@datagrok/peptides 1.13.3 → 1.14.0
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/CHANGELOG.md +11 -0
- package/dist/209.js +2 -2
- package/dist/521.js +2 -2
- package/dist/677.js +2 -0
- package/dist/729.js +2 -2
- package/dist/959.js +2 -2
- package/dist/package-test.js +2 -2
- package/dist/package.js +2 -2
- package/package.json +1 -1
- package/src/model.ts +34 -21
- package/src/package-test.ts +5 -5
- package/src/tests/core.ts +11 -66
- package/src/tests/model.ts +3 -12
- package/src/tests/table-view.ts +15 -12
- package/src/tests/viewers.ts +4 -31
- package/src/tests/widgets.ts +10 -43
- package/src/utils/misc.ts +33 -0
- package/src/viewers/logo-summary.ts +25 -11
- package/src/viewers/sar-viewer.ts +52 -3
- package/src/widgets/distribution.ts +5 -6
- package/src/widgets/mutation-cliffs.ts +32 -13
- package/src/widgets/selection.ts +27 -5
- package/dist/535.js +0 -2
package/package.json
CHANGED
package/src/model.ts
CHANGED
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@@ -4,7 +4,7 @@ import * as DG from 'datagrok-api/dg';
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import {splitAlignedSequences} from '@datagrok-libraries/bio/src/utils/splitter';
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import {SeqPalette} from '@datagrok-libraries/bio/src/seq-palettes';
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-
import {pickUpPalette, TAGS as bioTAGS} from '@datagrok-libraries/bio/src/utils/macromolecule';
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import {pickUpPalette, TAGS as bioTAGS, monomerToShort} from '@datagrok-libraries/bio/src/utils/macromolecule';
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import {calculateScores, SCORE} from '@datagrok-libraries/bio/src/utils/macromolecule/scoring';
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import {StringDictionary} from '@datagrok-libraries/utils/src/type-declarations';
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import {DistanceMatrix} from '@datagrok-libraries/ml/src/distance-matrix';
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@@ -266,7 +266,7 @@ export class PeptidesModel {
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this.df.tags['distributionSplit'] = `${splitByMonomerFlag}${flag ? 1 : 0}`;
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}
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-
get
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get isMutationCliffsSelectionEmpty(): boolean {
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for (const monomerList of Object.values(this.mutationCliffsSelection)) {
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if (monomerList.length !== 0)
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return false;
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@@ -274,6 +274,14 @@ export class PeptidesModel {
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return true;
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}
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get isInvariantMapSelectionEmpty(): boolean {
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for (const monomerList of Object.values(this.invariantMapSelection)) {
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if (monomerList.length !== 0)
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return false;
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}
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return true;
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}
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get isClusterSelectionEmpty(): boolean {
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return (this.clusterSelection[CLUSTER_TYPE.ORIGINAL].length + this.clusterSelection[CLUSTER_TYPE.CUSTOM].length) === 0;
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}
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@@ -453,29 +461,19 @@ export class PeptidesModel {
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const table = trueModel.df.filter.anyFalse ? trueModel.df.clone(trueModel.df.filter, null, true) : trueModel.df;
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acc.addPane('Mutation Cliffs pairs', () => mutationCliffsWidget(trueModel.df, trueModel).root);
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acc.addPane('Distribution', () => getDistributionWidget(table, trueModel).root);
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acc.addPane('Selection', () => getSelectionWidget(trueModel.df, trueModel)
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acc.addPane('Selection', () => getSelectionWidget(trueModel.df, trueModel));
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return acc;
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}
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updateGrid(): void {
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this.joinDataFrames();
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-
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this.createScaledCol();
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-
