@datagrok/helm 2.1.30 → 2.1.31

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@datagrok/helm",
   "friendlyName": "Helm",
-  "version": "2.1.30",
+  "version": "2.1.31",
   "author": {
     "name": "Oleksandra Serhiienko",
     "email": "oserhiienko@datagrok.ai"
@@ -15,8 +15,8 @@
     "helm/JSDraw/Pistoia.HELM-uncompressed.js"
   ],
   "dependencies": {
-    "@datagrok-libraries/bio": "^5.39.29",
-    "@datagrok-libraries/chem-meta": "^1.2.2",
+    "@datagrok-libraries/bio": "^5.40.0",
+    "@datagrok-libraries/chem-meta": "^1.2.3",
     "@datagrok-libraries/utils": "^4.1.45",
     "cash-dom": "^8.1.1",
     "datagrok-api": "^1.17.0",
@@ -37,8 +37,8 @@
     "@typescript-eslint/parser": "^5.11.0",
     "eslint": "^8.18.0",
     "eslint-config-google": "^0.14.0",
-    "@datagrok/bio": "^2.11.38",
-    "@datagrok/chem": "^1.8.13"
+    "@datagrok/bio": "^2.12.0",
+    "@datagrok/chem": "^1.9.0"
   },
   "scripts": {
     "link-all": "npm link @datagrok-libraries/chem-meta datagrok-api @datagrok-libraries/utils @datagrok-libraries/bio",

package/src/package.ts

@@ -7,7 +7,7 @@ import $ from 'cash-dom';
 
 import {errorToConsole} from '@datagrok-libraries/utils/src/to-console';
 import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
-import {GapSymbols, UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
+import {GapOriginals, SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
 import {IMonomerLib, Monomer} from '@datagrok-libraries/bio/src/types';
 import {IHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
 
@@ -156,17 +156,17 @@ export function helmCellRenderer(): HelmCellRenderer {
   return new HelmCellRenderer();
 }
 
-function checkMonomersAndOpenWebEditor(cell?: DG.Cell, value?: string, units?: string) {
+function checkMonomersAndOpenWebEditor(cell: DG.Cell, value?: string, units?: string) {
   const cellValue: string = !!cell && units === undefined ? cell.value : value;
   const monomerList: string[] = parseHelm(cellValue);
-  const monomers = findMonomers(monomerList);
-  if (monomers.size === 0)
+  const missedMonomerSet = findMonomers(monomerList);
+  if (missedMonomerSet.size === 0)
     webEditor(cell, value, units);
-  else if (monomers.size === 1 && monomers.has(GapSymbols[NOTATION.HELM]))
-    grok.shell.warning(`WebEditor doesn't support Helm with gaps '${GapSymbols[NOTATION.HELM]}'.`);
+  else if (missedMonomerSet.size === 1 && missedMonomerSet.has(GapOriginals[NOTATION.HELM]))
+    grok.shell.warning(`WebEditor doesn't support Helm with gaps '${GapOriginals[NOTATION.HELM]}'.`);
   else {
     grok.shell.warning(
-      `Monomers ${Array.from(monomers).map((m) => `'${m}'`).join(', ')} are absent! <br/>` +
+      `Monomers ${Array.from(missedMonomerSet).map((m) => `'${m}'`).join(', ')} are absent! <br/>` +
       `Please, upload the monomer library! <br/>` +
       `<a href="https://datagrok.ai/help/domains/bio/macromolecules" target="_blank">Learn more</a>`);
   }
@@ -187,11 +187,11 @@ export function editMoleculeCell(cell: DG.GridCell): void {
 export function openEditor(mol: string): void {
   const df = grok.shell.tv.grid.dataFrame;
   const col = df.columns.bySemType('Macromolecule')!;
-  const colUh = UnitsHandler.getOrCreate(col);
+  const colSh = SeqHandler.forColumn(col);
   const colUnits = col.getTag(DG.TAGS.UNITS);
   if (colUnits === NOTATION.HELM)
     checkMonomersAndOpenWebEditor(df.currentCell, undefined, undefined);
-  const convert = colUh.getConverter(NOTATION.HELM);
+  const convert = colSh.getConverter(NOTATION.HELM);
   const helmMol = convert(mol);
   checkMonomersAndOpenWebEditor(df.currentCell, helmMol, col.getTag(DG.TAGS.UNITS));
 }
@@ -204,11 +204,13 @@ export function propertiesWidget(sequence: DG.SemanticValue): DG.Widget {
   return getPropertiesWidget(sequence);
 }
 
