 @@ class StepSerializer < ActiveModel::Serializer
end
end
def open_vector_editor_context
if can_manage_step?(object)
{
new_sequence_asset_url: new_gene_sequence_asset_url(parent_type: 'Step', parent_id: object.id),
icon: image_path('icon_small/sequence-editor.svg')
}
end
end
def comments_count
object.comments.count
end

9
app/services/open_vector_editor_service.rb Normal file
View file

@ -0,0 +1,9 @@
# frozen_string_literal: true
class OpenVectorEditorService
class << self
def enabled?
ENV.fetch('SCINOTE_OVE_ENABLED') == 'true'
end
end
end

8
app/services/reports/docx/draw_result_table.rb
View file

@ -9,8 +9,8 @@ module Reports::Docx::DrawResultTable
table_data = JSON.parse(table.contents_utf_8)['data']
table_data = obj.add_headers_to_table(table_data, false)
if table.metadata.present?
table.metadata['cells']&.each do |cell|
if table.metadata.present? && table.metadata['cells'].is_a?(Array)
table.metadata['cells'].each do |cell|
next unless cell['row'].present? && cell['col'].present?
row_index = cell['row'].to_i + 1
@ -27,8 +27,8 @@ module Reports::Docx::DrawResultTable
cell_style rows[0], bold: true, background: color[:concrete]
cell_style cols[0], bold: true, background: color[:concrete]
if table.metadata.present?
table.metadata['cells']&.each do |cell|
if table.metadata.present? && table.metadata['cells'].is_a?(Array)
table.metadata['cells'].each do |cell|
next unless cell.present? && cell['row'].present? && cell['col'].present? && cell['className'].present?
cell_style rows.dig(cell['row'].to_i + 1, cell['col'].to_i + 1),

8
app/services/reports/docx/draw_step_table.rb
View file

@ -8,8 +8,8 @@ module Reports::Docx::DrawStepTable
table_data = JSON.parse(table.contents_utf_8)['data']
table_data = obj.add_headers_to_table(table_data, table_type == 'step_well_plates_table')
if table.metadata.present?
table.metadata['cells']&.each do |cell|
if table.metadata.present? && table.metadata['cells'].is_a?(Array)
table.metadata['cells'].each do |cell|
next unless cell['row'].present? && cell['col'].present?
row_index = cell['row'].to_i + 1
@ -26,8 +26,8 @@ module Reports::Docx::DrawStepTable
cell_style rows[0], bold: true, background: color[:concrete]
cell_style cols[0], bold: true, background: color[:concrete]
if table.metadata.present?
table.metadata['cells']&.each do |cell|
if table.metadata.present? && table.metadata['cells'].is_a?(Array)
table.metadata['cells'].each do |cell|
data = cell[1]
next unless data.present? && data['row'].present? && data['col'].present? && data['className'].present?

5
app/utilities/protocols_importer_v2.rb
View file

@ -115,6 +115,11 @@ class ProtocolsImporterV2
filename: asset_json['fileName'],
content_type: asset_json['fileType'],
metadata: JSON.parse(asset_json['fileMetadata'] || '{}'))
if asset_json['preview_image'].present?
asset.preview_image.attach(io: StringIO.new(Base64.decode64(asset_json.dig('preview_image', 'bytes'))),
filename: asset_json.dig('preview_image', 'fileName'))
end
asset.save!
asset_ids << asset.id

