Merge branch '333-localization-i18n' of https://github.com/cidgoh/Dat…

…aHarmonizer into 333-localization-i18n

.gitignore

@@ -150,7 +150,7 @@ cython_debug/
 #  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
-#.idea/
+.idea/
 
 # Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm, CLion, Android Studio, WebStorm and Rider
 # Reference: https://intellij-support.jetbrains.com/hc/en-us/articles/206544839

lib/DataHarmonizer.js

@@ -1,6 +1,5 @@
 import '@selectize/selectize';
 import Handsontable from 'handsontable';
-import SheetClip from 'sheetclip';
 import $ from 'jquery';
 import i18next from 'i18next';
 import { utils as XlsxUtils, read as xlsxRead } from 'xlsx/xlsx.mjs';
@@ -488,9 +487,6 @@ class DataHarmonizer {
   createHot() {
     const self = this;
 
-    this.clipboardCache = '';
-    this.sheetclip = new SheetClip();
-
     this.invalid_cells = {};
     if (this.hot) {
       this.hot.destroy(); // handles already existing data
@@ -506,42 +502,6 @@ class DataHarmonizer {
         rowHeaders: true,
         copyPaste: true,
         manualColumnResize: true,
-        //colWidths: [100], //Just fixes first column width
-        afterCopy: function (changes) {
-          self.clipboardCache = self.sheetclip.stringify(changes);
-        },
-        afterCut: function (changes) {
-          self.clipboardCache = self.sheetclip.stringify(changes);
-        },
-        afterPaste: function (changes) {
-          // we want to be sure that our cache is up to date, even if someone pastes data from another source than our tables.
-          self.clipboardCache = self.sheetclip.stringify(changes);
-        },
-        contextMenu: [
-          'copy',
-          'cut',
-          {
-            key: 'paste',
-            name: 'Paste',
-            disabled: function () {
-              return self.clipboardCache.length === 0;
-            },
-            callback: function () {
-              var plugin = this.getPlugin('copyPaste');
-
-              this.listen();
-              // BUG: It seems like extra lf is added by sheetclip, causing
-              // empty last row to be added and pasted. Exception is pasting
-              // of single empty cell
-              if (self.clipboardCache.length > 0)
-                self.clipboardCache = self.clipboardCache.slice(0, -1);
-              plugin.paste(self.clipboardCache);
-            },
-          },
-          'remove_row',
-          'row_above',
-          'row_below',
-        ],
         minRows: 100,
         minSpareRows: 100,
         width: '100%',

lib/editors/FlatpickrEditor.js

@@ -3,7 +3,8 @@ import flatpickr from 'flatpickr';
 import 'flatpickr/dist/themes/light.css';
 import { format, parse } from 'date-fns';
 
-const REF_DATE = new Date(0);
+const REF_DATE = new Date();
+REF_DATE.setHours(0, 0, 0, 0);
 
 class FlatpickrEditor extends Handsontable.editors.TextEditor {
   /**
@@ -29,12 +30,14 @@ class FlatpickrEditor extends Handsontable.editors.TextEditor {
   createElements() {
     super.createElements();
 
+    this.TEXTAREA.remove();
     this.TEXTAREA = this.hot.rootDocument.createElement('input');
     this.TEXTAREA.className = 'handsontableInput';
+    this.TEXTAREA.setAttribute('data-hot-input', true);
     this.textareaStyle = this.TEXTAREA.style;
     this.textareaStyle.width = 0;
     this.textareaStyle.height = 0;
-    Handsontable.dom.empty(this.TEXTAREA_PARENT);
+    this.TEXTAREA_PARENT.innerText = '';
     this.TEXTAREA_PARENT.appendChild(this.TEXTAREA);
 
     this.datePicker = this.hot.rootDocument.createElement('DIV');
@@ -52,10 +55,10 @@ class FlatpickrEditor extends Handsontable.editors.TextEditor {
      */
     const eventManager = new Handsontable.EventManager(this);
     eventManager.addEventListener(this.datePicker, 'mousedown', (event) => {
-      Handsontable.dom.stopImmediatePropagation(event);
+      event.stopPropagation();
     });
     eventManager.addEventListener(this.datePicker, 'keydown', (event) => {
-      Handsontable.dom.stopImmediatePropagation(event);
+      event.stopPropagation();
     });
     eventManager.addEventListener(this.TEXTAREA, 'keydown', (event) => {
       if (event.keyCode === Handsontable.helper.KEY_CODES.ENTER) {
@@ -75,7 +78,9 @@ class FlatpickrEditor extends Handsontable.editors.TextEditor {
   destroyElements() {
     const datePickerParentElement = this.datePicker.parentNode;
 
