@datagrok/bio 2.15.1 → 2.15.3

package/package.json

@@ -5,7 +5,7 @@
     "name": "Aleksandr Tanas",
     "email": "atanas@datagrok.ai"
   },
-  "version": "2.15.1",
+  "version": "2.15.3",
   "description": "Bioinformatics support (import/export of sequences, conversion, visualization, analysis). [See more](https://github.com/datagrok-ai/public/blob/master/packages/Bio/README.md) for details.",
   "repository": {
     "type": "git",
@@ -37,12 +37,12 @@
   ],
   "dependencies": {
     "@biowasm/aioli": "^3.1.0",
-    "@datagrok-libraries/bio": "^5.42.15",
+    "@datagrok-libraries/bio": "^5.43.1",
     "@datagrok-libraries/chem-meta": "^1.2.5",
     "@datagrok-libraries/math": "^1.2.0",
-    "@datagrok-libraries/ml": "^6.7.0",
+    "@datagrok-libraries/ml": "^6.7.1",
     "@datagrok-libraries/tutorials": "^1.4.0",
-    "@datagrok-libraries/utils": "^4.3.0",
+    "@datagrok-libraries/utils": "^4.3.3",
     "@webgpu/types": "^0.1.40",
     "ajv": "^8.12.0",
     "ajv-errors": "^3.0.0",
@@ -83,12 +83,12 @@
     "link-bio": "npm link @datagrok-libraries/bio",
     "link-ml": "npm link @datagrok-libraries/ml",
     "link-utils": "npm link @datagrok-libraries/utils",
-    "link-all": "npm link @datagrok-libraries/chem-meta datagrok-api @datagrok-libraries/utils @datagrok-libraries/math @datagrok-libraries/ml @datagrok-libraries/bio @datagrok-libraries/tutorials",
+    "link-all": "npm link @datagrok-libraries/chem-meta datagrok-api @datagrok-libraries/math @datagrok-libraries/utils @datagrok-libraries/ml @datagrok-libraries/bio @datagrok-libraries/tutorials",
     "debug-sequences1": "webpack && grok publish",
     "release-sequences1": "webpack && grok publish --release",
     "build-sequences1": "webpack",
     "build": "webpack",
-    "build-all": "npm --prefix ./../../libraries/chem-meta run build && npm --prefix ./../../js-api run build && npm --prefix ./../../libraries/utils run build && npm --prefix ./../../libraries/math run build && npm --prefix ./../../libraries/ml run build && npm --prefix ./../../libraries/bio run build && npm --prefix ./../../libraries/tutorials run build && npm run build",
+    "build-all": "npm --prefix ./../../libraries/chem-meta run build && npm --prefix ./../../js-api run build && npm --prefix ./../../libraries/math run build && npm --prefix ./../../libraries/utils run build && npm --prefix ./../../libraries/ml run build && npm --prefix ./../../libraries/bio run build && npm --prefix ./../../libraries/tutorials run build && npm run build",
     "debug-sequences1-local": "webpack && grok publish local",
     "release-sequences1-local": "webpack && grok publish local --release",
     "debug-sequences1-dev": "webpack && grok publish dev",
@@ -153,4 +153,4 @@
       }
     }
   }
-}
+}

package/src/package-test.ts

@@ -2,7 +2,7 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {runTests, TestContext, tests} from '@datagrok-libraries/utils/src/test';
+import {runTests, TestContext, tests, initAutoTests as initTests } from '@datagrok-libraries/utils/src/test';
 
 import './tests/_first-tests';
 import './tests/Palettes-test';
@@ -52,3 +52,8 @@ export async function test(category: string, test: string, testContext: TestCont
   const data = await runTests({category, test, testContext, stressTest});
   return DG.DataFrame.fromObjects(data)!;
 }
+
+//name: initAutoTests
+export async function initAutoTests() {
+  await initTests(_package, _package.getModule('package-test.js'));
+}

package/src/tests/pepsea-tests.ts

@@ -63,5 +63,5 @@ category('PepSeA', () => {
       logger.error(errMsg, undefined, errStack);
     }
     expect(logger.errorList[0].message, pepseaErrorError);
-  });
+  },{skipReason: 'GROK-16699'});
 });

package/src/utils/monomer-cell-renderer.ts

@@ -4,7 +4,8 @@ import * as ui from 'datagrok-api/ui';
 