30
app/views/gene_sequence_assets/edit.html.erb Normal file
View file

@ -0,0 +1,30 @@
<html>
<head>
<%= csp_meta_tag %>
<%= javascript_include_tag 'i18n_bundle' %>
<%= stylesheet_link_tag 'sn_icon_font' %>
<%= stylesheet_link_tag 'application' %>
<%= stylesheet_link_tag 'tailwind' %>
<%= stylesheet_link_tag 'open_vector_editor' %>
<style>
body {
margin: 0;
}
</style>
</head>
<body>
<% if @ove_enabled %>
<div id="open-vector-editor" data-behaviour="vue">
<open-vector-editor
file-url="<%= @file_url %>"
file-name="<%= @file_name %>"
update-url="<%= @asset ? gene_sequence_asset_url(@asset) : gene_sequence_assets_url(parent_type: params[:parent_type], parent_id: params[:parent_id]) %>"
can-edit-file="<%= asset_managable? %>"
ove-warning="<%= defined?(@warnings) ? @warnings : '' %>"
/>
</div>
<%= javascript_include_tag 'open_vector_editor' %>
<%= javascript_include_tag 'vue_components_open_vector_editor' %>
<% end %>
</body>
</html>

1
app/views/layouts/application.html.erb
View file

@ -109,6 +109,7 @@
<%= render "shared/file_preview/modal" %>
<%= render "shared/file_edit_modal" %>
<%= render "shared/marvinjs_modal" %>
<%= render "shared/iframe_modal" %>
<%= render "users/sessions/session_expire_modal" %>
<%= render "users/sessions/session_end_modal" %>
<%= render "label_printers/label_printer_modal" %>

4
app/views/my_module_tags/_index_edit.html.erb
View file

@ -68,9 +68,7 @@
:name,
{},
{ class: 'selectpicker' }) %>
<%= f.button class: 'btn btn-primary' do %>
<span><%= t("experiments.canvas.modal_manage_tags.create") %></span>
<% end %>
<%= f.submit t("experiments.canvas.modal_manage_tags.create"), class: 'btn btn-primary' %>
</div>
</div>
<% end %>

2
app/views/my_modules/modals/_new_modal.html.erb
View file

@ -80,7 +80,7 @@
<button type="button" class="btn btn-secondary" data-dismiss="modal">
<%= t('general.cancel') %>
</button>
<%= f.button t('experiments.canvas.new_my_module_modal.create'), class: "btn btn-primary" %>
<%= f.submit t('experiments.canvas.new_my_module_modal.create'), class: "btn btn-primary" %>
</div>
</div>
</div>

2
app/views/projects/index/modals/_new_project.html.erb
View file

@ -40,7 +40,7 @@
</div>
<div class="modal-footer">
<button type="button" class="btn btn-secondary" data-dismiss="modal"><%= t('general.cancel') %></button>
<%= f.button t('projects.index.modal_new_project.create'), class: "btn btn-primary" %>
<%= f.submit t('projects.index.modal_new_project.create'), class: "btn btn-primary" %>
</div>
</div>
</div>

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

@ -41,7 +41,7 @@
</div>
<div class="modal-footer">
<button type="button" class="btn btn-secondary" data-dismiss="modal"><%= t('general.cancel') %></button>
<%= f.button t("protocols.new_protocol_modal.create_#{type}") , class: "btn btn-primary create-protocol-button" %>
<%= f.submit t("protocols.new_protocol_modal.create_#{type}") , class: "btn btn-primary create-protocol-button" %>
</div>
</div>
</div>

3
app/views/result_assets/_edit.html.erb
View file

@ -17,8 +17,7 @@
<button type="button" class="btn btn-secondary cancel-edit">
<%= t("general.cancel")%>
</button>
<%= f.button t("general.save"),
class: 'btn btn-primary save-result' %>
<%= f.submit t("general.save"), class: 'btn btn-primary save-result' %>
</div>
<% end %>
</div>

3
app/views/result_tables/_edit.html.erb
View file

@ -18,8 +18,7 @@
<button type="button" class="btn btn-secondary cancel-edit">
<%= t("general.cancel")%>
</button>
<%= f.button t("general.save"),
class: 'btn btn-primary save-result' %>
<%= f.submit t("general.save"), class: 'btn btn-primary save-result' %>
</div>
<% end %>
</div>