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this.initInvariantMapSelection({notify: false});
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this.initMutationCliffsSelection({notify: false});
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this.initClusterSelection({notify: false});
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-
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this.setWebLogoInteraction();
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this.webLogoBounds = {};
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-
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this.setCellRenderers();
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-
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this.setTooltips();
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-
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this.setBitsetCallback();
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-
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this.setGridProperties();
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}
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@@ -965,20 +963,21 @@ export class PeptidesModel {
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const showAccordion = (): void => {
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const acc = this.createAccordion();
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if (acc
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if (acc === null)
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return;
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grok.shell.o = acc.root;
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for (const pane of acc.panes)
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pane.expanded = true;
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};
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selection.onChanged.subscribe(() => {
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DG.debounce(selection.onChanged, 500).subscribe(() => {
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if (!this.isUserChangedSelection)
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selection.copyFrom(getLatestSelection(), false);
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showAccordion();
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this.isUserChangedSelection = true;
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});
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filter.onChanged.subscribe(() => {
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DG.debounce(filter.onChanged, 500).subscribe(() => {
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const lstViewer = this.findViewer(VIEWER_TYPE.LOGO_SUMMARY_TABLE) as LogoSummaryTable | null;
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if (lstViewer !== null && typeof lstViewer.model !== 'undefined') {
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lstViewer.createLogoSummaryTableGrid();
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@@ -986,6 +985,7 @@ export class PeptidesModel {
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}
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showAccordion();
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});
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this.isBitsetChangedInitialized = true;
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}
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@@ -995,7 +995,6 @@ export class PeptidesModel {
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if (fireFilterChanged)
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this.df.filter.fireChanged();
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this.headerSelectedMonomers = calculateSelected(this.df);
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-
this.isUserChangedSelection = true;
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}
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setGridProperties(props?: DG.IGridLookSettings): void {
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@@ -1005,6 +1004,20 @@ export class PeptidesModel {
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sourceGridProps.allowEdit = props?.allowEdit ?? false;
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sourceGridProps.showCurrentRowIndicator = props?.showCurrentRowIndicator ?? false;
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this.df.temp[C.EMBEDDING_STATUS] = false;
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const positionCols = this.splitSeqDf.columns;
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let maxWidth = 10;
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const canvasContext = sourceGrid.canvas.getContext('2d');
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for (const positionCol of positionCols) {
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// Longest category
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const maxCategory = monomerToShort(positionCol.categories.reduce((a, b) => a.length > b.length ? a : b), 6);
