@datagrok/helm 2.1.3 → 2.1.5

package/package.json

@@ -1,17 +1,17 @@
 {
   "name": "@datagrok/helm",
   "friendlyName": "Helm",
-  "version": "2.1.3",
+  "version": "2.1.5",
   "author": {
     "name": "Oleksandra Serhiienko",
     "email": "oserhiienko@datagrok.ai"
   },
   "description": "",
   "dependencies": {
-    "@datagrok-libraries/bio": "^5.21.0",
+    "@datagrok-libraries/bio": "^5.22.0",
     "@datagrok-libraries/utils": "^1.19.1",
     "cash-dom": "^8.1.1",
-    "datagrok-api": "^1.11.1",
+    "datagrok-api": "^1.10.2",
     "dayjs": "^1.10.6",
     "rxjs": "^6.5.5"
   },

package/src/cell-renderer.ts

@@ -4,6 +4,7 @@ import * as DG from 'datagrok-api/dg';
 
 import {findMonomers, parseHelm, getParts} from './utils';
 import {printLeftOrCentered} from '@datagrok-libraries/bio/src/utils/cell-renderer';
+import {errorToConsole} from '@datagrok-libraries/utils/src/to-console';
 
 
 export class HelmCellRenderer extends DG.GridCellRenderer {
@@ -16,46 +17,51 @@ export class HelmCellRenderer extends DG.GridCellRenderer {
   get defaultHeight(): number | null { return 100; }
 
   onMouseMove(gridCell: DG.GridCell, e: MouseEvent): void {
-    const maxLengthWordsSum = gridCell.cell.column.temp['helm-sum-maxLengthWords'];
-    const maxIndex = Object.values(gridCell.cell.column.temp['helm-maxLengthWords']).length - 1;
-    const argsX = e.offsetX - gridCell.gridColumn.left + (gridCell.gridColumn.left - gridCell.bounds.x);
-    let left = 0;
-    let right = maxIndex;
-    let found = false;
-    maxLengthWordsSum[maxIndex + 1] = argsX + 1;
-    let mid = 0;
-    if (argsX > maxLengthWordsSum[0]) {
-      while (!found) {
-        mid = Math.floor((right + left) / 2);
-        if (argsX >= maxLengthWordsSum[mid] && argsX <= maxLengthWordsSum[mid + 1]) {
-          left = mid;
-          found = true;
-        } else if (argsX < maxLengthWordsSum[mid]) {
-          right = mid - 1;
-        } else if (argsX > maxLengthWordsSum[mid + 1]) {
-          left = mid + 1;
-        }
-        if (left == right) {
-          found = true;
+    try {
+      const maxLengthWordsSum = gridCell.cell.column.temp['helm-sum-maxLengthWords'];
+      const maxIndex = Object.values(gridCell.cell.column.temp['helm-maxLengthWords']).length - 1;
+      const argsX = e.offsetX - gridCell.gridColumn.left + (gridCell.gridColumn.left - gridCell.bounds.x);
+      let left = 0;
+      let right = maxIndex;
+      let found = false;
+      maxLengthWordsSum[maxIndex + 1] = argsX + 1;
+      let mid = 0;
+      if (argsX > maxLengthWordsSum[0]) {
+        while (!found) {
+          mid = Math.floor((right + left) / 2);
+          if (argsX >= maxLengthWordsSum[mid] && argsX <= maxLengthWordsSum[mid + 1]) {
+            left = mid;
+            found = true;
+          } else if (argsX < maxLengthWordsSum[mid]) {
+            right = mid - 1;
+          } else if (argsX > maxLengthWordsSum[mid + 1]) {
+            left = mid + 1;
+          }
+          if (left == right) {
+            found = true;
+          }
         }
       }
+      left = (argsX >= maxLengthWordsSum[left]) ? left + 1 : left;
+      const monomers = findMonomers(gridCell.cell.value);
+      let s: string = gridCell.cell.value ?? '';
+      let subParts: string[] = parseHelm(s);
+      let allParts: string[] = getParts(subParts, s);
+      let tooltipMessage: HTMLElement[] = [];
+      for (let i = 0; i < allParts.length; ++i) {
+        if (monomers.has(allParts[i]))
+          tooltipMessage[i] = ui.divV([
+            ui.divText(`Monomer ${allParts[i]} not found.`),
+            ui.divText('Open the Context Panel, then expand Manage Libraries')
+          ]);
+      }
+      (((tooltipMessage[left]?.childNodes.length ?? 0) > 0))
+        ? ui.tooltip.show(ui.div(tooltipMessage[left]), e.x + 16, e.y + 16)
+        : ui.tooltip.hide();
+    } catch (err: any) {
+      const errMsg: string = errorToConsole(err);
+      console.error('Helm: HelmCellRenderer.onMouseMove() error:\n' + errMsg);
     }
-    left = (argsX >= maxLengthWordsSum[left]) ? left + 1 : left;
-    const monomers = findMonomers(gridCell.cell.value);
-    let s: string = gridCell.cell.value ?? '';
-    let subParts: string[] = parseHelm(s);
-    let allParts: string[] = getParts(subParts, s);
-    let tooltipMessage: HTMLElement[] = [];
-    for (let i = 0; i < allParts.length; ++i) {
-      if (monomers.has(allParts[i]))
-        tooltipMessage[i] = ui.divV([
-          ui.divText(`Monomer ${allParts[i]} not found.`),
-          ui.divText('Open the Context Panel, then expand Manage Libraries')
-        ]);
-    }
-    (((tooltipMessage[left]?.childNodes.length ?? 0) > 0))
-      ? ui.tooltip.show(ui.div(tooltipMessage[left]), e.x + 16, e.y + 16)
-      : ui.tooltip.hide();
   }
 