3
app/views/result_tables/_new.html.erb
View file

@ -17,8 +17,7 @@
<button type="button" class="btn btn-secondary cancel-new">
<%= t("general.cancel")%>
</button>
<%= f.button t("result_tables.new.create"),
class: 'btn btn-primary save-result' %>
<%= f.submit t("result_tables.new.create"), class: 'btn btn-primary save-result' %>
</div>
<% end %>
</div>

3
app/views/result_texts/_edit.html.erb
View file

@ -19,8 +19,7 @@
<button type="button" class="btn btn-secondary cancel-edit">
<%= t("general.cancel")%>
</button>
<%= f.button t("general.save"),
class: 'btn btn-primary save-result' %>
<%= f.submit t("general.save"), class: 'btn btn-primary save-result' %>
</div>
<% end %>
</div>

3
app/views/result_texts/_new.html.erb
View file

@ -18,8 +18,7 @@
<button type="button" class="btn btn-secondary cancel-new">
<%= t("general.cancel")%>
</button>
<%= f.button t("result_texts.new.create"),
class: 'btn btn-primary save-result' %>
<%= f.submit t("result_texts.new.create"), class: 'btn btn-primary save-result' %>
</div>
<% end %>
</div>

4
app/views/search/results/_assets.html.erb
View file

@ -1,7 +1,9 @@
<% @asset_results.each do |asset| %>
<h5>
<h5 class="flex flex-row flex-nowrap items-center gap-1">
<% if asset.blob.metadata["asset_type"] == 'marvinjs' %>
<span class="mce-i-marvinjs"></span>
<% elsif asset.blob.metadata["asset_type"] == 'gene_sequence' %>
<span class="sn-file-ove"></span>
<% else %>
<% if wopi_file?(asset) %>
<%= file_extension_icon(asset) %>

2
app/views/shareable_links/my_module_results_show.html.erb
View file

@ -6,7 +6,7 @@
</span>
</div>
<div class="my-5 flex-1 bg-sn-white">
<div class="my-5 max-w-4xl flex-1 bg-sn-white">
<div class="content-pane flexible">
<%= render partial: 'shareable_links/my_modules/header_actions' %>
<div class="px-4">

4
app/views/shareable_links/my_modules/results/_comments_list.html.erb
View file

@ -2,13 +2,13 @@
<div class="comment-container">
<div class="avatar-placehodler">
<span class='global-avatar-container'>
<%= image_tag avatar_path(comment.user, :icon_small), class: 'avatar' %>
<%= image_tag user_avatar_absolute_url(comment.user, :icon_small, true), class: 'user-avatar' %>
</span>
</div>
<div class="content-placeholder">
<div class="comment-name"><%= comment.user.full_name %></div>
<div class="comment-right !w-fit">
<div class="comment-datetime !w-fit"><%= comment.created_at.iso8601 %></div>
<div class="comment-datetime !w-fit"><%= l(comment.created_at, format: :full) %></div>
</div>
<div class="comment-message">
<div class="view-mode"><%= smart_annotation_text(comment.message) %></div>

2
app/views/shareable_links/my_modules/step_elements/_table.html.erb
View file

@ -4,7 +4,7 @@
<% if element.name.present? %>
<div class="step-element-name">
<%= render partial: "shareable_links/my_modules/inline_view", locals: { text: element.name, smart_annotation_enabled: false } %>
</div>
</div>
<% end %>
</div>
<div class="step-table view locked" tabindex="0">

3
app/views/shared/_iframe_modal.html.erb Normal file
View file

@ -0,0 +1,3 @@
<div id="iFrameModal" class="fixed top-0 left-0 right-0 z-[2000] w-full h-full bg-sn-white hidden">
<iframe id="iFrameModalFrame" class="w-full h-full border-0"></iframe>
</div>

