@datagrok/helm 2.0.4 → 2.0.6

package/package.json

@@ -1,18 +1,19 @@
 {
   "name": "@datagrok/helm",
   "friendlyName": "Helm",
-  "version": "2.0.4",
+  "version": "2.0.6",
   "author": {
     "name": "Oleksandra Serhiienko",
     "email": "oserhiienko@datagrok.ai"
   },
   "description": "",
   "dependencies": {
-    "datagrok-api": "^1.6.0",
+    "@datagrok-libraries/utils": "^1.11.1",
+    "@datagrok-libraries/bio": "^5.5.0",
     "cash-dom": "^8.1.1",
+    "datagrok-api": "^1.7.2",
     "dayjs": "^1.10.6",
-    "@datagrok-libraries/utils": "^1.6.2",
-    "@datagrok-libraries/bio": "^5.1.0"
+    "rxjs": "^6.5.5"
   },
   "sources": [
     "css/helm.css",

package/src/helm-web-editor.ts

@@ -0,0 +1,45 @@
+import * as grok from 'datagrok-api/grok';
+import * as ui from 'datagrok-api/ui';
+import * as DG from 'datagrok-api/dg';
+
+export class HelmWebEditor {
+  editorView: any;
+  webEditor: any;
+  host: any;
+  editor: any;
+  w = 200;
+  h = 100;
+  constructor() {
+    this.editorView = ui.div();
+    org.helm.webeditor.MolViewer.molscale = 0.8;
+    this.webEditor = new scil.helm.App(this.editorView, {
+      showabout: false,
+      mexfontsize: '90%',
+      mexrnapinontab: true,
+      topmargin: 20,
+      mexmonomerstab: true,
+      sequenceviewonly: false,
+      mexfavoritefirst: true,
+      mexfilter: true
+    });
+    const sizes = this.webEditor.calculateSizes();
+    this.webEditor.canvas.resize(sizes.rightwidth - 100, sizes.topheight - 210);
+    let s = {width: sizes.rightwidth - 100 + 'px', height: sizes.bottomheight + 'px'};
+    //@ts-ignore
+    scil.apply(this.webEditor.sequence.style, s);
+    //@ts-ignore
+    scil.apply(this.webEditor.notation.style, s);
+    s = {width: sizes.rightwidth + 'px', height: (sizes.bottomheight + this.webEditor.toolbarheight) + 'px'};
+    //@ts-ignore
+    scil.apply(this.webEditor.properties.parent.style, s);
+    this.webEditor.structureview.resize(sizes.rightwidth, sizes.bottomheight + this.webEditor.toolbarheight);
+    this.webEditor.mex.resize(sizes.topheight - 80);
+    this.host = ui.div([], {style: {width: `${this.w}px`, height: `${this.h}px`}});
+    this.editor = new JSDraw2.Editor(this.host, {width: this.w, height: this.h, viewonly: true});
+  }
+
+  resizeEditor(w: number, h: number) {
+    this.editor.setSize(w, h);
+  }
+}
+

package/src/package-test.ts

@@ -1,6 +1,6 @@
 import * as DG from 'datagrok-api/dg';
 import * as grok from 'datagrok-api/grok';
-import {runTests, tests} from '@datagrok-libraries/utils/src/test';
+import {runTests, tests, TestContext} from '@datagrok-libraries/utils/src/test';
 import './tests/helm-tests.ts';
 
 export const _package = new DG.Package();
@@ -10,8 +10,9 @@ export {tests};
 //name: test
 //input: string category {optional: true}
 //input: string test {optional: true}
+//input: object testContext {optional: true}
 //output: dataframe result
-export async function test(category: string, test: string): Promise<DG.DataFrame> {
-  const data = await runTests({category, test});
+export async function test(category: string, test: string, testContext: TestContext): Promise<DG.DataFrame> {
+  const data = await runTests({category, test, testContext});
   return DG.DataFrame.fromObjects(data)!;
 }

package/src/package.ts

@@ -6,14 +6,14 @@ import * as bio from '@datagrok-libraries/bio';
 
 import {createJsonMonomerLibFromSdf} from './utils';
 import {MONOMER_MANAGER_MAP, RGROUPS, RGROUP_CAP_GROUP_NAME, RGROUP_LABEL, SMILES} from './constants';
-import {delay} from '@datagrok-libraries/utils/src/test';
+import {HelmWebEditor} from './helm-web-editor';
+import {Observable, Subject} from 'rxjs';
 
 export const _package = new DG.Package();
 
 const STORAGE_NAME = 'Libraries';
 const LIB_PATH = 'libraries/';
 
