@datagrok/helm 2.2.0 → 2.3.0

package/src/utils/helm-service.ts

@@ -2,25 +2,26 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import * as org from 'org';
-import * as scil from 'scil';
-import * as JSDraw2 from 'JSDraw2';
-
 import $ from 'cash-dom';
 import {Subject, Unsubscribable} from 'rxjs';
 
 import {errInfo} from '@datagrok-libraries/bio/src/utils/err-info';
-import {HelmAux, HelmProps, HelmServiceBase} from '@datagrok-libraries/bio/src/viewers/helm-service';
+import {IMonomerLib} from '@datagrok-libraries/bio/src/types/index';
+import {Editor, HelmType} from '@datagrok-libraries/bio/src/helm/types';
 import {RenderTask} from '@datagrok-libraries/bio/src/utils/cell-renderer-async-base';
+import {HelmAux, HelmProps, HelmServiceBase} from '@datagrok-libraries/bio/src/viewers/helm-service';
 import {svgToImage} from '@datagrok-libraries/utils/src/svg';
 
+import {JSDraw2HelmModule} from '../types';
+
 import {_package} from '../package';
-import {DummyWebEditorMonomer} from './dummy-monomer';
+
+declare const JSDraw2: JSDraw2HelmModule;
 
 export class HelmService extends HelmServiceBase {
   private readonly hostDiv: HTMLDivElement;
 
-  private editor: JSDraw2.Editor | null = null;
+  private editor!: Editor<HelmType>;
   private image: HTMLImageElement | null = null;
 
   constructor() {
@@ -57,46 +58,18 @@ export class HelmService extends HelmServiceBase {
     this.editor.options.height = task.props.height;
     this.editor.resize(task.props.width, task.props.height);
     const helmStr = task.props.helm;
-    let hasMissing: boolean = false;
     if (helmStr) {
-      const monomers = org.helm.webeditor.Monomers;
-      const originalGetMonomer = monomers.getMonomer;
-      const originalAlert = scil.Utils.alert;
-      try {
-        org.helm.webeditor.Monomers.getMonomer = (a: org.helm.IAtom | string, name: string): org.helm.IAtom | null => {
-          let resAtom: any = originalGetMonomer.bind(monomers)(a, name);
-
-          if (!resAtom) {
-            // Input logic
-            if (a == null && name == null)
-              return null;
-
-            let s: string;
-            let biotype: string;
-            if (name == null) {
-              biotype = (a as org.helm.IAtom).biotype();
-              s = (a as org.helm.IAtom).elem;
-            } else {
-              biotype = a as string;
-              s = org.helm.webeditor.IO.trimBracket(name);
-            }
-            resAtom = new DummyWebEditorMonomer(biotype, s);
-            //hasMissing = true;
-          }
-          return resAtom;
-        };
-        // Preventing alert message box for missing monomers with compressed Scilligence.JSDraw2.Lite.js
-        scil.Utils.alert = (s: string): void => {
-          this.logger.warning(`${logPrefix}, scil.Utils.alert() s = 's'.`);
-        };
-        this.logger.debug(`${logPrefix}, editor.setData( '${helmStr}' )`);
-        this.editor.setData(helmStr, 'helm');
-      } finally {
-        monomers.getMonomer = originalGetMonomer;
-        scil.Utils.alert = originalAlert;
-      }
+      // getMonomerOverrideAndLogAlert(
+      //   this.monomerLib,
+      //   getMonomerPatched,
+      //   () => {
+      //     this.logger.debug(`${logPrefix}, editor.setData( '${helmStr}' )`);
+      //     this.editor.setData(helmStr, 'helm');
+      //   }, this.logger);
+      this.logger.debug(`${logPrefix}, editor.setData( '${helmStr}' )`);
+      this.editor.setData(helmStr, 'helm');
     }
-    if (!helmStr || hasMissing)
+    if (!helmStr)
       this.editor.reset();
 
     const bBox = (this.editor.div.children[0] as SVGSVGElement).getBBox();
@@ -155,3 +128,4 @@ export class HelmService extends HelmServiceBase {
 
   async reset(): Promise<void> { }
 }
+

package/src/utils/index.ts

@@ -1,9 +1,8 @@
+import * as grok from 'datagrok-api/grok';
+import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import * as scil from 'scil';
-import * as org from 'org';
-
-import {_package} from '../package';
+import {OrgHelmModule, ScilModule} from '../types';
 
 import {
   RGROUP_CAP_GROUP_NAME,
@@ -16,6 +15,11 @@ import {
   SDF_MONOMER_NAME
 } from '../constants';
 