12
app/views/shared/file_preview/_content.html.erb
View file

@ -22,6 +22,14 @@
<%= t('assets.file_preview.edit_in_marvinjs') %>
</button>
<% elsif asset.blob.metadata["asset_type"] == 'gene_sequence' %>
<button class="btn btn-light gene-sequence-edit-button"
data-sequence-edit-url="<%= edit_gene_sequence_asset_path(asset) %>"
>
<span class="sn-icon sn-icon-sequence-editor"></span>
<%= t('open_vector_editor.edit_sequence') %>
</button>
<% elsif asset.editable_image? %>
<button class="btn btn-light image-edit-button"
data-image-id="<%= asset.id %>"
@ -54,8 +62,8 @@
<%= render partial: 'shared/pdf_viewer', locals: { asset: asset, report_document: false } %>
<% else %>
<%= image_tag asset.large_preview,
class: 'asset-image',
style: 'opacity: 0' %>
class: class_names('asset-image', 'gene-sequence-asset': asset.blob&.metadata["asset_type"] == 'gene_sequence'),
style: 'opacity: 0' %>
<% end %>
<% else %>
<%= render partial: 'shared/file_preview/file_icon', locals: { asset: asset } %>

6
config/initializers/assets.rb
View file

@ -131,5 +131,11 @@ Rails.application.config.assets.precompile += %w(big.min.js)
# JQuery related includes
Rails.application.config.assets.precompile += %w(jquery_bundle.js)
# Separate icon font file
Rails.application.config.assets.precompile += %w(sn_icon_font.css)
# Separate translations file
Rails.application.config.assets.precompile += %w(i18n_bundle.js)
# Add stuff installed by yarn
Rails.application.config.assets.paths << Rails.root.join('node_modules')

14
config/initializers/extends.rb
View file

@ -449,7 +449,15 @@ class Extends
team_sharing_tasks_disabled: 245,
task_link_sharing_enabled: 246,
task_link_sharing_disabled: 247,
shared_task_message_edited: 248
shared_task_message_edited: 248,
task_sequence_asset_added: 249,
task_sequence_asset_edit_started: 250,
task_sequence_asset_edit_finished: 251,
task_sequence_asset_deleted: 252,
protocol_sequence_asset_added: 253,
protocol_sequence_asset_edit_started: 254,
protocol_sequence_asset_edit_finished: 255,
protocol_sequence_asset_deleted: 256
}
ACTIVITY_GROUPS = {
@ -458,7 +466,7 @@ class Extends
task: [8, 58, 9, 59, *10..14, 35, 36, 37, 53, 54, *60..63, 138, 139, 140, 64, 66, 106, 126, 120, 132,
*146..148, 166, 246, 247, 248],
task_protocol: [15, 22, 16, 18, 19, 20, 21, 17, 38, 39, 100, 111, 45, 46, 47, 121, 124, 115, 118, 127, 130, 137,
217, 168, 171, 177, 184, 185, 188, 189, *192..203, 222, 224, 225, 226, 236],
217, 168, 171, 177, 184, 185, 188, 189, *192..203, 222, 224, 225, 226, 236, *249..252],
task_inventory: [55, 56, 146, 147, 183],
experiment: [*27..31, 57, 141, 165],
reports: [48, 50, 49, 163, 164],
@ -466,7 +474,7 @@ class Extends
78, 96, 107, 113, 114, *133..136, 180, 181, 182],
protocol_repository: [80, 103, 89, 87, 79, 90, 91, 88, 85, 86, 84, 81, 82,
83, 101, 112, 123, 125, 117, 119, 129, 131, 170, 173, 179, 187, 186,
190, 191, *204..215, 220, 221, 223, 227, 228, 229, *230..235, *237..240],
190, 191, *204..215, 220, 221, 223, 227, 228, 229, *230..235, *237..240, *253..256],
team: [92, 94, 93, 97, 104, 244, 245],
label_templates: [*216..219]
}

