Merge branch 'main' into move-thunor-core

thunorweb/templates/base-inner.html

@@ -112,16 +112,8 @@
 </div>
 <div class="powered-by">Powered by <i class="fa fa-bolt"></i> Thunor</div>
 
-{% load webpack_loader %}{% get_files 'sentry' 'js' as sentry_js %}
-<script src="{{ sentry_js.0.url }}" crossorigin="anonymous"></script>
-
-<script>{% load thunorweb_tags %}Sentry.init({
-    dsn: '{% sentry_public_dsn %}',
-    environment: '{% sentry_environment %}', release: '{% thunorweb_version %}'
-});
-{% if user.is_authenticated %}Sentry.setUser({email: '{{ user.email }}',
-    id: '{{ user.id }}'});{% endif %}</script>
-
+{% load webpack_loader %}
+{% include "sentry_init.html" %}
 {% render_bundle 'vendor' 'js' %}
 <script>$('.tt').tooltip();
 $('.help-link').click(function(e) {

thunorweb/templates/plotly_plot.html

@@ -12,14 +12,8 @@
 </div>
 <div class="powered-by"><i class="fa fa-bolt"></i> Thunor</div>
 
-{% load webpack_loader %}{% get_files 'sentry' 'js' as sentry_js %}
-<script src="{{ sentry_js.0.url }}" crossorigin="anonymous"></script>
-<script>{% load thunorweb_tags %}Sentry.init({
-    dsn: '{% sentry_public_dsn %}',
-    environment: '{% sentry_environment %}', release: '{% thunorweb_version %}'
-});
-{% if user.is_authenticated %}Sentry.setUser({email: '{{ user.email }}',
-    id: '{{ user.id }}'});{% endif %}</script>
+{% load webpack_loader %}
+{% include "sentry_init.html" %}
 {% render_bundle 'vendor' 'js' %}
 {% render_bundle 'app' 'js' %}
 {% render_bundle 'plots' 'js' %}

thunorweb/templates/sentry_init.html

@@ -0,0 +1,10 @@
+{% load webpack_loader %}
+{% get_files 'sentry' 'js' as sentry_js %}
+<script src="{{ sentry_js.0.url }}" crossorigin="anonymous"></script>
+
+<script>{% load thunorweb_tags %}Sentry.init({
+    dsn: '{% sentry_public_dsn %}',
+    environment: '{% sentry_environment %}', release: '{% thunorweb_version %}'
+});
+{% if user.is_authenticated %}Sentry.setUser({email: '{{ user.email }}',
+ id: '{{ user.id }}'});{% endif %}</script>

thunorweb/webpack/Dockerfile

@@ -11,6 +11,7 @@ COPY package.json $BUILD_DIR
 RUN npm install
 
 COPY webpack.config.js $BUILD_DIR
+COPY sentry.js $BUILD_DIR
 COPY plotly.js $BUILD_DIR
 COPY .bootstraprc $BUILD_DIR
 COPY bootstrap-customisations.scss $BUILD_DIR

thunorweb/webpack/sentry.js

@@ -0,0 +1 @@
+export * from "@sentry/browser"

thunorweb/webpack/thunorweb/js/dataset.js

@@ -1,9 +1,7 @@
-"use strict";
+import { ajax } from './modules/ajax'
+import { ui } from './modules/ui'
 
-var ui = require("./modules/ui"),
-    ajax = require("./modules/ajax");
-
-var delete_dataset = function() {
+const delete_dataset = function() {
     ui.loadingModal.show();
     $.ajax({type: 'POST',
             url: ajax.url("delete_dataset"),
@@ -19,7 +17,7 @@ var delete_dataset = function() {
             dataType: 'json'});
 };
 
-var accept_license = function() {
+const accept_license = function() {
     ui.loadingModal.show();
     $.ajax({type: 'POST',
             url: ajax.url("accept_license", $('#dataset-id').val()),
@@ -32,23 +30,23 @@ var accept_license = function() {
 };
 
