@datagrok/helm 2.2.0 → 2.3.0

package/src/package.ts

@@ -3,161 +3,138 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-// import '@datagrok-libraries/bio/src/types/dojo';
-// import * as dojo from 'DOJO';
-import '@datagrok-libraries/bio/src/types/helm';
-import * as scil from 'scil';
-import * as org from 'org';
-import '@datagrok-libraries/bio/src/types/jsdraw2';
-import * as JSDraw2 from 'JSDraw2';
-
 import $ from 'cash-dom';
 
+import {testEvent} from '@datagrok-libraries/utils/src/test';
 import {errorToConsole} from '@datagrok-libraries/utils/src/to-console';
+import {errInfo} from '@datagrok-libraries/bio/src/utils/err-info';
 import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
-import {GapOriginals, SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
-import {IMonomerLib, Monomer} from '@datagrok-libraries/bio/src/types';
+import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
+import {IMonomerLib} from '@datagrok-libraries/bio/src/types';
+import {App, HweWindow} from '@datagrok-libraries/bio/src/helm/types';
 import {IHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
 import {HelmServiceBase} from '@datagrok-libraries/bio/src/viewers/helm-service';
+import {getMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
 
-import {findMonomers, parseHelm} from './utils';
 import {HelmCellRenderer} from './cell-renderer';
 import {HelmHelper} from './helm-helper';
 import {getPropertiesWidget} from './widgets/properties-widget';
 import {HelmGridCellRenderer, HelmGridCellRendererBack} from './utils/helm-grid-cell-renderer';
-import {_getHelmService} from './package-utils';
+import {_getHelmService, HelmPackage, initHelmLoadAndPatchDojo} from './package-utils';
+import {RGROUP_CAP_GROUP_NAME, RGROUP_LABEL, SMILES} from './constants';
+import {getRS} from './utils/get-monomer-dummy';
 
-import {WebEditorMonomer, RGROUP_CAP_GROUP_NAME, RGROUP_LABEL, SMILES} from './constants';
+// Do not import anything than types from @datagrok/helm-web-editor/src/types
+import {buildWebEditorApp} from './helm-web-editor';
+import {JSDraw2HelmModule, OrgHelmModule, ScilModule} from './types';
+
+export const _package = new HelmPackage();
 
 let monomerLib: IMonomerLib | null = null;
 
-export const _package = new DG.Package();
-
-function initHelmPatchDojo(): void {
-  // patch window.dojox.gfx.svg.Text.prototype.getTextWidth hangs
-  /** get the text width in pixels */
-  // @ts-ignore
-  window.dojox.gfx.svg.Text.prototype.getTextWidth = function() {
-    const rawNode = this.rawNode;
-    const oldParent = rawNode.parentNode;
-    const _measurementNode = rawNode.cloneNode(true);
-    _measurementNode.style.visibility = 'hidden';
-
-    // solution to the "orphan issue" in FF
-    let _width = 0;
-    const _text = _measurementNode.firstChild.nodeValue;
-    oldParent.appendChild(_measurementNode);
-
-    // solution to the "orphan issue" in Opera
-    // (nodeValue == "" hangs firefox)
-    if (_text != '') {
-      let watchdogCounter = 100;
-      while (!_width && --watchdogCounter > 0) { // <-- hangs
-        //Yang: work around svgweb bug 417 -- http://code.google.com/p/svgweb/issues/detail?id=417
-        if (_measurementNode.getBBox)
-          _width = parseInt(_measurementNode.getBBox().width);
-        else
-          _width = 68;
-      }
-    }
-    oldParent.removeChild(_measurementNode);
-    return _width;
-  };
-}
+/*
+  Loading modules:
+  Through Helm/package.json/sources section
+    dojo from ajax.googleapis.com
+    HELMWebEditor
+      JSDraw.Lite is embedded into HELMWebEditor bundle (dist/package.js)
+ */
+
+declare const window: Window & HweWindow;
+declare const scil: ScilModule;
+declare const JSDraw2: JSDraw2HelmModule;
+declare const org: OrgHelmModule;
 