   render(g: CanvasRenderingContext2D, x: number, y: number, w: number, h: number,

package/src/package.ts

@@ -8,7 +8,8 @@ import {HelmWebEditor} from './helm-web-editor';
 import {HelmCellRenderer} from './cell-renderer';
 import {IMonomerLib, Monomer} from '@datagrok-libraries/bio/src/types';
 import {NotationConverter} from '@datagrok-libraries/bio/src/utils/notation-converter';
-import { findMonomers } from './utils';
+import {findMonomers} from './utils';
+import {errorToConsole} from '@datagrok-libraries/utils/src/to-console';
 
 export const _package = new DG.Package();
 let monomerLib: IMonomerLib | null = null;
@@ -20,18 +21,32 @@ export async function initHelm(): Promise<void> {
     dojo.ready(function() { resolve(null); });
   }), await grok.functions.call('Bio:getBioLib')]).then(([_, lib]: [void, IMonomerLib]) => {
     monomerLib = lib;
-    rewriteLibraries();
+    rewriteLibraries(); // initHelm()
     monomerLib.onChanged.subscribe((_) => {
-      rewriteLibraries();
-    })
+      try {
+        rewriteLibraries(); // initHelm()
+
+        const monTypeList: string[] = monomerLib.getTypes();
+        const msgStr: string = 'Monomer lib updated:<br />' + (
+          monTypeList.length == 0 ? 'empty' : monTypeList.map((monType) => {
+            return `${monType} ${monomerLib.getMonomerNamesByType(monType).length}`;
+          }).join('<br />'));
+
+        grok.shell.info(msgStr);
+      } catch (err: any) {
+        const errMsg = errorToConsole(err);
+        console.error('Helm: initHelm monomerLib.onChanged() error:\n' + errMsg);
+        // throw err; // Prevent disabling event handler
+      }
+    });
   });
 }
 
 function rewriteLibraries() {
   org.helm.webeditor.Monomers.clear();
-  monomerLib.getTypes().forEach(type => {
+  monomerLib.getTypes().forEach((type) => {
     const mms = monomerLib.getMonomerNamesByType(type);
-    mms.forEach(symbol => {
+    mms.forEach((symbol) => {
       let isBroken = false;
       const monomer: Monomer = monomerLib.getMonomer(type, symbol);
       const webEditorMonomer: WebEditorMonomer = {
@@ -43,29 +58,30 @@ function rewriteLibraries() {
         type: monomer.polymerType,
         mt: monomer.monomerType,
         at: {}
-      }; 
+      };
 
-      if(monomer.rgroups.length > 0) {
+      if (monomer.rgroups.length > 0) {
         webEditorMonomer.rs = monomer.rgroups.length;
         const at = {};
         monomer.rgroups.forEach(it => {
           at[it[RGROUP_LABEL]] = it[RGROUP_CAP_GROUP_NAME];
         });
         webEditorMonomer.at = at;
-      } else if (monomer.data[SMILES] != null){
+      } else if (monomer.data[SMILES] != null) {
         webEditorMonomer.rs = Object.keys(getRS(monomer.data[SMILES].toString())).length;
         webEditorMonomer.at = getRS(monomer.data[SMILES].toString());
-      } else
+      } else {
         isBroken = true;
+      }
 
-      if(!isBroken)
+      if (!isBroken)
         org.helm.webeditor.Monomers.addOneMonomer(webEditorMonomer);
     });
   });
 
   // Obsolete
   let grid: DG.Grid = grok.shell.tv.grid;
-  grid.invalidate();
+  if (grid) grid.invalidate();
 }
 
 //name: helmCellRenderer
@@ -78,14 +94,15 @@ export function helmCellRenderer(): HelmCellRenderer {
 }
 
 //tags: cellEditor
-//description: Macromolecule
+//description: Macromolecule  
 //input: grid_cell cell
 export function editMoleculeCell(cell: DG.GridCell): void {
   const monomers = findMonomers(cell.cell.value);
-  if (cell.gridColumn.column.tags[DG.TAGS.UNITS] === 'helm' && monomers.size === 0) 
-    webEditor(cell);
-  else
-    grok.shell.warning(`Monomers ${Array.from(monomers).join(', ')} are absent!`);
+  if (cell.gridColumn.column.tags[DG.TAGS.UNITS] === 'helm')
+    if (monomers.size == 0) 
+      webEditor(cell);
+    else
+      grok.shell.warning(`Monomers ${Array.from(monomers).join(', ')} are absent!`);
 }
 
 //name: Open Helm Web Editor
@@ -96,7 +113,11 @@ export function openEditor(mol: string): void {
   let df = grok.shell.tv.grid.dataFrame;
   let converter = new NotationConverter(df.columns.bySemType('Macromolecule'));
   const resStr = converter.convertStringToHelm(mol, '/');
-  webEditor(undefined, resStr);
+  const monomers = findMonomers(resStr);
+  if (monomers.size == 0) 
+    webEditor(undefined, resStr);
+  else
+    grok.shell.warning(`Monomers ${Array.from(monomers).join(', ')} are absent!`);
 }
 
 //name: Properties