@datagrok/sequence-translator 1.10.17 → 1.10.19

package/src/tests/oligo-cell-editor-tests.ts

@@ -0,0 +1,83 @@
+import {after, category, test, expect, awaitCheck, delay} from '@datagrok-libraries/test/src/test';
+import * as grok from 'datagrok-api/grok';
+import * as DG from 'datagrok-api/dg';
+
+import $ from 'cash-dom';
+
+import {tagAsOligoNucleotide} from '../oligo-renderer/converters';
+
+const SAMPLE_HELM =
+  'RNA1{r(A)p.r(C)p.r(G)p.r(U)p}|RNA2{r(U)p.r(C)p.r(G)p.r(A)p}$$$$';
+
+function dialogCount(): number {
+  return $('.d4-dialog').length;
+}
+
+function closeAllDialogs(): void {
+  $('.d4-dialog .ui-btn-cancel, .d4-dialog .d4-dialog-header .grok-icon.fa-times').trigger('click');
+}
+
+category('OligoCellEditor', () => {
+  after(async () => {
+    closeAllDialogs();
+    grok.shell.closeAll();
+  });
+
+  test('cellEditor opens HELM editor for OligoNucleotide cell and saves on OK', async () => {
+    const col = DG.Column.fromStrings('seq', [SAMPLE_HELM]);
+    tagAsOligoNucleotide(col);
+    const df = DG.DataFrame.fromColumns([col]);
+    df.name = 'oligo-edit-test';
+    const tv = grok.shell.addTableView(df);
+
+    await awaitCheck(() => $(tv.root).find('.d4-grid canvas').length > 0,
+      'Grid canvas did not appear', 5000);
+
+    // Find the cellEditor that the platform would dispatch on double-click for
+    // a column tagged quality=OligoNucleotide. Pre-fix: zero matches (the
+    // registration didn't exist). Post-fix: exactly one — editOligoNucleotideCell.
+    const matches = DG.Func.find({tags: ['cellEditor'], package: 'SequenceTranslator'})
+      .filter((f) => f.description === 'OligoNucleotide');
+    expect(matches.length, 1);
+    expect(matches[0].name, 'editOligoNucleotideCell');
+
+    const gridCell = tv.grid.cell('seq', 0);
+    expect(gridCell != null, true);
+    expect(gridCell.cell.value, SAMPLE_HELM);
+
+    const dialogsBefore = dialogCount();
+
+    // Invoke the cellEditor as the platform would on double-click.
+    // Pre-fix (delegating to Helm:editMoleculeCell): throws synchronously
+    //   "The column of notation 'helm' must be 'Macromolecule'" — dialog never opens.
+    // Post-fix (using helmHelper.createWebEditorApp directly): dialog opens.
+    await matches[0].apply({cell: gridCell});
+
+    await awaitCheck(() => dialogCount() > dialogsBefore,
+      'HELM editor dialog did not open within 15s', 15000);
+
+    // Wait for HWE async init (Dojo + JSDraw2 + monomer lib) to mount the editor.
+    // JSDraw2 renders to SVG, so wait for the OK button to be wired up — that's
+    // a reliable signal that the dialog footer is fully constructed.
+    await awaitCheck(() => $('.d4-dialog .ui-btn-ok, .d4-dialog button.ui-btn.ui-btn-ok').length > 0,
+      'OK button did not appear in HELM editor dialog within 15s', 15000);
+
+    // Allow the editor a moment to load the HELM string into the canvas before we read it back.
+    await delay(1000);
+
+    const okBtn = $('.d4-dialog .ui-btn-ok, .d4-dialog button.ui-btn.ui-btn-ok').first();
+    expect(okBtn.length > 0, true, 'OK button not found in dialog');
+
+    okBtn.trigger('click');
+
+    await awaitCheck(() => dialogCount() <= dialogsBefore,
+      'Dialog did not close after OK', 5000);
+
+    // After OK: cell.setValue(helmValue) must have run with the editor's HELM.
+    // The editor may canonicalize formatting, so we don't require byte-equality —
+    // we require it remains a valid two-strand HELM string for our input.
+    const after = gridCell.cell.value as string;
+    expect(typeof after === 'string' && after.includes('RNA1{') && after.includes('RNA2{') && after.includes('$$$$'), true,
+      `Expected cell value to remain valid HELM after OK; got: ${after}`);
+  });
+});

package/src/tests/oligo-renderer-tests.ts

@@ -1,6 +1,7 @@
 import {category, test, expect} from '@datagrok-libraries/test/src/test';
 
