@datagrok/helm 1.0.10 → 2.0.2
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
package/package.json
CHANGED
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@@ -2,14 +2,14 @@
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"name": "@datagrok/helm",
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"beta": false,
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"friendlyName": "Helm",
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"version": "
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"version": "2.0.2",
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"description": "",
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"dependencies": {
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"datagrok-api": "^1.
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"datagrok-api": "^1.5.0",
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"cash-dom": "latest",
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"dayjs": "latest",
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"@datagrok-libraries/utils": "^1.4.0",
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"@datagrok-libraries/bio": "^
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"@datagrok-libraries/bio": "^3.0.1",
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"ts-loader": "^9.2.5",
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"typescript": "^4.4.2"
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},
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package/src/package.ts
CHANGED
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@@ -3,7 +3,8 @@ import * as grok from 'datagrok-api/grok';
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import * as ui from 'datagrok-api/ui';
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import * as DG from 'datagrok-api/dg';
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//import {lru} from '../../Bio/src/utils/cell-renderer';
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import {NotationConverter
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import {NotationConverter} from '@datagrok-libraries/bio/src/utils/notation-converter';
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import {NOTATION} from '@datagrok-libraries/bio/src/utils/units-handler';
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import {WebLogo} from '@datagrok-libraries/bio/src/viewers/web-logo';
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import {createJsonMonomerLibFromSdf} from './utils';
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import {MONOMER_MANAGER_MAP, RGROUPS, RGROUP_CAP_GROUP_NAME, RGROUP_LABEL, SMILES} from './constants';
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@@ -26,6 +27,11 @@ export async function initHelm(): Promise<void> {
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grid.invalidate();
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}
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//name: initHelp
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export function initHelp() {
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return;
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}
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//name: getLru
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export async function getLru() {
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return await grok.functions.call('Bio:Lru');
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@@ -129,19 +135,36 @@ export async function libraryPanel(helmColumn: DG.Column) {
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//@ts-ignore
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let loadButton = ui.button('Load Library');
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loadButton.addEventListener('click', loadDialog);
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//@ts-ignore
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let filesButton = ui.button('Manage');
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filesButton.addEventListener('click', manageFiles);
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let list = (await _package.files.list(`${LIB_PATH}`, false, '')).map(it => it.fileName);
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let usedLibraries = [];
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for (let j = 0; j <= i; j++) {
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usedLibraries.push(await grok.dapi.userDataStorage.getValue(STORAGE_NAME, j.toString(), true));
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}
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let unusedLibraries = list.filter(x => !usedLibraries.includes(x));
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return new DG.Widget(
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ui.
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return new DG.Widget(ui.splitV([
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ui.splitH([
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ui.tableFromMap({
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'Uploaded libraries': ui.divText(usedLibraries.toString()),
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'Not used libraries': ui.divText(unusedLibraries.toString()),
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})
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]),
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ui.splitH([
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ui.divH([loadButton]),
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ui.divH([filesButton]),
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])
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]));
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}
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//name: manageFiles
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function manageFiles() {
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const a = ui.dialog({title: 'Manage files'})
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//@ts-ignore
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.add(ui.fileBrowser({path: 'System:AppData/Helm/libraries'}).root)
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.addButton('OK', () => a.close())
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.show();
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}
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async function accessServer(url: string, key: string) {
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@@ -296,3 +319,10 @@ class HelmCellRenderer extends DG.GridCellRenderer {
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lru.set(gridCell.cell.value, result);
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}
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}
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//name: getMonomerLib
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//input: string type
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//output: string monomerSetJSON
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export function getMonomerLib(type: string): string {