 
-var dataset = function(showLicense) {
+const activate = function(showLicense) {
     $('#dataset-name-edit').click(function() {
         var datasetName = $('.dataset-name').first().text();
         $('#dataset-name').hide();
         $('#dataset-rename').show().find("input[name=datasetName]").val(datasetName).select();
     });
 
     $('#dataset-rename-cancel').click(function() {
-       $('#dataset-rename').hide();
-       $('#dataset-name').show();
+    $('#dataset-rename').hide();
+    $('#dataset-name').show();
     });
 
     $('#dataset-rename-form').submit(function(e) {
-       e.preventDefault();
-       ui.loadingModal.show();
+    e.preventDefault();
+    ui.loadingModal.show();
 
-       $.ajax({type: 'POST',
+    $.ajax({type: 'POST',
         url: ajax.url("rename_dataset"),
         headers: { 'X-CSRFToken': ajax.getCsrfToken() },
         data: $(this).serialize(),
@@ -108,6 +106,6 @@ var dataset = function(showLicense) {
     }
 };
 
-module.exports = {
-    activate: dataset
-};
+export const dataset = {
+    activate: activate
+}

thunorweb/webpack/thunorweb/js/dataset_permissions.js

@@ -1,9 +1,7 @@
-"use strict";
+import { ajax } from './modules/ajax'
+import { ui } from './modules/ui'
 
-var ui = require("./modules/ui"),
-    ajax = require("./modules/ajax");
-
-var set_dataset_group_permission = function(dataset_id, group_id, perm_id,
+const set_dataset_group_permission = function(dataset_id, group_id, perm_id,
                                             state, $caller) {
     ui.loadingModal.show();
     $.ajax({type: 'POST',
@@ -27,7 +25,7 @@ var set_dataset_group_permission = function(dataset_id, group_id, perm_id,
             dataType: 'json'});
 };
 
-var dataset_permissions = function() {
+export const dataset_permissions = function() {
     $("input[type=checkbox]").bootstrapSwitch({
         'onSwitchChange': function(event, state) {
             var $target = $(event.currentTarget);
@@ -41,7 +39,3 @@ var dataset_permissions = function() {
         }
     });
 };
-
-module.exports = {
-    activate: dataset_permissions
-};

thunorweb/webpack/thunorweb/js/home.js

@@ -1,14 +1,12 @@
-var ajax = require("./modules/ajax"),
-    datasetTable = require("./modules/dataset_table");
+import { ajax } from './modules/ajax'
+import { initDatasetTable } from './modules/dataset_table'
 
-var home = function() {
-    var callbackFn = function (data, type, full, meta) {
-        return "<a href=\"" + ajax.url("page_view_dataset",
-                full.id) +  "\">" + full.name + "</a>";
-    };
-    datasetTable.initDatasetTable(callbackFn);
-};
-
-module.exports = {
-    activate: home
-};
+export const home = {
+    activate: function() {
+        var callbackFn = function (data, type, full, meta) {
+            return "<a href=\"" + ajax.url("page_view_dataset",
+                    full.id) +  "\">" + full.name + "</a>";
+        };
+        initDatasetTable(callbackFn);
+    }
+}

thunorweb/webpack/thunorweb/js/modules/ajax.js

@@ -1,8 +1,6 @@
-"use strict";
+import { ui } from "./ui"
 
-var ui = require("./ui");
-
-var ajax = (function () {
+export const ajax = (function () {
     var csrfToken = null;
 
     var getCookie = function (name) {
@@ -174,4 +172,3 @@ var ajax = (function () {
         url: url
     }
 })();
-module.exports = ajax;

thunorweb/webpack/thunorweb/js/modules/dataset_table.js

@@ -1,11 +1,11 @@
-var ajax = require("./ajax"),
-    util = require("./util");
+import { ajax } from './ajax'
+import { util } from './util'
 
-var formatISODate = function(data) {
+const formatISODate = function(data) {
     return data.replace('T', ' ').slice(0, -5) + ' UTC';
 };
 