-function webEditor(cell?: DG.Cell, value?: string, units?: string) {
+function webEditor(cell: DG.Cell, value?: string, units?: string) {
   const view = ui.div();
-  const df = grok.shell.tv.grid.dataFrame;
-  const col = df.columns.bySemType('Macromolecule')!;
-  const uh = UnitsHandler.getOrCreate(col);
+  // const df = grok.shell.tv.grid.dataFrame;
+  // const col = df.columns.bySemType('Macromolecule')!;
+  const col = cell.column;
+  const sh = SeqHandler.forColumn(col);
+  const rowIdx = cell.rowIndex;
   // @ts-ignore
   org.helm.webeditor.MolViewer.molscale = 0.8;
   // @ts-ignore
@@ -244,13 +246,13 @@ function webEditor(cell?: DG.Cell, value?: string, units?: string) {
   ui.dialog({showHeader: false, showFooter: true})
     .add(view)
     .onOK(() => {
-      const helmValue = app.canvas.getHelm(true).replace(/<\/span>/g, '')
+      const helmValue: string = app.canvas.getHelm(true).replace(/<\/span>/g, '')
         .replace(/<span style='background:#bbf;'>/g, '');
       if (!!cell) {
         if (units === undefined)
           cell.value = helmValue;
         else {
-          const convertedRes = uh.convertHelmToFastaSeparator(helmValue, units!);
+          const convertedRes = sh.convertHelmToFastaSeparator(helmValue, units!, sh.separator);
           cell.value = convertedRes;
         }
       }

package/src/tests/properties-widget-tests.ts

@@ -4,7 +4,7 @@ import * as grok from 'datagrok-api/grok';
 
 import {category, expect, expectObject, test} from '@datagrok-libraries/utils/src/test';
 import {ALPHABET, NOTATION, TAGS as bioTAGS} from '@datagrok-libraries/bio/src/utils/macromolecule';
-import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
+import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
 
 import {getPropertiesDict} from '../widgets/properties-widget';
 
@@ -75,7 +75,7 @@ function testPropertiesDict(
   col.setTag(DG.TAGS.UNITS, units);
   if (separator) col.setTag(bioTAGS.separator, separator);
   if (alphabet) col.setTag(bioTAGS.alphabet, alphabet);
-  const uh = UnitsHandler.getOrCreate(col);
+  const uh = SeqHandler.forColumn(col);
   const actPropDict = getPropertiesDict(seq, uh);
   expectObject(actPropDict, expPropDict);
 }

package/src/widgets/properties-widget.ts

@@ -4,13 +4,13 @@ import * as DG from 'datagrok-api/dg';
 
 import $ from 'cash-dom';
 
-import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
+import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
 import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
 
 import {removeGapsFromHelm} from '../utils';
 
-export function getPropertiesDict(seq: string, uh: UnitsHandler): {} {
-  const helmString = uh.isHelm() ? seq : uh.getConverter(NOTATION.HELM)(seq);
+export function getPropertiesDict(seq: string, sh: SeqHandler): {} {
+  const helmString = sh.isHelm() ? seq : sh.getConverter(NOTATION.HELM)(seq);
   // Remove gap symbols for compatibility with WebEditor
   const helmString2 = removeGapsFromHelm(helmString);
 
@@ -36,8 +36,8 @@ export function getPropertiesDict(seq: string, uh: UnitsHandler): {} {
 
 
 export function getPropertiesWidget(value: DG.SemanticValue): DG.Widget {
-  const uh = UnitsHandler.getOrCreate(value.cell.column);
-  const propDict = getPropertiesDict(value.value, uh);
+  const sh = SeqHandler.forColumn(value.cell.column);
+  const propDict = getPropertiesDict(value.value, sh);
   return new DG.Widget(
     ui.tableFromMap(propDict)
   );