19
config/locales/en.yml
View file

@ -2696,9 +2696,9 @@ en:
body_html: "The process of importing has started. Please wait..."
not_yet_done:
title: "Importing in progress"
body_html: "The import is taking longer than expected. You'll get a notice in <i class=\"sn-icon sn-icon-notifications\"></i> Notifications when your protocol template is ready. You can close the window and continue with your work."
body_html: "The import is taking longer than expected. You'll get a notice in Notifications when your protocol template is ready. You can close the window and continue with your work."
done:
title: "Importing completed"
title: "Importing finished"
body_html: 'The protocol has been successfully imported. You can access the draft of protocol template <a href="%{url}">here.</a>'
failed:
title: "Import failed"
@ -3097,7 +3097,7 @@ en:
drag_zone_title: "Upload a file from your PC"
drag_zone_description: "You can also drag & drop files to here or into steps to upload"
drag_zone_notification: "Drop files to add to step %{position}"
or: "OR"
or: "or create new"
new:
description: 'New'
uploading: 'Uploading'
@ -3277,7 +3277,7 @@ en:
wopi_supported_table_formats_title: 'Only .xlsx, .xlsm, .xlsb, .ods file formats are supported for editing in Excel Online.'
wopi_supported_presentation_formats_title: 'Only .pptx, ppsx, .odp file formats are supported for editing in PowerPoint Online.'
create_wopi_file:
button_text: 'Create an MS Office file'
button_text: 'MS Office file'
li_text: "Office file"
modal_title: 'Create new Microsoft Office Online document'
text_field_label: 'Document name'
@ -3701,9 +3701,18 @@ en:
new_li_button: "Chemical drawing"
structure_placeholder: "Click here to enter Chemical Drawing name"
modal_name_title: "Chemical Drawing name:"
checmical_drawing: "Chemical drawings"
chemical_drawing: "Chemical drawings"
no_sketches_found: "No Sketches Found"
open_vector_editor:
new_sequence: "Sequence"
new_sequence_file: "New sequence"
default_sequence_name: "New sequence"
edit_sequence: "Edit in Sequence editor"
sequence_name_placeholder: "Click here to enter sequence name"
editor:
tooltips:
importTool: "Click or drag to import and view files (.fasta .gb .dna .json)"
pdf_preview:
fit_to_screen: 'Fit to screen'
pages:

16
config/locales/global_activities/en.yml
View file

@ -273,6 +273,14 @@ en:
task_link_sharing_enabled_html: "%{user} enabled link sharing for task %{my_module}."
task_link_sharing_disabled_html: "%{user} disabled link sharing for task %{my_module}."
shared_task_message_edited_html: "%{user} edited message for shared task %{my_module}."
task_sequence_asset_added_html: "%{user} created sequence <strong>%{asset_name}</strong> on protocol’s step <strong>%{step_position}</strong> <strong>%{step}</strong> on task <strong>%{my_module}</strong>."
task_sequence_asset_edit_started_html: "%{user} edited sequence <strong>%{asset_name}</strong> on protocol’s step <strong>%{step_position}</strong> <strong>%{step}</strong> on task <strong>%{my_module}</strong>: editing started."
task_sequence_asset_edit_finished_html: "%{user} edited sequence <strong>%{asset_name}</strong> on protocol’s step <strong>%{step_position}</strong> <strong>%{step}</strong> on task <strong>%{my_module}</strong>: editing finished."
task_sequence_asset_deleted_html: "%{user} deleted sequence <strong>%{asset_name}</strong> on protocol’s step <strong>%{step_position}</strong> <strong>%{step}</strong> on task <strong>%{my_module}</strong>."
protocol_sequence_asset_added_html: "%{user} created sequence <strong>%{asset_name}</strong> on protocol’s step <strong>%{step_position}</strong> <strong>%{step}</strong> in Protocol repository."
protocol_sequence_asset_edit_started_html: "%{user} edited sequence <strong>%{asset_name}</strong> on protocol’s step <strong>%{step_position}</strong> <strong>%{step}</strong> in Protocol repository: editing started."
protocol_sequence_asset_edit_finished_html: "%{user} edited sequence <strong>%{asset_name}</strong> on protocol’s step <strong>%{step_position}</strong> <strong>%{step}</strong> in Protocol repository: editing finished."
protocol_sequence_asset_deleted_html: "%{user} deleted sequence <strong>%{asset_name}</strong> on protocol’s step <strong>%{step_position}</strong> <strong>%{step}</strong> in Protocol repository."
activity_name:
create_project: "Project created"
rename_project: "Project renamed"
@ -500,6 +508,14 @@ en:
task_link_sharing_enabled: "Task link sharing enabled"
task_link_sharing_disabled: "Task link sharing disabled"
shared_task_message_edited: "Shared task message edited"
task_sequence_asset_added: "Task sequence asset added"
task_sequence_asset_edit_started: "Task sequence asset editing started"
task_sequence_asset_edit_finished: "Task sequence asset editing finished"
task_sequence_asset_deleted: "Task sequence asset deleted"
protocol_sequence_asset_added: "Protocol sequence asset added"
protocol_sequence_asset_edit_started: "Protocol sequence asset editing started"
protocol_sequence_asset_edit_finished: "Protocol sequence asset editing finished"
protocol_sequence_asset_deleted: "Protocol sequence asset deleted"
activity_group:
projects: "Projects"
task_results: "Task results"