-
 //tags: init
 export async function initHelm(): Promise<void> {
   return new Promise(async (resolve, reject) => {
@@ -23,11 +23,11 @@ export async function initHelm(): Promise<void> {
   });
 }
 
+
 async function loadLibraries() {
   let uploadedLibraries: string[] = Object.values(await grok.dapi.userDataStorage.get(STORAGE_NAME, true));
-  for (let i = 0; i < uploadedLibraries.length; ++i) {
-    await monomerManager(await grok.dapi.userDataStorage.getValue(STORAGE_NAME, uploadedLibraries[i], true));
-  }
+  for (let i = 0; i < uploadedLibraries.length; ++i)
+    await monomerManager(uploadedLibraries[i]);
 }
 
 //name: helmCellRenderer
@@ -283,6 +283,12 @@ export async function monomerManager(value: string) {
     }
     org.helm.webeditor.Monomers.addOneMonomer(m);
   });
+
+  // Now after updating org.helm.webeditor.Monomers we update MonomerLib window singleton (fires onChanged event)
+  (getMonomerLibObj() as MonomerLib).update(getAllLibsData());
+  //grok.events.fireCustomEvent('monomersLibChanged', null);
+
+  // Obsolete
   let grid: DG.Grid = grok.shell.tv.grid;
   grid.invalidate();
 }
@@ -442,6 +448,54 @@ export function findMonomers(helmString: string) {
   return new Set(split_string.filter(val => !monomer_names.includes(val)));
 }
 
+
+class MonomerLib implements bio.IMonomerLib {
+  private _monomers: { [type: string]: { [name: string]: bio.Monomer } };
+  private _onChanged = new Subject<any>();
+
+  get(monomerType: string, monomerName: string): bio.Monomer | null {
+    if (monomerType in this._monomers && monomerName in this._monomers[monomerType])
+      return this._monomers[monomerType][monomerName];
+    else
+      return null;
+  }
+
+  get onChanged(): Observable<any> {
+    return this._onChanged;
+  }
+
+  public update(monomers: { [type: string]: { [name: string]: bio.Monomer } }): void {
+    this._monomers = monomers;
+    this._onChanged.next();
+  }
+}
+
+function getAllLibsData(): { [type: string]: { [name: string]: bio.Monomer } } {
+  //@ts-ignore
+  const types = Object.keys(org.helm.webeditor.monomerTypeList());
+  //const monomers: any = [];
+  const monomers: { [type: string]: { [name: string]: bio.Monomer } } = {};
+  for (let i = 0; i < types.length; i++) {
+    monomers[types[i]] = new scil.helm.Monomers.getMonomerSet(types[i]);
+    //@ts-ignore
+    //monomers.push(new scil.helm.Monomers.getMonomerSet(types[i]));
+  }
+
+  return monomers;
+}
+
+//name: getMonomerLibObj
+//description: Get object of IMonomerLib interface (singleton)
+//output: object result
+export function getMonomerLibObj(): bio.IMonomerLib {
+  if (!('monomerLib' in window)) {
+    window['monomerLib'] = new MonomerLib();
+    window['monomerLib'].update(getAllLibsData()); // TODO: refactor
+  }
+
+  return window['monomerLib'];
+}
+
 //name: getMolfiles
 //input: column col {semType: Macromolecule}
 //output: column res 
@@ -584,5 +638,13 @@ class HelmCellRenderer extends DG.GridCellRenderer {
 //input: string type
 //output: string monomerSetJSON
 export function getMonomerLib(type: string): string {
+  // TODO: deprecate
   return JSON.stringify(scil.helm.Monomers.getMonomerSet(type));
 }
+
+
+//name: helmWebEditor
+//output: object
+export function helmWebEditor(): HelmWebEditor {
+  return new HelmWebEditor();
+}

package/{test-Helm-916a90d7d48b-481b4bd5.html → test-Helm-49ff04f38f57-48c80158.html}