-import {parseHelmDuplex, looksLikeHelm} from '../oligo-renderer/helm-parser';
+import {parseHelmDuplex, looksLikeHelm, canonicalizeHelm} from '../oligo-renderer/helm-parser';
+import {ParsedNucleotide} from '../oligo-renderer/types';
 import {computeLayout, hitTest, drawDuplex} from '../oligo-renderer/canvas-renderer';
 import {
   resolveSugar, resolvePhosphate, resolveConjugate,
@@ -94,6 +95,68 @@ category('OligoRenderer: parser', () => {
       expect(m0.phosphate, 'zp');
     }
   });
+
+  test('parser strips brackets from multi-char base in parens', async () => {
+    // Bug: pre-fix, cleanupHelmSymbol was not called on the base, so base === '[5Br-dC]'.
+    // Post-fix: cleanupHelmSymbol('[5Br-dC]') → '5Br-dC'.
+    const dup = parseHelmDuplex('RNA1{r([5Br-dC])p}$$$$');
+    const m = dup.sense.monomers[0] as ParsedNucleotide;
+    expect(m.kind, 'nucleotide');
+    expect(m.sugar, 'r');
+    // pre-fix: '[5Br-dC]'  post-fix: '5Br-dC'
+    expect(m.base, '5Br-dC');
+    expect(m.phosphate, 'p');
+  });
+
+  test('parser strips brackets from multi-char base on both strands', async () => {
+    // Covers both strands and different modification combinations.
+    // pre-fix: base === '[5meC]', '[5Br-dC]', '[5fU]'  post-fix: '5meC', '5Br-dC', '5fU'
+    const dup = parseHelmDuplex('RNA1{r([5meC])p.[fl2r]([5Br-dC])[sp]}|RNA2{r([5fU])p}$$$$');
+    const senseFirst = dup.sense.monomers[0] as ParsedNucleotide;
+    const senseSecond = dup.sense.monomers[1] as ParsedNucleotide;
+    const antiFirst = dup.antisense!.monomers[0] as ParsedNucleotide;
+    // pre-fix: '[5meC]'  post-fix: '5meC'
+    expect(senseFirst.base, '5meC');
+    expect(senseSecond.sugar, 'fl2r');
+    // pre-fix: '[5Br-dC]'  post-fix: '5Br-dC'
+    expect(senseSecond.base, '5Br-dC');
+    expect(senseSecond.phosphate, 'sp');
+    // pre-fix: '[5fU]'  post-fix: '5fU'
+    expect(antiFirst.base, '5fU');
+  });
+
+  test('parser leaves bare-letter base unchanged', async () => {
+    // Regression guard: single-letter bases must NOT be transformed.
+    // A, G, C, T, U are all single-char and do not have brackets → unchanged by cleanupHelmSymbol.
+    const dup = parseHelmDuplex('RNA1{r(A)p.r(G)p.r(C)p.r(T)p.r(U)p}$$$$');
+    const bases = dup.sense.monomers.map((m) => (m as ParsedNucleotide).base);
+    // Expected: ['A', 'G', 'C', 'T', 'U'] — unchanged for all five bases.
+    expect(bases.join(','), 'A,G,C,T,U');
+  });
+
+  test('canonicalizeHelm re-brackets multi-char base on output', async () => {
+    // serializeCanonicalMonomer emits `([${base}])` when base.length > 1.
+    // pre-fix: emitted '(5Br-dC)' (invalid HELM, missing brackets).
+    // post-fix: emits '([5Br-dC])' — round-trip is valid HELM.
+    const out = canonicalizeHelm('RNA1{r([5Br-dC])p}$$$$');
+    // Must contain the bracketed base form.
+    expect(out.includes('([5Br-dC])'), true,
+      `expected canonicalized HELM to contain '([5Br-dC])', got: ${out}`);
+    // Must NOT contain the bare (unbracketed) form.
+    expect(out.includes('(5Br-dC)') && !out.includes('([5Br-dC])'), false,
+      `must not emit unbracketed (5Br-dC) without wrapping brackets, got: ${out}`);
+  });
+
+  test('canonicalizeHelm keeps single-letter base unbracketed', async () => {
+    // serializeCanonicalMonomer: base.length === 1 → `(${base})`, not `([${base}])`.
+    // Expected output contains 'r(A)p' — single letter stays bare.
+    const out = canonicalizeHelm('RNA1{r(A)p}$$$$');
+    expect(out.includes('r(A)p'), true,
+      `expected single-letter base to stay unbracketed, got: ${out}`);
+    // Single-letter base must NOT get double-bracketed.
+    expect(out.includes('([A])'), false,
+      `single-letter base must NOT be wrapped in brackets, got: ${out}`);
+  });
 });
 
 category('OligoRenderer: modification dictionary', () => {