2
config/routes.rb
View file

@ -991,4 +991,6 @@ Rails.application.routes.draw do
get 'wopi/files/:id', to: 'wopi#file_get_endpoint', as: 'wopi_rest_endpoint'
post 'wopi/files/:id', to: 'wopi#post_file_endpoint'
end
resources :gene_sequence_assets, only: %i(new create edit update)
end

5
config/tailwind.config.js
View file

@ -19,7 +19,10 @@ module.exports = {
},
colors: {
transparent: 'transparent',
current: 'currentColor'
current: 'currentColor',
'brand-warning': '#f0ad4e',
'sn-blue': '#104DA9',
'sn-grey': '#98a2b3'
}
}
},

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

@ -16,6 +16,7 @@ const entryList = {
emoji_button: './app/javascript/packs/emoji_button.js',
fontawesome: './app/javascript/packs/fontawesome.scss',
prism: './app/javascript/packs/prism.js',
open_vector_editor: './app/javascript/packs/open_vector_editor.js',
tiny_mce: './app/javascript/packs/tiny_mce.js',
tiny_mce_styles: './app/javascript/packs/tiny_mce_styles.scss',
tui_image_editor: './app/javascript/packs/tui_image_editor.js',
@ -36,8 +37,9 @@ const entryList = {
vue_share_task_container: './app/javascript/packs/vue/share_task_container.js',
vue_navigation_top_menu: './app/javascript/packs/vue/navigation/top_menu.js',
vue_navigation_navigator: './app/javascript/packs/vue/navigation/navigator.js',
vue_navigation_breadcrumbs: './app/javascript/packs/vue/navigation/breadcrumbs.js',
vue_components_action_toolbar: './app/javascript/packs/vue/action_toolbar.js',
vue_components_open_vector_editor: './app/javascript/packs/vue/open_vector_editor.js',
vue_navigation_breadcrumbs: './app/javascript/packs/vue/navigation/breadcrumbs.js',
vue_protocol_file_import_modal: './app/javascript/packs/vue/protocol_file_import_modal.js'
}

2
package.json
View file

@ -49,8 +49,10 @@
"@babel/preset-env": "^7.20.2",
"@fortawesome/fontawesome-free": "^5.2.0",
"@joeattardi/emoji-button": "^4.6.2",
"@teselagen/ove": "^0.3.15",
"ajv": "6.12.6",
"autoprefixer": "10.4.14",
"axios": "^1.4.0",
"babel-loader": "^8.2.5",
"babel-plugin-macros": "^3.1.0",
"bootstrap": "^3.4.1",