 //tags: init
 export async function initHelm(): Promise<void> {
-  const logPrefix: string = 'Helm: initHelm()';
+  const logPrefix: string = 'Helm: _package.initHelm()';
   _package.logger.debug(`${logPrefix}, start`);
-  org.helm.webeditor.kCaseSensitive = true; // GROK-13880
-
-  return Promise.all([
-    new Promise((resolve, reject) => {
-      // @ts-ignore
-      dojo.ready(function() { resolve(null); });
-    }).then(() => {
-      initHelmPatchDojo();
-    }),
-    grok.functions.call('Bio:getBioLib'),
-  ])
-    .then(([_, lib]: [unknown, IMonomerLib]) => {
-      _package.logger.debug(`${logPrefix}, then(), lib loaded`);
-      monomerLib = lib;
-      rewriteLibraries(); // initHelm()
-      monomerLib.onChanged.subscribe((_) => {
-        try {
-          const logPrefixInt = `${logPrefix} monomerLib.onChanged()`;
-          _package.logger.debug(`${logPrefixInt}, start, org,helm.webeditor.Monomers updating`);
-          rewriteLibraries(); // initHelm()
-
-          const libSummary: string = monomerLib!.getSummary()
-            .replaceAll('\n', '<br />\n')
-            .replaceAll(',', ' ');
-          const libMsg: string = `Monomer lib updated:<br /> ${libSummary}'`;
-          grok.shell.info(libMsg);
-
-          _package.logger.debug(`${logPrefixInt}, end, org.helm.webeditor.Monomers completed`);
-        } catch (err: any) {
-          const errMsg = errorToConsole(err);
-          console.error('Helm: initHelm monomerLib.onChanged() error:\n' + errMsg);
-          // throw err; // Prevent disabling event handler
-        }
-      });
-    })
-    .catch((err: any) => {
-      const errMsg: string = err instanceof Error ? err.message : !!err ? err.toString() : 'Exception \'undefined\'';
-      grok.shell.error(`Package \'Helm\' init initHelm() error: ${errMsg}`);
-      const errRes = new Error(errMsg);
-      errRes.stack = err.stack;
-      throw errRes;
-    });
-}
 