-var initDatasetTable = function(tableRowCallbackFn, loadingCompleteCallbackFn) {
+export const initDatasetTable = function(tableRowCallbackFn, loadingCompleteCallbackFn) {
     var $tabContent = $(".tab-content");
     $tabContent.loadingOverlay("show");
 
@@ -63,7 +63,3 @@ var initDatasetTable = function(tableRowCallbackFn, loadingCompleteCallbackFn) {
         $this.addClass("active");
     });
 };
-
-module.exports = {
-    initDatasetTable: initDatasetTable
-};

thunorweb/webpack/thunorweb/js/modules/ui.js

@@ -1,5 +1,4 @@
-"use strict";
-var ui = (function() {
+export const ui = (function() {
     var modalBase = $(
         '<div class="modal fade" tabindex="-1" role="dialog"' +
         ' aria-hidden="true" data-success="false">' +
@@ -160,4 +159,3 @@ var ui = (function() {
         loadingModal: loadingModal
     }
 })();
-module.exports = ui;

thunorweb/webpack/thunorweb/js/modules/util.js

@@ -1,6 +1,4 @@
-"use strict";
-
-var util = (function() {
+export const util = (function() {
     var onlyUnique = function (value, index, self) {
         return self.indexOf(value) === index;
     };
@@ -197,4 +195,3 @@ var util = (function() {
         }
     }
 })();
-module.exports = util;

thunorweb/webpack/thunorweb/js/plate_mapper.js

@@ -1,8 +1,7 @@
-"use strict";
-
-var ui = require('./modules/ui'),
-    util = require('./modules/util'),
-    ajax = require('./modules/ajax');
+import { ui } from './modules/ui'
+import { util } from './modules/util'
+import { ajax } from './modules/ajax'
+import { tsvParse } from 'd3-dsv'
 
 var Well = function(well) {
     if(well === undefined) {
@@ -372,13 +371,15 @@ PlateMap.prototype = {
     }
 };
 
-var check_loading = function() {
+export { PlateMap }
+
+export const checkLoading = function() {
     if(pyHTS.state.plates.length > 0 && pyHTS.state.plates[0] !== "MASTER") {
         ui.loadingModal.show();
     }
 };
 
-var plate_mapper = function () {
+const activate = function () {
     var setWellSizes = function() {
         var numWells = pyHTS.state.plateMap.wells.length;
         var $plate = $('#hts-well-plate-inner');
@@ -1728,8 +1729,7 @@ var plate_mapper = function () {
     });
 
     var tsvToJson = function(tsv) {
-        var d3 = require("d3-dsv");
-        var rows = d3.tsvParse(tsv);
+        var rows = tsvParse(tsv);
         var rLen = rows.length;
         if(rLen !== pyHTS.state.plateMap.wells.length) {
             return upErr('File has '+rLen+' wells, but current plate map has '+pyHTS.state.plateMap.wells.length+' wells');
@@ -1980,8 +1980,10 @@ var plate_mapper = function () {
         }
     }
 };
-module.exports = {
-    activate: plate_mapper,
-    checkLoading: check_loading,
+
+export const plate_mapper = {
+    activate: activate,
+    checkLoading: checkLoading,
     PlateMap: PlateMap
-};
+}
+

thunorweb/webpack/thunorweb/js/plate_upload.js

@@ -1,9 +1,7 @@
-"use strict";
+import { ui } from './modules/ui'
+import { ajax } from './modules/ajax'
 
-var ui = require("./modules/ui"),
-    ajax = require("./modules/ajax");
-
-var plate_upload = function () {
+const activate = function () {
     var ajaxSettings = {
         headers: {"X-CSRFToken": ajax.getCsrfToken()}
     };
@@ -111,6 +109,6 @@ var plate_upload = function () {
     }
 };
 
-module.exports = {
-    activate: plate_upload
+export const plate_upload = {
+    activate: activate
 };