-    this.fp.destroy();
+    if (this.fp?.destroy) {
+      this.fp.destroy();
+    }
 
     if (datePickerParentElement) {
       datePickerParentElement.removeChild(this.datePicker);
@@ -141,8 +146,10 @@ class FlatpickrEditor extends Handsontable.editors.TextEditor {
    */
   showDatepicker(event) {
     const offset = this.TD.getBoundingClientRect();
-    const isMouseDown = this.instance.view.isMouseDown();
-    const isMeta = event ? Handsontable.helper.isMetaKey(event.keyCode) : false;
+    const isMouseDown = this.hot.view.isMouseDown();
+    const isMeta = event
+      ? Handsontable.helper.isFunctionKey(event.keyCode)
+      : false;
 
     const defaultConfig = this.getFlatpickrConfig();
     const cellConfig =
@@ -153,14 +160,20 @@ class FlatpickrEditor extends Handsontable.editors.TextEditor {
     const mandatoryConfig = {
       appendTo: this.datePicker,
       allowInput: true,
-      allowInvalidPreload: true,
+      allowInvalidPreload: false,
       inline: true,
       clickOpens: false,
       // Inject date-fns formatter & parser here for better consistency when
       // parsing and formatting of exported data
-      formatDate: format,
-      parseDate: (dateString, formatString) =>
-        parse(dateString, formatString, REF_DATE),
+      formatDate: (dateObj, formatString) => {
+        if (!(dateObj instanceof Date && !isNaN(dateObj.getTime()))) {
+          return '';
+        }
+        return format(dateObj, formatString);
+      },
+      parseDate: (dateString, formatString) => {
+        return parse(dateString, formatString, REF_DATE);
+      },
       onChange: (dates, datestr) => {
         this.setValue(datestr);
       },

lib/utils/files.js

@@ -1,4 +1,4 @@
-import { utils as XlsxUtils, writeFile } from 'xlsx';
+import { utils as XlsxUtils, writeFile } from 'xlsx/xlsx.mjs';
 import { saveAs } from 'file-saver';
 
 /**

package.json

@@ -1,6 +1,6 @@
 {
   "name": "data-harmonizer",
-  "version": "1.6.0",
+  "version": "1.6.1",
   "description": "A standardized spreadsheet editor and validator that can be run offline and locally",
   "repository": "[email protected]:cidgoh/DataHarmonizer.git",
   "license": "MIT",

web/templates/canada_covid19/schema.json

@@ -2,7 +2,7 @@
   "name": "CanCOGeN_Covid-19",
   "description": "",
   "id": "https://example.com/CanCOGeN_Covid-19",
-  "version": "2.1.3",
+  "version": "2.2.3",
   "prefixes": {
     "linkml": {
       "prefix_prefix": "linkml",
@@ -4128,6 +4128,9 @@
         "Newfoundland and Labrador - Eastern Health": {
           "text": "Newfoundland and Labrador - Eastern Health"
         },
+        "Newfoundland and Labrador - Newfoundland and Labrador Health Services": {
+          "text": "Newfoundland and Labrador - Newfoundland and Labrador Health Services"
+        },
         "Nova Scotia Health Authority": {
           "text": "Nova Scotia Health Authority"
         },
@@ -4220,6 +4223,9 @@
         "Newfoundland and Labrador - Eastern Health": {
           "text": "Newfoundland and Labrador - Eastern Health"
         },
+        "Newfoundland and Labrador - Newfoundland and Labrador Health Services": {
+          "text": "Newfoundland and Labrador - Newfoundland and Labrador Health Services"
+        },
         "Nova Scotia Health Authority": {
           "text": "Nova Scotia Health Authority"
         },