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// Measure text width of longest category
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const width = Math.ceil(canvasContext!.measureText(maxCategory).width);
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maxWidth = Math.max(maxWidth, width);
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}
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setTimeout(() => {
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for (const positionCol of positionCols)
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sourceGrid.col(positionCol.name)!.width = maxWidth + 15;
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}, 1000);
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}
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closeViewer(viewerType: VIEWER_TYPE): void {
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package/src/package-test.ts
CHANGED
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@@ -1,14 +1,14 @@
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1
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import * as DG from 'datagrok-api/dg';
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import {runTests, tests, TestContext} from '@datagrok-libraries/utils/src/test';
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import './tests/core';
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// import './tests/core';
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//FIXME: fails on CI; crashes browser
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// import './tests/peptide-space-test';
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import './tests/algorithms';
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import './tests/viewers';
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import './tests/widgets';
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import './tests/table-view';
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import './tests/model';
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// import './tests/viewers';
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// import './tests/widgets';
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// import './tests/table-view';
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// import './tests/model';
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export const _package = new DG.Package();
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export {tests};
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package/src/tests/core.ts
CHANGED
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@@ -1,7 +1,7 @@
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import * as grok from 'datagrok-api/grok';
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import * as DG from 'datagrok-api/dg';
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import {category, test, expect, awaitCheck} from '@datagrok-libraries/utils/src/test';
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import {category, test, expect, awaitCheck, delay} from '@datagrok-libraries/utils/src/test';
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import {_package} from '../package-test';
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import {startAnalysis} from '../widgets/peptides';
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@@ -45,16 +45,9 @@ category('Core', () => {
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grok.log.debug('Overlay initialized');
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});
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// Ensure grid finished initializing to prevent Unhandled exceptions
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let accrodionInit = false;
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grok.events.onAccordionConstructed.subscribe((_) => accrodionInit = true);
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await awaitCheck(() => model!.df.currentRowIdx === 0, 'Grid cell never finished initializing', 2000);
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await awaitCheck(() => grok.shell.o instanceof DG.Column, 'Shell object never changed', 2000);
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await awaitCheck(() => accrodionInit, 'Accordion never finished initializing', 2000);
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await awaitCheck(() => overlayInit, 'Overlay never finished initializing', 2000);
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model!.mutationCliffsSelection = {'11': ['D']};
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await delay(500);
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});
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test('Start analysis: сomplex', async () => {
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const complexActivityColName = 'Activity';
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@@ -77,17 +70,11 @@ category('Core', () => {
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grok.log.debug('Overlay initialized');
