Merge branch 'dh2-beta-release' into dh2-i18n-rc1

cidgoh · Dec 18, 2024 · 43c6a41 · 43c6a41
2 parents e8895b5 + 7736fe9
commit 43c6a41
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Showing 29 changed files with 227 additions and 152 deletions.
diff --git a/.eslintrc.js b/.eslintrc.js
@@ -2,6 +2,7 @@ module.exports = {
   ignorePatterns: [
     '.eslintrc.js',
     'web/webpack.config.js',
+    'web/webpack.schemas.js',
     'lib/rollup.config.js',
     '**/dist/**/*.js',
     '.venv',

diff --git a/lib/AppContext.js b/lib/AppContext.js
@@ -1,16 +1,17 @@
 import * as $ from 'jquery';
 import i18n from 'i18next';
 
-import { DataHarmonizer } from '@/lib';
-import { findLocalesForLangcodes } from '@/lib/utils/i18n';
+import { DataHarmonizer } from '.';
+import { findLocalesForLangcodes } from './utils/i18n';
 import {
   Template,
   findSlotNamesForClass,
   getTemplatePathInScope,
-} from '@/lib/utils/templates';
-import { wait } from '@/lib/utils/general';
-import { invert, removeNumericKeys, consolidate } from '@/lib/utils/objects';
-import { createDataHarmonizerContainer, createDataHarmonizerTab } from '@/web';
+} from '../lib/utils/templates';
+import { wait } from '../lib/utils/general';
+import { invert, removeNumericKeys, consolidate } from '../lib/utils/objects';
+import { createDataHarmonizerContainer, createDataHarmonizerTab } from '../web';
+import { getExportFormats } from 'schemas';
 
 // COMMENTED OUT: WIP FEATURE
 // import { buildAppContext, setup1M } from '@/lib/utils/1m';
@@ -409,9 +410,7 @@ export default class AppContext {
   }
 
   async loadExportFormats(schema) {
-    this.exportFormats = (
-      await import(`@/web/templates/${schema}/export.js`)
-    ).default;
+    this.exportFormats = await getExportFormats(schema);
     return this.exportFormats;
   }
 

diff --git a/lib/DataHarmonizer.js b/lib/DataHarmonizer.js
@@ -7,18 +7,18 @@ import 'jquery-ui/dist/themes/base/jquery-ui.css';
 
 import i18next from 'i18next';
 import { utils as XlsxUtils, read as xlsxRead } from 'xlsx/xlsx.js';
-import { renderContent, urlToClickableAnchor } from '@/lib/utils/content';
-import { readFileAsync, updateSheetRange } from '@/lib/utils/files';
-import { findSlotNamesForClass } from '@/lib/utils/templates';
+import { renderContent, urlToClickableAnchor } from './utils/content';
+import { readFileAsync, updateSheetRange } from '../lib/utils/files';
+import { findSlotNamesForClass } from '../lib/utils/templates';
 import {
   isValidHeaderRow,
   rowIsEmpty,
   wait,
   stripDiv,
   isEmptyUnitVal,
   pascalToLowerWithSpaces,
-} from '@/lib/utils/general';
-import { invert, deepMerge, looseMatchInObject } from '@/lib/utils/objects';
+} from '../lib/utils/general';
+import { invert, deepMerge, looseMatchInObject } from '../lib/utils/objects';
 
 import {
   changeCase,
@@ -31,40 +31,42 @@ import {
   MULTIVALUED_DELIMITER,
   parseMultivaluedValue,
   titleOverText,
-} from '@/lib/utils/fields';
+} from './utils/fields';
 
 import {
   checkProvenance,
   itemCompare,
   validateValAgainstVocab,
   validateValsAgainstVocab,
   // validateUniqueValues,
-} from '@/lib/utils/validation';
+} from './utils/validation';
 
 import 'handsontable/dist/handsontable.full.css';
-import '@/lib/data-harmonizer.css';
+import './data-harmonizer.css';
 import '@selectize/selectize/dist/css/selectize.bootstrap4.css';
 
-import specifyHeadersModal from '@/lib/specifyHeadersModal.html';
-import unmappedHeadersModal from '@/lib/unmappedHeadersModal.html';
-import fieldDescriptionsModal from '@/lib/fieldDescriptionsModal.html';
+import specifyHeadersModal from './specifyHeadersModal.html';
+import unmappedHeadersModal from './unmappedHeadersModal.html';
+import fieldDescriptionsModal from './fieldDescriptionsModal.html';
 