 import {PolymerType} from '@datagrok-libraries/bio/src/helm/types';
 import {ALPHABET, getPaletteByType, monomerToShort} from '@datagrok-libraries/bio/src/utils/macromolecule';
-import {TAGS as bioTAGS} from '@datagrok-libraries/bio/src/utils/macromolecule/consts';
+import {TAGS as bioTAGS, } from '@datagrok-libraries/bio/src/utils/macromolecule/consts';
+import {MONOMER_RENDERER_TAGS} from '@datagrok-libraries/bio/src/utils/cell-renderer';
 import {MonomerWorks} from '@datagrok-libraries/bio/src/monomer-works/monomer-works';
 
 import * as C from './constants';
@@ -92,7 +93,7 @@ export class MonomerCellRenderer extends DG.GridCellRenderer {
   ): void {
     if (gridCell.gridRow < 0) return;
     MonomerTooltipHandler.getOrCreate(gridCell.gridColumn);
-
+    const applyToBackground = gridCell.cell?.column && gridCell.cell.column.getTag(MONOMER_RENDERER_TAGS.applyToBackground) === 'true';
 
     g.font = `12px monospace`;
     g.textBaseline = 'middle';
@@ -103,11 +104,14 @@ export class MonomerCellRenderer extends DG.GridCellRenderer {
     if (!s)
       return;
     const color = palette.get(s);
-
-    g.fillStyle = color;
     //cell width of monomer should dictate how many characters can be displayed
     // for width 40, 6 characters can be displayed (0.15 is 6 / 40)
     const maxChars = Math.max(2, Math.floor(w * 0.15));
+    g.fillStyle = color;
+    if (applyToBackground) {
+      g.fillRect(x, y, w, h);
+      g.fillStyle = DG.Color.toHtml(DG.Color.getContrastColor(DG.Color.fromHtml(color)));
+    }
     g.fillText(monomerToShort(s, maxChars), x + (w / 2), y + (h / 2), w);
   }
 }

package/src/utils/monomer-lib/monomer-manager/monomer-manager.ts

@@ -907,6 +907,13 @@ function capSmiles(smiles: string, rgroups: RGroup[]) {
 }
 
 function monomerFromDfRow(dfRow: DG.Row): Monomer {
+  // hacky way for now, but meta object for now only supports key value pairs and not nested objects
+  const metaJSON = JSON.parse(dfRow.get(MONOMER_DF_COLUMN_NAMES.META) ?? '{}');
+  for (const key in metaJSON) {
+    if (typeof metaJSON[key] === 'object')
+      metaJSON[key] = JSON.stringify(metaJSON[key]);
+  }
+
   return {
     symbol: dfRow.get(MONOMER_DF_COLUMN_NAMES.SYMBOL),
     name: dfRow.get(MONOMER_DF_COLUMN_NAMES.NAME),
@@ -917,7 +924,7 @@ function monomerFromDfRow(dfRow: DG.Row): Monomer {
     naturalAnalog: dfRow.get(MONOMER_DF_COLUMN_NAMES.NATURAL_ANALOG),
     id: dfRow.get(MONOMER_DF_COLUMN_NAMES.ID),
     rgroups: JSON.parse(dfRow.get(MONOMER_DF_COLUMN_NAMES.R_GROUPS) ?? '[]'),
-    meta: JSON.parse(dfRow.get(MONOMER_DF_COLUMN_NAMES.META) ?? '{}'),
+    meta: metaJSON,
     author: dfRow.get(MONOMER_DF_COLUMN_NAMES.AUTHOR),
     createDate: dfRow.get(MONOMER_DF_COLUMN_NAMES.CREATE_DATE),
   };

package/src/utils/pepsea.ts

@@ -7,6 +7,7 @@ import {Subject} from 'rxjs';
 
 import {testEvent} from '@datagrok-libraries/utils/src/test';
 import {NOTATION, TAGS as bioTAGS, ALIGNMENT, ALPHABET} from '@datagrok-libraries/bio/src/utils/macromolecule';
+import { fetchWrapper } from '@datagrok-libraries/utils/src/fetch-utils';
 import {ILogger} from '@datagrok-libraries/bio/src/utils/logger';
 
 import {checkForSingleSeqClusters} from './multiple-sequence-alignment';
@@ -79,7 +80,7 @@ export async function runPepsea(srcCol: DG.Column<string>, unUsedName: string,
 
   const alignedSequences: string[] = new Array(peptideCount);
   for (const body of bodies) { // getting aligned sequences for each cluster
-    const alignedObject = await requestAlignedObjects(pepseaContainer.id, body, method, gapOpen, gapExtend, logger);
+    const alignedObject = await fetchWrapper(() => requestAlignedObjects(pepseaContainer.id, body, method, gapOpen, gapExtend, logger));
     const alignments = alignedObject.Alignment;
 
     for (const alignment of alignments) { // filling alignedSequencesCol