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});
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// Ensure grid finished initializing to prevent Unhandled exceptions
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let accrodionInit = false;
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grok.events.onAccordionConstructed.subscribe((_) => accrodionInit = true);
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await awaitCheck(() => model!.df.currentRowIdx === 0, 'Grid cell never finished initializing', 2000);
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await awaitCheck(() => grok.shell.o instanceof DG.Column, 'Shell object never changed', 2000);
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await awaitCheck(() => accrodionInit, 'Accordion never finished initializing', 2000);
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await awaitCheck(() => overlayInit, 'Overlay never finished initializing', 2000);
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if (model !== null)
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model.mutationCliffsSelection = {'13': ['-']};
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await delay(500);
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});
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test('Save and load project', async () => {
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const simpleActivityColName = 'IC50';
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@@ -100,20 +87,9 @@ category('Core', () => {
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simpleAlignedSeqCol.setTag(bioTAGS.aligned, ALIGNMENT.SEQ_MSA);
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simpleScaledCol = scaleActivity(simpleActivityCol, C.SCALING_METHODS.MINUS_LG);
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model = await startAnalysis(
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simpleActivityCol, simpleAlignedSeqCol, null, simpleTable, simpleScaledCol, C.SCALING_METHODS.MINUS_LG);
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model = await startAnalysis(simpleActivityCol, simpleAlignedSeqCol, null, simpleTable, simpleScaledCol, C.SCALING_METHODS.MINUS_LG);
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let v = grok.shell.getTableView('Peptides analysis');
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let overlayInit = false;
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v.grid.onAfterDrawOverlay.subscribe(() => overlayInit = true);
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// Ensure grid finished initializing to prevent Unhandled exceptions
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let accrodionInit = false;
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grok.events.onAccordionConstructed.subscribe((_) => accrodionInit = true);
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await awaitCheck(() => v.table!.currentRowIdx === 0, 'Grid cell never finished initializing', 2000);
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await awaitCheck(() => grok.shell.o instanceof DG.Column, 'Shell object never changed', 2000);
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await awaitCheck(() => accrodionInit, 'Accordion never finished initializing', 2000);
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await awaitCheck(() => overlayInit, 'Overlay never finished initializing', 2000);
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const d = v.dataFrame;
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const layout = v.saveLayout();
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@@ -133,19 +109,12 @@ category('Core', () => {
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await sp.open();
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v = grok.shell.getTableView('Peptides analysis');
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overlayInit = false;
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v.grid.onAfterDrawOverlay.subscribe(() => overlayInit = true);
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await grok.dapi.layouts.delete(sl);
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await grok.dapi.tables.delete(sti);
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await grok.dapi.projects.delete(sp);
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accrodionInit = false;
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grok.events.onAccordionConstructed.subscribe((_) => accrodionInit = true);
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await awaitCheck(() => v.table!.currentRowIdx === 0, 'Grid cell never finished initializing', 2000);
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await awaitCheck(() => grok.shell.o instanceof DG.Column, 'Shell object never changed', 2000);
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await awaitCheck(() => overlayInit, 'Overlay never finished initializing', 2000);
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await delay(500);
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});
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test('Cluster stats - Benchmark HELM 5k', async () => {