-import HelpSidebar from '@/lib/HelpSidebar';
+import HelpSidebar from './HelpSidebar';
 
 // NOTE: this is odd! package.json is a developer file. why should a UI component care about it?
-import pkg from '@/package.json';
-import Validator from '@/lib/Validator';
+import pkg from '../package.json';
+import Validator from './Validator';
 
 const VERSION = pkg.version;
 const VERSION_TEXT = 'DataHarmonizer v' + VERSION;
 
-import { DateEditor, DatetimeEditor, TimeEditor } from '@/lib/editors';
 import {
+  DateEditor,
+  DatetimeEditor,
+  TimeEditor,
   KeyValueListEditor,
   keyValueListValidator,
   keyValueListRenderer,
   multiKeyValueListRenderer,
-} from '@/lib/editors';
+} from './editors';
 
 Handsontable.cellTypes.registerCellType('key-value-list', {
   editor: KeyValueListEditor,
@@ -2236,7 +2238,7 @@ class DataHarmonizer {
       // if sources exist, fetch transformed Value
       if (field.sources) {
         if (field.multivalued === true) {
-          //Map list of semicolon-delimited choices
+          // Map list of semicolon-delimited choices
           // ISSUE: relying on semicolon delimiter in input
           for (let cellVal of mappedCellVal.split(';')) {
             mappedCell.push(
@@ -2655,7 +2657,6 @@ class DataHarmonizer {
         if (number >= 0) {
           // Here we have the 3 field call, with units sandwitched in the middle
           if (binOffset === 2) {
-
             const unit = matrix[row][hotRowNextCol];
             // Host age unit is interpreted by default to be year.
             // If user selects month, value is converted into years for binning.
@@ -2693,7 +2694,7 @@ class DataHarmonizer {
           const bin_values = fields[hotRowBinCol].flatVocabulary;
           if (value in bin_values && (!bin_value || bin_value === '')) {
             selection = value;
-            console.log("no bin value", value);
+            console.log('no bin value', value);
           }
           // If a unit field exists, then set that to metadata too.
           if (binOffset == 2) {
@@ -2742,7 +2743,7 @@ class DataHarmonizer {
   doPreValidationRepairs(data) {
     return new Promise((resolve) => {
       const cellChanges = [];
-      const whitespace_minimized_re = new RegExp(/\s+/,'g');
+      const whitespace_minimized_re = new RegExp(/\s+/, 'g');
       let fullVersion =
         VERSION_TEXT +
         ', ' +
@@ -2762,15 +2763,16 @@ class DataHarmonizer {
           const datatype = field.datatype;
 
           if (cellVal && datatype === 'xsd:token') {
-
-            const minimized = cellVal.replace(whitespace_minimized_re, ' ').trim();
+            const minimized = cellVal
+              .replace(whitespace_minimized_re, ' ')
+              .trim();
             // Update cellVal in advance of validateVal(s) below
             if (minimized !== cellVal) {
               cellVal = minimized;
               data[row][col] = cellVal;
               cellChanges.push([row, col, minimized, 'thisChange']);
             }
-          };
+          }
 
           if (datatype === 'Provenance') {
             checkProvenance(cellChanges, fullVersion, cellVal, row, col);

diff --git a/lib/HelpSidebar.js b/lib/HelpSidebar.js
@@ -1,6 +1,6 @@
 import $ from 'jquery';
-import { renderContent } from '@/lib/utils/content';
-import '@/lib/HelpSidebar.css';
+import { renderContent } from './utils/content';
+import './HelpSidebar.css';
 
 const DEFAULT_OPTIONS = {
   width: 300,

diff --git a/lib/Toolbar.js b/lib/Toolbar.js
@@ -13,27 +13,24 @@ import {
   exportWorkbook,
   importJsonFile,
   prependToSheet,
-} from '@/lib/utils/files';
-import { nullValuesToString, isEmptyUnitVal } from '@/lib/utils/general';
-import { MULTIVALUED_DELIMITER, titleOverText } from '@/lib/utils/fields';
-import { takeKeys, invert } from '@/lib/utils/objects';
+} from '../lib/utils/files';
+import { nullValuesToString, isEmptyUnitVal } from '../lib/utils/general';
+import { MULTIVALUED_DELIMITER, titleOverText } from '../lib/utils/fields';
+import { takeKeys, invert } from '../lib/utils/objects';
 import {
   findBestLocaleMatch,
   templatePathForSchemaURI,
   rangeToContainerClass,
   LocaleNotSupportedError,
-} from '@/lib/utils/templates';
+} from '../lib/utils/templates';
 