+import {getMonomerLib} from '../package';
+
+declare const scil: ScilModule;
+declare const org: OrgHelmModule;
+
 // Global flag is for replaceAll
 const helmGapStartRe = /\{(\*\.)+/g;
 const helmGapIntRe = /\.(\*\.)+/g;
@@ -109,19 +113,9 @@ export function parseHelm(s: string): string[] {
 // }
 
 /** Searches monomers of helmString for missed. */
-export function findMonomers(monomerSymbolList: string[]): Set<string> {
-  const types = Object.keys(org.helm.webeditor.monomerTypeList());
-  const monomers: any = [];
-  const monomerNames: any = [];
-  for (let i = 0; i < types.length; i++) {
-    // @ts-ignore
-    // eslint-disable-next-line new-cap
-    monomers.push(new org.helm.webeditor.Monomers.getMonomerSet(types[i]));
-    Object.keys(monomers[i]).forEach((k) => {
-      monomerNames.push(monomers[i][k].id);
-    });
-  }
-  return new Set(monomerSymbolList.filter((val) => !monomerNames.includes(val)));
+export function findMonomers(seqMonomerSymbolList: string[]): Set<string> {
+  const monomerLib = getMonomerLib();
+  return new Set(seqMonomerSymbolList.filter((s) => monomerLib?.getMonomer(null, s)));
 }
 
 function findClosing(s: string, start: number, open: string, close: string) {

package/src/widgets/properties-widget.ts

@@ -7,22 +7,34 @@ import $ from 'cash-dom';
 import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
 import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
 
+import {JSDraw2HelmModule} from '../types';
 import {removeGapsFromHelm} from '../utils';
 
-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);
+declare const JSDraw2: JSDraw2HelmModule;
 
+export class SeqPropertiesError extends Error {
+  constructor(message?: string, options?: ErrorOptions) {
+    super(message, options);
+  }
+}
+
+export function getPropertiesDict(seq: string, sh: SeqHandler): {} {
   const host = ui.div([], {style: {width: '0', height: '0'}});
   document.documentElement.appendChild(host);
   try {
+    if (seq.length > 1000)
+      throw new SeqPropertiesError('Too long sequence to calculate molecular properties.');
+
+    const helmString = sh.isHelm() ? seq : sh.getConverter(NOTATION.HELM)(seq);
+    // Remove gap symbols for compatibility with WebEditor
+    const helmString2 = removeGapsFromHelm(helmString);
+
     const editor = new JSDraw2.Editor(host, {viewonly: true});
     editor.setHelm(helmString2);
 
     const formula = editor.getFormula(true);
     const molWeight = Math.round(editor.getMolWeight() * 100) / 100;
-    const coef = Math.round(editor.getExtinctionCoefficient(true) * 100) / 100;
+    const coef = Math.round(editor.getExtinctionCoefficient() * 100) / 100;
     return {
       'formula': formula.replace(/<sub>/g, '').replace(/<\/sub>/g, ''),
       'molecular weight': molWeight,
@@ -37,8 +49,16 @@ export function getPropertiesDict(seq: string, sh: SeqHandler): {} {
 
 export function getPropertiesWidget(value: DG.SemanticValue): DG.Widget {
   const sh = SeqHandler.forColumn(value.cell.column);
-  const propDict = getPropertiesDict(value.value, sh);
-  return new DG.Widget(
-    ui.tableFromMap(propDict)
-  );
+  try {
+    const propDict = getPropertiesDict(value.value, sh);
+    return new DG.Widget(
+      ui.tableFromMap(propDict)
+    );
+  } catch (err: any) {
+    if (err instanceof SeqPropertiesError) {
+      // Display warning from err.message
+      return new DG.Widget(ui.divText(err.message));
+    }
+    throw err;
+  }
 }

package/tsconfig.json

@@ -65,7 +65,7 @@
     "emitDecoratorMetadata": true,                  /* Enables experimental support for emitting type metadata for decorators. */
 
     /* Advanced Options */
-    "skipLibCheck": false,                          /* Skip type checking of declaration files. */
+    "skipLibCheck": true,                           /* Skip type checking of declaration files. */
     "forceConsistentCasingInFileNames": true,       /* Disallow inconsistently-cased references to the same file. */
     //"jsx": "react"
   }