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const sequenceCol = df.getCol('HELM');
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sequenceCol.semType = DG.SEMTYPE.MACROMOLECULE;
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sequenceCol.setTag(DG.TAGS.UNITS, NOTATION.HELM);
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const model = await startAnalysis(
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activityCol, sequenceCol, clustersCol, df, scaledActivityCol, C.SCALING_METHODS.NONE);
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// Ensure grid finished initializing to prevent Unhandled exceptions
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let accrodionInit = false;
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grok.events.onAccordionConstructed.subscribe((_) => accrodionInit = true);
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await awaitCheck(() => model!.df.currentRowIdx === 0, 'Grid cell never finished initializing', 2000);
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await awaitCheck(() => grok.shell.o instanceof DG.Column, 'Shell object never changed', 2000);
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await awaitCheck(() => accrodionInit, 'Accordion never finished initializing', 2000);
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const model = await startAnalysis(activityCol, sequenceCol, clustersCol, df, scaledActivityCol, C.SCALING_METHODS.NONE);
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for (let i = 0; i < 5; ++i)
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DG.time('Cluster stats', () => model?.calculateClusterStatistics());
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@@ -184,15 +145,7 @@ category('Core', () => {
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const sequenceCol = df.getCol('HELM');
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sequenceCol.semType = DG.SEMTYPE.MACROMOLECULE;
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sequenceCol.setTag(DG.TAGS.UNITS, NOTATION.HELM);
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const model = await startAnalysis(
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activityCol, sequenceCol, clustersCol, df, scaledActivityCol, C.SCALING_METHODS.NONE);
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// Ensure grid finished initializing to prevent Unhandled exceptions
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let accrodionInit = false;
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grok.events.onAccordionConstructed.subscribe((_) => accrodionInit = true);
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await awaitCheck(() => model!.df.currentRowIdx === 0, 'Grid cell never finished initializing', 2000);
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await awaitCheck(() => grok.shell.o instanceof DG.Column, 'Shell object never changed', 2000);
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await awaitCheck(() => accrodionInit, 'Accordion never finished initializing', 2000);
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const model = await startAnalysis(activityCol, sequenceCol, clustersCol, df, scaledActivityCol, C.SCALING_METHODS.NONE);
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for (let i = 0; i < 5; ++i)
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DG.time('Monomer position stats', () => model?.calculateMonomerPositionStatistics());
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@@ -212,15 +165,7 @@ category('Core', () => {
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166
|
for (let i = 0; i < 5; ++i) {
|
|
214
167
|
await DG.timeAsync('Analysis start', async () => {
|
|
215
|
-
const model = await startAnalysis(
|
|
216
|
-
activityCol, sequenceCol, clustersCol, df, scaledActivityCol, C.SCALING_METHODS.NONE);
|
|
217
|
-
|
|
218
|
-
// Ensure grid finished initializing to prevent Unhandled exceptions
|
|
219
|
-
let accrodionInit = false;
|
|
220
|
-
grok.events.onAccordionConstructed.subscribe((_) => accrodionInit = true);
|
|
221
|
-
await awaitCheck(() => model!.df.currentRowIdx === 0, 'Grid cell never finished initializing', 2000);
|
|
222
|
-
await awaitCheck(() => grok.shell.o instanceof DG.Column, 'Shell object never changed', 2000);
|
|
223
|
-
await awaitCheck(() => accrodionInit, 'Accordion never finished initializing', 2000);
|
|
168
|
+
const model = await startAnalysis(activityCol, sequenceCol, clustersCol, df, scaledActivityCol, C.SCALING_METHODS.NONE);
|
|
224
169
|
|
|
225
170
|
if (model)
|
|
226
171
|
grok.shell.closeTable(model.df);
|
package/src/tests/model.ts
CHANGED
|
@@ -1,7 +1,6 @@
|
|
|
1
|
-
import * as grok from 'datagrok-api/grok';
|
|
2
1
|
import * as DG from 'datagrok-api/dg';
|
|
3
2
|
|
|
4
|
-
import {category, test, before, expect, expectFloat, awaitCheck} from '@datagrok-libraries/utils/src/test';
|
|
3
|
+
import {category, test, before, expect, expectFloat, awaitCheck, delay} from '@datagrok-libraries/utils/src/test';
|
|
5
4
|
import {_package} from '../package-test';
|