10
public/images/icon_small/sequence-editor.svg Normal file
View file

@ -0,0 +1,10 @@
<svg width="24" height="24" viewBox="0 0 24 24" fill="none" xmlns="http://www.w3.org/2000/svg">
<path d="M11.4923 3.51517C10.0704 3.60025 8.69275 4.04129 7.48581 4.79777C6.27887 5.55426 5.28139 6.60192 4.58502 7.84452C3.88865 9.08711 3.51572 10.4848 3.50049 11.9091C3.48526 13.3335 3.82822 14.7388 4.49786 15.996" stroke="#1D2939" stroke-linecap="round"/>
<path d="M11.5501 6.51843C10.6743 6.59031 9.8284 6.87102 9.08335 7.33704C8.3383 7.80307 7.71577 8.44084 7.26789 9.19694C6.82001 9.95304 6.55984 10.8055 6.50916 11.6828C6.45847 12.5601 6.61875 13.4368 6.97658 14.2395" stroke="#1D2939" stroke-linecap="round"/>
<path d="M10.7142 14.144C11.0835 14.3654 11.5036 14.4878 11.934 14.4991C12.3644 14.5105 12.7904 14.4105 13.1708 14.2089" stroke="#1D2939" stroke-linecap="round"/>
<path d="M11.5231 9.54591C11.0365 9.64048 10.5889 9.87759 10.2374 10.2271C9.88584 10.5766 9.64613 11.0227 9.54873 11.5088" stroke="#1D2939" stroke-linecap="round"/>
<path d="M16.4528 15.2284C17.2432 14.1382 17.6062 12.7958 17.473 11.4558" stroke="#1D2939" stroke-linecap="round"/>
<path d="M8.8669 16.5204C9.66189 17.0714 10.5881 17.403 11.5522 17.4817C12.5163 17.5605 13.4841 17.3836 14.358 16.9689" stroke="#1D2939" stroke-linecap="round"/>
<path d="M19.4459 7.90013C18.6397 6.43599 17.4197 5.24203 15.9386 4.46756" stroke="#1D2939" stroke-linecap="round"/>
<path d="M6.52764 18.5041C7.79803 19.573 9.35364 20.2464 11.0024 20.4413C12.6512 20.6361 14.3209 20.3439 15.8054 19.6006C17.29 18.8573 18.5244 17.6955 19.3562 16.2587C20.188 14.8219 20.5808 13.1729 20.4862 11.5154" stroke="#1D2939" stroke-linecap="round"/>
</svg>
Side by side

After

Width:  |  Height:  |  Size: 1.6 KiB

BIN
vendor/assets/stylesheets/fonts/SN-icon-font.eot vendored
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Binary file not shown.

26
vendor/assets/stylesheets/fonts/SN-icon-font.svg vendored
View file

@ -10,9 +10,9 @@
"description": "SN icon font\nFont generated by IcoMoon.",
"copyright": "SciNote LLC",
"majorVersion": 1,
"minorVersion": 12,
"minorVersion": 14,
"fontURL": "https://www.scinote.net",
"version": "Version 1.12",
"version": "Version 1.14",
"fontId": "SN-icon-font",
"psName": "SN-icon-font",
"subFamily": "Regular",
@ -64,19 +64,19 @@
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BIN
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vendor/assets/stylesheets/fonts/SN-icon-font.woff2 vendored Normal file
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35
vendor/assets/stylesheets/sn-icon-font.css vendored
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@ -1,10 +1,11 @@
@font-face {
font-family: 'SN-icon-font';
src: url('fonts/SN-icon-font.eot?n7qhkp');
src: url('fonts/SN-icon-font.eot?n7qhkp#iefix') format('embedded-opentype'),
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src: url('fonts/SN-icon-font.eot?x922k8');
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font-weight: normal;
font-style: normal;
font-display: block;
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font-size: 16px !important;
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content: "\e900";
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@ -279,10 +272,10 @@
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content: "\e951";
}
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content: "\e952";
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content: "\e953";
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yarn.lock
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