web/templates/canada_covid19/schema.yaml

@@ -1,7 +1,7 @@
 id: https://example.com/CanCOGeN_Covid-19
 name: CanCOGeN_Covid-19
 description: ''
-version: 2.1.3
+version: 2.2.3
 imports:
 - linkml:types
 prefixes:
@@ -5762,6 +5762,8 @@ enums:
         text: "New Brunswick - Vitalit\xE9 Health Network"
       Newfoundland and Labrador - Eastern Health:
         text: Newfoundland and Labrador - Eastern Health
+      Newfoundland and Labrador - Newfoundland and Labrador Health Services:
+        text: Newfoundland and Labrador - Newfoundland and Labrador Health Services
       Nova Scotia Health Authority:
         text: Nova Scotia Health Authority
       Ontario Institute for Cancer Research (OICR):
@@ -5823,6 +5825,8 @@ enums:
         text: "New Brunswick - Vitalit\xE9 Health Network"
       Newfoundland and Labrador - Eastern Health:
         text: Newfoundland and Labrador - Eastern Health
+      Newfoundland and Labrador - Newfoundland and Labrador Health Services:
+        text: Newfoundland and Labrador - Newfoundland and Labrador Health Services
       Nova Scotia Health Authority:
         text: Nova Scotia Health Authority
       Nunavut:

web/templates/canada_covid19/schema_core.yaml

@@ -1,7 +1,7 @@
 id: https://example.com/CanCOGeN_Covid-19
 name: CanCOGeN_Covid-19
 description: ""
-version: 2.1.3
+version: 2.2.3
 imports:
 - 'linkml:types'
 prefixes:

web/templates/canada_covid19/schema_enums.tsv

@@ -887,6 +887,7 @@ sequence submitted by menu		Alberta Precision Labs (APL)
 		National Microbiology Laboratory (NML)										
 		New Brunswick - Vitalité Health Network										
 		Newfoundland and Labrador - Eastern Health										
+		Newfoundland and Labrador - Newfoundland and Labrador Health Services										
 		Nova Scotia Health Authority										
 		Ontario Institute for Cancer Research (OICR)										
 		Prince Edward Island - Health PEI										
@@ -917,6 +918,7 @@ sequence submitted by menu		Alberta Precision Labs (APL)
 		National Microbiology Laboratory (NML)										
 		New Brunswick - Vitalité Health Network										
 		Newfoundland and Labrador - Eastern Health										
+		Newfoundland and Labrador - Newfoundland and Labrador Health Services										
 		Nova Scotia Health Authority										
 		Nunavut										
 		Ontario Institute for Cancer Research (OICR)										
@@ -1202,6 +1204,4 @@ geo_loc_name (country) menu	GAZ:00006882	Afghanistan
 	GAZ:00000564	Western Sahara										
 	GAZ:00005284	Yemen										
 	GAZ:00001107	Zambia										
-	GAZ:00001106	Zimbabwe										
-
-
+	GAZ:00001106	Zimbabwe										

web/templates/canada_covid19/schema_slots.tsv

@@ -158,5 +158,4 @@ CanCOGeN Covid-19		GENEPIO:0001122	Database Identifiers
 
 		GENEPIO:0001516	Contributor acknowledgement																			
 	Contributor acknowledgement	GENEPIO:0001517	authors		WhitespaceMinimizedString					TRUE					Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission.	Include the first and last names of all individuals that should be attributed, separated by a comma.	Tejinder Singh, Fei Hu, Joe Blogs	Authors	Authors	PH_CANCOGEN_AUTHORS		
-	Contributor acknowledgement	GENEPIO:0001518	DataHarmonizer provenance		Provenance										The DataHarmonizer software and template version provenance.	The current software and template version information will be automatically generated in this field after the user utilizes the "validate" function. This information will be generated regardless as to whether the row is valid of not.	DataHarmonizer v1.4.3, CanCOGeN Covid-19 v1.0.0	DataHarmonizer provenance	Additional Comments	HC_COMMENTS		
-
+	Contributor acknowledgement	GENEPIO:0001518	DataHarmonizer provenance		Provenance										The DataHarmonizer software and template version provenance.	The current software and template version information will be automatically generated in this field after the user utilizes the "validate" function. This information will be generated regardless as to whether the row is valid of not.	DataHarmonizer v1.4.3, CanCOGeN Covid-19 v1.0.0	DataHarmonizer provenance	Additional Comments	HC_COMMENTS