|
6
5
|
import {PeptidesModel, VIEWER_TYPE, getAggregatedColName} from '../model';
|
|
7
6
|
import {startAnalysis} from '../widgets/peptides';
|
|
@@ -35,16 +34,8 @@ category('Model: Settings', () => {
|
|
|
35
34
|
if (tempModel === null)
|
|
36
35
|
throw new Error('Model is null');
|
|
37
36
|
model = tempModel;
|
|
38
|
-
|
|
39
|
-
|
|
40
|
-
|
|
41
|
-
// Ensure grid finished initializing to prevent Unhandled exceptions
|
|
42
|
-
let accrodionInit = false;
|
|
43
|
-
grok.events.onAccordionConstructed.subscribe((_) => accrodionInit = true);
|
|
44
|
-
await awaitCheck(() => model!.df.currentRowIdx === 0, 'Grid cell never finished initializing', 2000);
|
|
45
|
-
await awaitCheck(() => grok.shell.o instanceof DG.Column, 'Shell object never changed', 2000);
|
|
46
|
-
await awaitCheck(() => accrodionInit, 'Accordion never finished initializing', 2000);
|
|
47
|
-
await awaitCheck(() => overlayInit, 'Overlay never finished initializing', 2000);
|
|
37
|
+
|
|
38
|
+
await delay(500);
|
|
48
39
|
});
|
|
49
40
|
|
|
50
41
|
test('Activity scaling', async () => {
|
package/src/tests/table-view.ts
CHANGED
|
@@ -1,7 +1,6 @@
|
|
|
1
|
-
import * as grok from 'datagrok-api/grok';
|
|
2
1
|
import * as DG from 'datagrok-api/dg';
|
|
3
2
|
|
|
4
|
-
import {category, test, before, expect,
|
|
3
|
+
import {category, test, before, expect, delay} from '@datagrok-libraries/utils/src/test';
|
|
5
4
|
import {_package} from '../package-test';
|
|
6
5
|
import {CLUSTER_TYPE, PeptidesModel} from '../model';
|
|
7
6
|
import {startAnalysis} from '../widgets/peptides';
|
|
@@ -36,16 +35,8 @@ category('Table view', () => {
|
|
|
36
35
|
if (tempModel === null)
|
|
37
36
|
throw new Error('Model is null');
|
|
38
37
|
model = tempModel;
|
|
39
|
-
|
|
40
|
-
|
|
41
|
-
|
|
42
|
-
// Ensure grid finished initializing to prevent Unhandled exceptions
|
|
43
|
-
let accrodionInit = false;
|
|
44
|
-
grok.events.onAccordionConstructed.subscribe((_) => accrodionInit = true);
|
|
45
|
-
await awaitCheck(() => model!.df.currentRowIdx === 0, 'Grid cell never finished initializing', 2000);
|
|
46
|
-
await awaitCheck(() => grok.shell.o instanceof DG.Column, 'Shell object never changed', 2000);
|
|
47
|
-
await awaitCheck(() => accrodionInit, 'Accordion never finished initializing', 2000);
|
|
48
|
-
await awaitCheck(() => overlayInit, 'Overlay never finished initializing', 2000);
|
|
38
|
+
|
|
39
|
+
await delay(500);
|
|
49
40
|
});
|
|
50
41
|
|
|
51
42
|
test('Tooltip', async () => {
|
|
@@ -74,6 +65,7 @@ category('Table view', () => {
|
|
|
74
65
|
|
|
75
66
|
// Select first monomer-position pair
|
|
76
67
|
model.modifyMutationCliffsSelection(firstPair);
|
|
68
|
+
await delay(500);
|
|
77
69
|
expect(model.mutationCliffsSelection[firstPair.positionOrClusterType].includes(firstPair.monomerOrCluster), true,
|
|
78
70
|
`Monomer ${firstPair.monomerOrCluster} is not selected at position ${firstPair.positionOrClusterType}`);
|
|
79
71
|
expect(selection.trueCount, firstPair.mcCount, `Selection count is not equal to ${firstPair.mcCount} ` +
|
|
@@ -81,6 +73,7 @@ category('Table view', () => {
|
|
|
81
73
|
|
|
82
74
|
// Select second monomer-position pair
|
|
83
75
|
model.modifyMutationCliffsSelection(secondPair, {shiftPressed: true, ctrlPressed: false});
|
|
76
|
+
await delay(500);
|
|
84
77
|
expect(model.mutationCliffsSelection[secondPair.positionOrClusterType].includes(secondPair.monomerOrCluster), true,
|
|
85
78
|
`Monomer ${secondPair.monomerOrCluster} is not selected at position ${secondPair.positionOrClusterType}`);
|
|
86
79
|
expect(selection.trueCount, secondPair.mcCount + firstPair.mcCount, `Selection count is not equal ` +
|
|
@@ -89,6 +82,7 @@ category('Table view', () => {
|
|
|
89
82
|
|
|
90
83
|
// Deselect second monomer-position pair
|
|
91
84
|
model.modifyMutationCliffsSelection(secondPair, {shiftPressed: true, ctrlPressed: true});
|
|
85
|
+
await delay(500);
|
|
92
86
|
expect(model.mutationCliffsSelection[secondPair.positionOrClusterType].includes(secondPair.monomerOrCluster), false,
|
|
93
87
|
`Monomer ${secondPair.monomerOrCluster} is still selected at position ${secondPair.positionOrClusterType} after deselection`);
|
|
94
88
|
expect(selection.trueCount, firstPair.mcCount, `Selection count is not equal to ${firstPair.mcCount} ` +
|
|
@@ -96,6 +90,7 @@ category('Table view', () => {
|
|
|
96
90
|
|
|
97
91
|
// Clear monomer-position selection
|
|
98
92
|
model.initMutationCliffsSelection();
|
|
93
|
+
await delay(500);
|
|
99
94
|
for (const [position, selectedMonomers] of Object.entries(model.mutationCliffsSelection)) {
|
|
100
95
|
expect(selectedMonomers.length, 0, `Selection is not empty for position ${position} after clearing ` +
|
|
101
96
|
`monomer-position selection`);
|
|
@@ -104,6 +99,7 @@ category('Table view', () => {
|
|
|
104
99
|
|
|
105
100
|
// Select first cluster
|
|
106
101
|
model.modifyClusterSelection(firstCluster);
|
|
102
|
+
await delay(500);
|
|
107
103
|
expect(model.clusterSelection[firstCluster.positionOrClusterType].includes(firstCluster.monomerOrCluster), true,
|
|
108
104
|