@@ -1,4 +1,4 @@
-<html><head><meta charset="utf-8"/><title>Helm Test Report. Datagrok version datagrok/datagrok:latest SHA=916a90d7d48b. Commit 481b4bd5.</title><style type="text/css">html,
+<html><head><meta charset="utf-8"/><title>Helm Test Report. Datagrok version datagrok/datagrok:latest SHA=49ff04f38f57. Commit 48c80158.</title><style type="text/css">html,
 body {
   font-family: Arial, Helvetica, sans-serif;
   font-size: 1rem;
@@ -229,7 +229,7 @@ header {
   font-size: 1rem;
   padding: 0 0.5rem;
 }
-</style></head><body><div id="jesthtml-content"><header><h1 id="title">Helm Test Report. Datagrok version datagrok/datagrok:latest SHA=916a90d7d48b. Commit 481b4bd5.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-10-14 10:03:25</div><div id="summary"><div id="suite-summary"><div class="summary-total">Suites (1)</div><div class="summary-passed">1 passed</div><div class="summary-failed summary-empty">0 failed</div><div class="summary-pending summary-empty">0 pending</div></div><div id="test-summary"><div class="summary-total">Tests (1)</div><div class="summary-passed">1 passed</div><div class="summary-failed summary-empty">0 failed</div><div class="summary-pending summary-empty">0 pending</div></div></div></div><div id="suite-1" class="suite-container"><div class="suite-info"><div class="suite-path">/home/runner/work/public/public/packages/Helm/src/__jest__/remote.test.ts</div><div class="suite-time warn">20.521s</div></div><div class="suite-tests"><div class="test-result passed"><div class="test-info"><div class="test-suitename"> </div><div class="test-title">TEST</div><div class="test-status">passed</div><div class="test-duration">5.136s</div></div></div></div><div class="suite-consolelog"><div class="suite-consolelog-header">Console Log</div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/Helm/src/__jest__/test-node.ts:61:11)
+</style></head><body><div id="jesthtml-content"><header><h1 id="title">Helm Test Report. Datagrok version datagrok/datagrok:latest SHA=49ff04f38f57. Commit 48c80158.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-10-25 11:59:02</div><div id="summary"><div id="suite-summary"><div class="summary-total">Suites (1)</div><div class="summary-passed">1 passed</div><div class="summary-failed summary-empty">0 failed</div><div class="summary-pending summary-empty">0 pending</div></div><div id="test-summary"><div class="summary-total">Tests (1)</div><div class="summary-passed">1 passed</div><div class="summary-failed summary-empty">0 failed</div><div class="summary-pending summary-empty">0 pending</div></div></div></div><div id="suite-1" class="suite-container"><div class="suite-info"><div class="suite-path">/home/runner/work/public/public/packages/Helm/src/__jest__/remote.test.ts</div><div class="suite-time warn">14.844s</div></div><div class="suite-tests"><div class="test-result passed"><div class="test-info"><div class="test-suitename"> </div><div class="test-title">TEST</div><div class="test-status">passed</div><div class="test-duration">5.034s</div></div></div></div><div class="suite-consolelog"><div class="suite-consolelog-header">Console Log</div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/Helm/src/__jest__/test-node.ts:61:11)
     at Generator.next (&lt;anonymous&gt;)
     at fulfilled (/home/runner/work/public/public/packages/Helm/src/__jest__/test-node.ts:28:58)
     at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Using web root: http://localhost:8080</pre></div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at /home/runner/work/public/public/packages/Helm/src/__jest__/remote.test.ts:40:11
@@ -242,8 +242,7 @@ header {
     at new Promise (&lt;anonymous&gt;)</pre><pre class="suite-consolelog-item-message">Testing Helm package</pre></div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at /home/runner/work/public/public/packages/Helm/src/__jest__/remote.test.ts:66:11
     at Generator.next (&lt;anonymous&gt;)
     at fulfilled (/home/runner/work/public/public/packages/Helm/src/__jest__/remote.test.ts:31:58)
-    at runMicrotasks (&lt;anonymous&gt;)
-    at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Test result : Success : 90 : Helm.Helm.manageFiles : OK
-Test result : Success : 1897 : Helm.Helm.monomerManager : OK
-Test result : Success : 1 : Helm.Helm.parseHelm : OK
+    at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Test result : Success : 48 : Helm.Helm.manageFiles : OK
+Test result : Success : 839 : Helm.Helm.monomerManager : OK
+Test result : Success : 2 : Helm.Helm.parseHelm : OK
 </pre></div></div></div></div></body></html>