-import {
-  findLocalesForLangcodes,
-  interface_translation,
-} from '@/lib/utils/i18n';
+import { findLocalesForLangcodes, interface_translation } from './utils/i18n';
 import i18next from 'i18next';
 
-import template from '@/lib/toolbar.html';
-import '@/lib//toolbar.css';
+import template from './toolbar.html';
+import './/toolbar.css';
 
-import menu from '@/web/templates/menu.json';
+import { menu } from 'schemas';
 import pkg from '../package.json';
 
 const VERSION = pkg.version;

diff --git a/lib/Validator.js b/lib/Validator.js
@@ -1,6 +1,6 @@
-import { Datatypes } from '@/lib/utils/datatypes';
-import { validateUniqueValues } from '@/lib/utils/validation';
-import { rowIsEmpty } from '@/lib/utils/general';
+import { Datatypes } from './utils/datatypes';
+import { validateUniqueValues } from './utils/validation';
+import { rowIsEmpty } from './utils/general';
 
 class Validator {
   #schema;
@@ -58,7 +58,7 @@ class Validator {
         return;
       }
       // todos is an array of strings.
-      const slotType = this.getSlotType(slotDefinition);// LinkML schema.type object
+      const slotType = this.getSlotType(slotDefinition); // LinkML schema.type object
 
       // Slot type could be:
       // a number, string, date ...
@@ -74,11 +74,15 @@ class Validator {
         }
       }
 
-      // Cycle through each slotDefinition any_of etc. object entries and get 
+      // Cycle through each slotDefinition any_of etc. object entries and get
       // the datatype of its .range (or recurse) and in LinkML fashion attach
       // minimum_value and maximum_value to the slotDefinition OR its any_of
       // etc array BASED ON top level todos. E.g. inheriting min/max criteria.
-      for (const def of slotDefinition.any_of ?? slotDefinition.all_of ?? slotDefinition.exactly_one_of ?? slotDefinition.none_of ?? []) {
+      for (const def of slotDefinition.any_of ??
+        slotDefinition.all_of ??
+        slotDefinition.exactly_one_of ??
+        slotDefinition.none_of ??
+        []) {
         processTodos(def, todos);
       }
     };
@@ -248,8 +252,7 @@ class Validator {
 
     const validate = (value) => {
       if (!value) {
-        if (slotDefinition.required) 
-          return 'This field is required';
+        if (slotDefinition.required) return 'This field is required';
         // value_presence is subject to dynamic rules?
         if (slotDefinition.value_presence === 'PRESENT')
           return 'Value is not present';
@@ -283,7 +286,8 @@ class Validator {
       // Message needs
       for (const value of splitValues) {
         let parse_error = false;
-        if (slotType) {// Doesn't pertain to slots which are ONLY enumerations.
+        if (slotType) {
+          // Doesn't pertain to slots which are ONLY enumerations.
           const parsed = this.#parser.parse(value, slotType.uri);
 
           // Issue: parse can fail on decimal but menu has "Missing"
@@ -297,15 +301,14 @@ class Validator {
           // All these cases have encountered an item which matches basic data
           // datatype and so sudden death is ok.
           else {
-
             if (slotMinimumValue !== undefined && parsed < slotMinimumValue) {
               return 'Value is less than minimum value';
             }
-            
+
             if (slotMaximumValue !== undefined && parsed > slotMaximumValue) {
               return 'Value is greater than maximum value';
             }
-            
+
             if (
               (slotDefinition.equals_string !== undefined &&
                 parsed !== slotDefinition.equals_string) ||
@@ -322,14 +325,12 @@ class Validator {
               return 'Value does not match pattern';
             }
 
-            // Here slotType value tested and is ok!      
+            // Here slotType value tested and is ok!
             continue;
           }
 