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return JSON.stringify(scil.helm.Monomers.getMonomerSet(type));
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}
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package/src/tests/helm-tests.ts
CHANGED
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@@ -28,19 +28,21 @@ category('Helm', () => {
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// expect(await helmToPeptide('PEPTIDE1{A.R.C.A.A.K.T.C.D.A}$PEPTIDE1,PEPTIDE1,8:R3-3:R3$$$'), 'ARCAAKTCDA');
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// });
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// detectMacromolecule is a function of Bio package
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// test('detectMacromolecule', async () => {
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// const file = await _package.files.readAsText('tests/test.csv');
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// const df = DG.DataFrame.fromCsv(file);
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// const col = df.columns.byName('HELM string');
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// await grok.data.detectSemanticTypes(df);
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// expect(col.semType, DG.SEMTYPE.MACROMOLECULE);
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// });
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// semType and units tags are detecting by Bio package function detectMacromolecule
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// test('detectHelm', async () => {
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// const file = await _package.files.readAsText('tests/test.csv');
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// const df = DG.DataFrame.fromCsv(file);
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// const col = df.columns.byName('HELM string');
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// await grok.data.detectSemanticTypes(df);
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// expect(col.tags[DG.TAGS.UNITS], 'HELM');
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// });
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});
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@@ -1,4 +1,4 @@
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<html><head><meta charset="utf-8"/><title>Helm Test Report. Datagrok version datagrok/datagrok:latest SHA=
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<html><head><meta charset="utf-8"/><title>Helm Test Report. Datagrok version datagrok/datagrok:latest SHA=4f0c8bae6479. Commit a2fd943e.</title><style type="text/css">html,
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body {
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font-family: Arial, Helvetica, sans-serif;
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font-size: 1rem;
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@@ -229,13 +229,11 @@ header {
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font-size: 1rem;
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padding: 0 0.5rem;
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}
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</style></head><body><div id="jesthtml-content"><header><h1 id="title">Helm Test Report. Datagrok version datagrok/datagrok:latest SHA=
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at /
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at
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at fulfilled (/home/runner/work/public/public/packages/Helm/src/__jest__/remote.test.ts:31:58)
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at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre></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.<anonymous> (/home/runner/work/public/public/packages/Helm/src/__jest__/test-node.ts:61:11)
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</style></head><body><div id="jesthtml-content"><header><h1 id="title">Helm Test Report. Datagrok version datagrok/datagrok:latest SHA=4f0c8bae6479. Commit a2fd943e.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-08-04 07:38:43</div><div id="summary"><div id="suite-summary"><div class="summary-total">Suites (1)</div><div class="summary-passed summary-empty">0 passed</div><div class="summary-failed">1 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 summary-empty">0 passed</div><div class="summary-failed">1 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">14.855s</div></div><div class="suite-tests"><div class="test-result failed"><div class="test-info"><div class="test-suitename"> </div><div class="test-title">TEST</div><div class="test-status">failed</div><div class="test-duration">0.393s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: Evaluation failed: TypeError: Cannot read properties of null (reading 'columns')
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at __puppeteer_evaluation_script__:4:34
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at ExecutionContext._evaluateInternal (/home/runner/work/public/public/packages/Helm/node_modules/puppeteer/src/common/ExecutionContext.ts:273:13)
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at processTicksAndRejections (internal/process/task_queues.js:97:5)
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at ExecutionContext.evaluate (/home/runner/work/public/public/packages/Helm/node_modules/puppeteer/src/common/ExecutionContext.ts:140:12)</pre></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.<anonymous> (/home/runner/work/public/public/packages/Helm/src/__jest__/test-node.ts:61:11)
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at Generator.next (<anonymous>)
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at fulfilled (/home/runner/work/public/public/packages/Helm/src/__jest__/test-node.ts:28:58)
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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
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at Object.<anonymous>.__awaiter (/home/runner/work/public/public/packages/Helm/src/__jest__/remote.test.ts:30:12)
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at Object.<anonymous> (/home/runner/work/public/public/packages/Helm/src/__jest__/remote.test.ts:38:23)
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at Promise.then.completed (/home/runner/work/public/public/packages/Helm/node_modules/jest-circus/build/utils.js:391:28)
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at new Promise (<anonymous>)</pre><pre class="suite-consolelog-item-message">Testing Helm package</pre></div
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at Generator.next (<anonymous>)
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at fulfilled (/home/runner/work/public/public/packages/Helm/src/__jest__/remote.test.ts:31:58)
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at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message"/></div></div></div></div></body></html>
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at new Promise (<anonymous>)</pre><pre class="suite-consolelog-item-message">Testing Helm package</pre></div></div></div></div></body></html>
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