-export function getMonomerLib(): IMonomerLib {
-  return monomerLib!;
-}
-
-/** Fills org.helm.webeditor.Monomers dictionary for WebEditor */
-function rewriteLibraries() {
-  org.helm.webeditor.Monomers.clear();
-  monomerLib!.getPolymerTypes().forEach((polymerType) => {
-    const monomerSymbols = monomerLib!.getMonomerSymbolsByType(polymerType);
-    monomerSymbols.forEach((monomerSymbol) => {
-      let isBroken = false;
-      const monomer: Monomer = monomerLib!.getMonomer(polymerType, monomerSymbol)!;
-      const webEditorMonomer: WebEditorMonomer = {
-        id: monomerSymbol,
-        m: monomer.molfile,
-        n: monomer.name,
-        na: monomer.naturalAnalog,
-        rs: monomer.rgroups.length,
-        type: monomer.polymerType,
-        mt: monomer.monomerType,
-        at: {}
-      };
-
-      if (monomer.rgroups.length > 0) {
-        webEditorMonomer.rs = monomer.rgroups.length;
-        const at: { [prop: string]: any } = {};
-        monomer.rgroups.forEach((it) => {
-          at[it[RGROUP_LABEL]] = it[RGROUP_CAP_GROUP_NAME];
-        });
-        webEditorMonomer.at = at;
-      } else if (monomer[SMILES] != null) {
-        webEditorMonomer.rs = Object.keys(getRS(monomer[SMILES].toString())).length;
-        webEditorMonomer.at = getRS(monomer[SMILES].toString());
-      } else
-        isBroken = true;
-
-      if (!isBroken) {
-        org.helm.webeditor.Monomers.addOneMonomer(webEditorMonomer);
+  try {
+    const [_, lib]: [void, IMonomerLib] = await Promise.all([
+      Promise.all([
+        new Promise<void>((resolve, reject) => {
+          // @ts-ignore
+          // try { dojo.ready(function() { resolve(null); }); } catch (err: any) { reject(err); }
+          resolve();
+        }),
+        (async () => {
+          _package.logger.debug(`${logPrefix}, dependence loading …`);
+          const t1: number = performance.now();
+
+          _package.logger.debug(`${logPrefix}, dojox loading and patching …`);
+          await initHelmLoadAndPatchDojo();
+          _package.logger.debug(`${logPrefix}, dojox loaded and patched`);
+
+          // through webpack.config.ts/alias
+          require('vendor/helm-web-editor');
+
+          _package.logger.debug(`${logPrefix}, HelmWebEditor awaiting …`);
+          await window.helmWebEditor$.initPromise;
+          _package.logger.debug(`${logPrefix}, HelmWebEditor loaded`);
+          org.helm.webeditor.kCaseSensitive = true; // GROK-13880
+
+          _package.logger.debug(`${logPrefix}, scil.Utils.alert patch`);
+          _package.initHelmPatchScilAlert(); // patch immediately
+
+          const t2: number = performance.now();
+          _package.logger.debug(`${logPrefix}, dependence loaded, ET: ${(t2 - t1)} ms`);
+        })()
+      ]).then(() => {
+
+        // settings
+      }),
+      (async () => {
+        const libHelper = await getMonomerLibHelper();
+        return libHelper.getBioLib();
+      })()
+    ]);
+
+    _package.logger.debug(`${logPrefix}, then(), lib loaded`);
+    monomerLib = lib;
+    // rewriteLibraries(); // initHelm()
+    await _package.initHelmPatchPistoia(monomerLib);
+
+    monomerLib.onChanged.subscribe((_) => {
+      const logPrefixInt = `${logPrefix} monomerLib.onChanged()`;
+      try {
+        const libSummary = monomerLib!.getSummaryObj();
+        const isLibEmpty = Object.keys(libSummary).length == 0;
+        const libSummaryLog = isLibEmpty ? 'empty' : Object.entries(libSummary)
+          .map(([pt, count]) => `${pt}: ${count}`)
+          .join(', ');
+        _package.logger.debug(`${logPrefixInt}, start, lib: { ${libSummaryLog} }`);
+
+        const libSummaryHtml = isLibEmpty ? 'empty' : Object.entries(libSummary)
+          .map(([pt, count]) => `${pt} ${count}`)
+          .join('<br />');
+        const libMsg: string = `Monomer lib updated:<br /> ${libSummaryHtml}`;
+        grok.shell.info(libMsg);
+
+        // _package.logger.debug(`${logPrefixInt}, org,helm.webeditor.Monomers updating ...`);
+        // rewriteLibraries(); // initHelm() monomerLib.onChanged()
+        // _package.logger.debug(`${logPrefixInt}, end, org.helm.webeditor.Monomers completed`);
+      } catch (err: any) {
+        const errMsg = errorToConsole(err);
+        console.error(`${logPrefixInt} error:\n` + errMsg);
+        // throw err; // Prevent disabling event handler
       }
     });
-  });
+  } catch (err: any) {
+    const [errMsg, errStack] = errInfo(err);
+    // const errMsg: string = err instanceof Error ? err.message : !!err ? err.toString() : 'Exception \'undefined\'';
+    grok.shell.error(`Package \'Helm\' init error:\n${errMsg}`);
+    const errRes = new Error(`${logPrefix} error:\n  ${errMsg}\n${errStack}`);
+    errRes.stack = errStack;
+    throw errRes;
+  } finally {
+    _package.logger.debug(`${logPrefix}, finally`);
+  }
+  _package.logger.debug(`${logPrefix}, end`);
+}
 
-  // Obsolete
-  const grid: DG.Grid = grok.shell.tv?.grid;
-  if (grid) grid.invalidate();
+export function getMonomerLib(): IMonomerLib | null {
+  return monomerLib;
 }
 