           // Here value didn't parse to slotType
-
-        }
-        else {
+        } else {
           // No basic slot type here so only enumeration handling.
         }
 
@@ -378,17 +379,20 @@ class Validator {
           }
         }
 
-        if (anyOfValidators.length || allOfValidators.length || exactlyOneOfValidators.length || noneOfValidators.length) {
+        if (
+          anyOfValidators.length ||
+          allOfValidators.length ||
+          exactlyOneOfValidators.length ||
+          noneOfValidators.length
+        ) {
           // We passed validation here which means a parse error can be overriden
-        }
-        else if (parse_error.length) {
-          //There were no other ranges besides basic slotType so 
+        } else if (parse_error.length) {
+          //There were no other ranges besides basic slotType so
           return parse_error;
         }
       }
     };
 
-
     return validate;
   }
 

diff --git a/lib/editors/DateEditor.js b/lib/editors/DateEditor.js
@@ -1,4 +1,4 @@
-import FlatpickrEditor from '@/lib/editors/FlatpickrEditor';
+import FlatpickrEditor from './FlatpickrEditor';
 
 class DateEditor extends FlatpickrEditor {
   getFlatpickrConfig() {

diff --git a/lib/editors/DatetimeEditor.js b/lib/editors/DatetimeEditor.js
@@ -1,4 +1,4 @@
-import FlatpickrEditor from '@/lib/editors/FlatpickrEditor';
+import FlatpickrEditor from './FlatpickrEditor';
 
 class DatetimeEditor extends FlatpickrEditor {
   getFlatpickrConfig() {

diff --git a/lib/editors/KeyValueEditor.js b/lib/editors/KeyValueEditor.js
@@ -1,6 +1,6 @@
 import Handsontable from 'handsontable';
-import { MULTIVALUED_DELIMITER, titleOverText } from '@/lib/utils/fields';
-import { isEmptyUnitVal } from '@/lib/utils/general';
+import { MULTIVALUED_DELIMITER, titleOverText } from '../utils/fields';
+import { isEmptyUnitVal } from '../utils/general';
 
 // Derived from: https://jsfiddle.net/handsoncode/f0b41jug/
 

diff --git a/lib/editors/TimeEditor.js b/lib/editors/TimeEditor.js
@@ -1,4 +1,4 @@
-import FlatpickrEditor from '@/lib/editors/FlatpickrEditor';
+import FlatpickrEditor from './FlatpickrEditor';
 
 class TimeEditor extends FlatpickrEditor {
   getFlatpickrConfig() {

diff --git a/lib/editors/index.js b/lib/editors/index.js
@@ -1,10 +1,10 @@
-export { default as DateEditor } from '@/lib/editors/DateEditor';
-export { default as DatetimeEditor } from '@/lib/editors/DatetimeEditor';
-export { default as TimeEditor } from '@/lib/editors/TimeEditor';
-export { default as FlatpickrEditor } from '@/lib/editors/FlatpickrEditor';
+export { default as DateEditor } from './DateEditor.js';
+export { default as DatetimeEditor } from './DatetimeEditor.js';
+export { default as TimeEditor } from './TimeEditor.js';
+export { default as FlatpickrEditor } from './FlatpickrEditor.js';
 export {
   default as KeyValueListEditor,
   keyValueListRenderer,
   keyValueListValidator,
   multiKeyValueListRenderer,
-} from '@/lib/editors/KeyValueEditor';
+} from './KeyValueEditor.js';
diff --git a/lib/index.js b/lib/index.js
@@ -1,9 +1,5 @@
-export { default as Footer } from '@/lib/Footer';
-export { default as Toolbar } from '@/lib/Toolbar';
-export { default as DataHarmonizer } from '@/lib/DataHarmonizer';
-export { default as AppContext } from '@/lib/AppContext';
-export {
-  DATE_OBJECT,
-  JSON_SCHEMA_FORMAT,
-  INPUT_FORMAT,
-} from '@/lib/utils/fields';
+export { default as Footer } from './Footer';
+export { default as Toolbar } from './Toolbar';
+export { default as DataHarmonizer } from './DataHarmonizer';
+export { default as AppContext } from './AppContext';
+export { DATE_OBJECT, JSON_SCHEMA_FORMAT, INPUT_FORMAT } from './utils/fields';