 //name: getHelmService
@@ -172,24 +149,14 @@ export function getHelmService(): HelmServiceBase {
 //meta.columnTags: quality=Macromolecule, units=helm
 //output: grid_cell_renderer result
 export function helmCellRenderer(): HelmCellRenderer {
+  const logPrefix = `Helm: _package.getHelmCellRenderer()`;
+  _package.logger.debug(`${logPrefix}, start`);
   // return new HelmCellRenderer(); // old
   return new HelmGridCellRenderer(); // new
 }
 
 function checkMonomersAndOpenWebEditor(cell: DG.Cell, value?: string, units?: string) {
-  const cellValue: string = !!cell && units === undefined ? cell.value : value;
-  const monomerList: string[] = parseHelm(cellValue);
-  const missedMonomerSet = findMonomers(monomerList);
-  if (missedMonomerSet.size === 0)
-    webEditor(cell, value, units);
-  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 ${Array.from(missedMonomerSet).map((m) => `'${m}'`).join(', ')} are not found. <br/>` +
-      `Please specify the monomer library to use. <br/>` +
-      `<a href="https://datagrok.ai/help/datagrok/solutions/domains/bio/#manage-monomer-libraries" target="_blank">Learn more</a>`);
-  }
+  openWebEditor(cell, value, units);
 }
 
 //tags: cellEditor
@@ -224,41 +191,23 @@ export function propertiesWidget(sequence: DG.SemanticValue): DG.Widget {
   return getPropertiesWidget(sequence);
 }
 
-function webEditor(cell: DG.Cell, value?: string, units?: string) {
+function openWebEditor(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 col = cell.column as DG.Column<string>;
   const sh = SeqHandler.forColumn(col);
   const rowIdx = cell.rowIndex;
-  org.helm.webeditor.MolViewer.molscale = 0.8;
-  const app = new org.helm.webeditor.App(view, {
-    showabout: false,
-    mexfontsize: '90%',
-    mexrnapinontab: true,
-    topmargin: 20,
-    mexmonomerstab: true,
-    sequenceviewonly: false,
-    mexfavoritefirst: true,
-    mexfilter: true
-  });
-  const sizes = app.calculateSizes();
-  app.canvas.resize(sizes.rightwidth - 100, sizes.topheight - 210);
-  let s = {width: sizes.rightwidth - 100 + 'px', height: sizes.bottomheight + 'px'};
-  scil.apply(app.sequence.style, s);
-  scil.apply(app.notation.style, s);
-  s = {width: sizes.rightwidth + 'px', height: (sizes.bottomheight + app.toolbarheight) + 'px'};
-  scil.apply(app.properties.parent.style, s);
-  app.structureview.resize(sizes.rightwidth, sizes.bottomheight + app.toolbarheight);
-  app.mex.resize(sizes.topheight - 80);
-  setTimeout(() => {
+  let app: App;
+  setTimeout(async () => {
+    app = await buildWebEditorApp(view);
     if (!!cell && units === undefined)
       app.canvas.helm.setSequence(cell.value, 'HELM');
     else
       app.canvas.helm.setSequence(value!, 'HELM');
-  }, 200);
-  ui.dialog({showHeader: false, showFooter: true})
-    .add(view)
+  }, 20);
+  const dlg = ui.dialog({showHeader: false, showFooter: true});
+  dlg.add(view)
     .onOK(() => {
       const helmValue: string = app.canvas.getHelm(true).replace(/<\/span>/g, '')
         .replace(/<span style='background:#bbf;'>/g, '');
@@ -271,30 +220,10 @@ function webEditor(cell: DG.Cell, value?: string, units?: string) {
         }
       }
     }).show({modal: true, fullScreen: true});
-}
 
-function getRS(smiles: string) {
-  const newS = smiles.match(/(?<=\[)[^\][]*(?=])/gm);
-  const res: { [name: string]: string } = {};
-  let el = '';
-  let digit;
-  if (!!newS) {
-    for (let i = 0; i < newS.length; i++) {
-      if (newS[i] != null) {
-        if (/\d/.test(newS[i])) {
-          digit = newS[i][newS[i].length - 1];
-          newS[i] = newS[i].replace(/[0-9]/g, '');
-          for (let j = 0; j < newS[i].length; j++) {
-            if (newS[i][j] != ':')
-              el += newS[i][j];
-          }
-          res['R' + digit] = el;
-          el = '';
-        }
-      }
-    }
-  }
-  return res;
+  // Quick fix for full screen dialog
+  const dlgCntDiv = $(dlg.root).find('div').get()[0] as HTMLDivElement;
+  dlgCntDiv.className = dlgCntDiv.className.replace('dlg- ui-form', 'dlg-ui-form');
 }
 
 //name: getMolfiles
@@ -324,12 +253,9 @@ export function getMolfiles(col: DG.Column): DG.Column {
 //name: getHelmHelper
 //output: object result
 export async function getHelmHelper(): Promise<IHelmHelper> {
-  return HelmHelper.getInstance();
+  return _package.hh;
 }
 
-import {testEvent} from '@datagrok-libraries/utils/src/test';
-import {CellRendererBackAsyncBase} from '@datagrok-libraries/bio/src/utils/cell-renderer-async-base';
-
 //name: measureCellRenderer
 export async function measureCellRenderer(): Promise<void> {
   const grid = grok.shell.tv.grid;

package/src/tests/findMonomers-tests.ts

@@ -10,6 +10,7 @@ import {
 } from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
 
 import {findMonomers, parseHelm} from '../utils';
+import {initHelmMainPackage} from './utils';
 
 
 /** Tests with default monomer library */
@@ -19,6 +20,7 @@ category('findMonomers', () => {
   let userLibSettings: UserLibSettings;
 
   before(async () => {
+    await initHelmMainPackage();
     monomerLibHelper = await getMonomerLibHelper();
     userLibSettings = await getUserLibSettings();
 

package/src/tests/get-all-parts-tests.ts

@@ -5,6 +5,7 @@ import * as DG from 'datagrok-api/dg';
 import {after, before, category, delay, expect, test, expectArray} from '@datagrok-libraries/utils/src/test';
 
 import {getAllParts} from '../helm-monomer-placer';
+import {initHelmMainPackage} from './utils';
 
 category('getAllParts', () => {
   /** All parts of Helm string are required for fallback rendering. */
@@ -21,6 +22,10 @@ category('getAllParts', () => {
     }
   };
 
+  before(async () => {
+    await initHelmMainPackage();
+  });
+
   for (const [testName, testData] of Object.entries(tests)) {
     test(`${testName}`, async () => {
       await _testAllParts(testData.seq, testData.tgt);

package/src/tests/{get-molfiles.ts → get-molfiles-tests.ts}

@@ -3,6 +3,7 @@ import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
 import {after, before, category, delay, expect, test, expectArray, testEvent} from '@datagrok-libraries/utils/src/test';
+import {getHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
 import {
   getUserLibSettings, setUserLibSettings, setUserLibSettingsForTests
 } from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
@@ -11,7 +12,7 @@ import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/sr
 import {MolfileHandler} from '@datagrok-libraries/chem-meta/src/parsing-utils/molfile-handler';
 import {MolfileHandlerBase} from '@datagrok-libraries/chem-meta/src/parsing-utils/molfile-handler-base';
 
-import {awaitGrid} from './utils';
+import {awaitGrid, initHelmMainPackage} from './utils';
 
 import {_package} from '../package-test';
 
@@ -20,6 +21,7 @@ category('getMolfiles', () => {
   let userLibSettings: UserLibSettings;
 
   before(async () => {
+    await initHelmMainPackage();
     monomerLibHelper = await getMonomerLibHelper();
     userLibSettings = await getUserLibSettings();
     await setUserLibSettingsForTests();