`Cluster ${firstCluster.monomerOrCluster} is not selected`);
|
|
109
105
|
expect(selection.trueCount, firstCluster.count, `Selection count is not equal to ${firstCluster.count} for ` +
|
|
@@ -111,6 +107,7 @@ category('Table view', () => {
|
|
|
111
107
|
|
|
112
108
|
// Select second cluster
|
|
113
109
|
model.modifyClusterSelection(secondCluster, {shiftPressed: true, ctrlPressed: false});
|
|
110
|
+
await delay(500);
|
|
114
111
|
expect(model.clusterSelection[secondCluster.positionOrClusterType].includes(secondCluster.monomerOrCluster), true,
|
|
115
112
|
`Cluster ${secondCluster.monomerOrCluster} is not selected`);
|
|
116
113
|
expect(selection.trueCount, firstCluster.count + secondCluster.count, `Selection count is not equal to ` +
|
|
@@ -118,6 +115,7 @@ category('Table view', () => {
|
|
|
118
115
|
|
|
119
116
|
// Deselect first cluster
|
|
120
117
|
model.modifyClusterSelection(firstCluster, {shiftPressed: true, ctrlPressed: true});
|
|
118
|
+
await delay(500);
|
|
121
119
|
expect(model.clusterSelection[firstCluster.positionOrClusterType].includes(firstCluster.monomerOrCluster), false,
|
|
122
120
|
`Cluster ${firstCluster.monomerOrCluster} is still selected after deselection`);
|
|
123
121
|
expect(selection.trueCount, secondCluster.count, `Selection count is not equal to ${secondCluster.count} for ` +
|
|
@@ -125,6 +123,7 @@ category('Table view', () => {
|
|
|
125
123
|
|
|
126
124
|
// Clear selection
|
|
127
125
|
model.initClusterSelection();
|
|
126
|
+
await delay(500);
|
|
128
127
|
expect(model.isClusterSelectionEmpty, true, `Selection is not empty after clearing cluster selection`);
|
|
129
128
|
expect(selection.trueCount, 0, `Selection count is not equal to 0 after clearing cluster selection`);
|
|
130
129
|
});
|
|
@@ -137,6 +136,7 @@ category('Table view', () => {
|
|
|
137
136
|
|
|
138
137
|
// Select by second monomer-position pair
|
|
139
138
|
model.modifyInvariantMapSelection(secondPair);
|
|
139
|
+
await delay(500);
|
|
140
140
|
expect(model.invariantMapSelection[secondPair.positionOrClusterType].includes(secondPair.monomerOrCluster), true,
|
|
141
141
|
`Monomer ${secondPair.monomerOrCluster} is not filtered at position ${secondPair.positionOrClusterType}`);
|
|
142
142
|
expect(selection.trueCount, secondPair.imCount, `Filter count is not equal to ${secondPair.imCount} ` +
|
|
@@ -144,6 +144,7 @@ category('Table view', () => {
|
|
|
144
144
|
|
|
145
145
|
// Select by first monomer-position pair
|
|
146
146
|
model.modifyInvariantMapSelection(firstPair, {shiftPressed: true, ctrlPressed: false});
|
|
147
|
+
await delay(500);
|
|
147
148
|
expect(model.invariantMapSelection[firstPair.positionOrClusterType].includes(firstPair.monomerOrCluster), true,
|
|
148
149
|
`Monomer ${firstPair.monomerOrCluster} is not filtered at position ${firstPair.positionOrClusterType}`);
|
|
149
150
|
expect(selection.trueCount, secondPair.imCount, `Filter count is not equal to ${secondPair.imCount} ` +
|
|
@@ -151,6 +152,7 @@ category('Table view', () => {
|
|
|
151
152
|
|
|
152
153
|
// Deselect filter for second monomer-position pair
|
|
153
154
|
model.modifyInvariantMapSelection(secondPair, {shiftPressed: true, ctrlPressed: true});
|
|
155
|
+
await delay(500);
|
|
154
156
|
expect(model.invariantMapSelection[secondPair.positionOrClusterType].includes(secondPair.monomerOrCluster), false,
|
|
155
157
|
`Monomer ${secondPair.monomerOrCluster} is still filtered at position ${secondPair.positionOrClusterType} after ` +
|
|
156
158
|
`deselection`);
|
|
@@ -160,6 +162,7 @@ category('Table view', () => {
|
|
|
160
162
|
|
|
161
163
|
// Clear selection
|
|
162
164
|
model.initInvariantMapSelection();
|
|
165
|
+
await delay(500);
|
|
163
166
|
expect(selection.trueCount, 0, `Filter count is not equal to ${0} after clearing monomer-position filter`);
|
|
164
167
|
|
|
165
168
|
for (const [position, filteredMonomers] of Object.entries(model.invariantMapSelection)) {
|
package/src/tests/viewers.ts
CHANGED
|
@@ -1,7 +1,6 @@
|
|
|
1
|
-
import * as grok from 'datagrok-api/grok';
|
|
2
1
|
import * as DG from 'datagrok-api/dg';
|
|
3
2
|
|
|
4
|
-
import {
|
|
3
|
+
import {before, category, delay, expect, test, testViewer} from '@datagrok-libraries/utils/src/test';
|
|
5
4
|
import {aligned1} from './test-data';
|
|
6
5
|
import {CLUSTER_TYPE, PeptidesModel, VIEWER_TYPE} from '../model';
|
|
7
6
|
import {_package} from '../package-test';
|
|
@@ -46,18 +45,9 @@ category('Viewers: Monomer-Position', () => {
|
|
|
46
45
|
if (tempModel === null)
|
|
47
46
|
throw new Error('Model is null');
|
|
48
47
|
model = tempModel;
|
|
49
|
-
let overlayInit = false;
|
|
50
|
-
model._analysisView!.grid.onAfterDrawOverlay.subscribe(() => overlayInit = true);
|
|
51
|
-
|
|
52
48
|
mpViewer = model.findViewer(VIEWER_TYPE.MONOMER_POSITION) as MonomerPosition;
|
|
53
49
|
|
|
54
|
-
|
|
55
|
-
let accrodionInit = false;
|
|
56
|
-
grok.events.onAccordionConstructed.subscribe((_) => accrodionInit = true);
|
|
57
|
-
await awaitCheck(() => model!.df.currentRowIdx === 0, 'Grid cell never finished initializing', 2000);
|
|
58
|
-
await awaitCheck(() => grok.shell.o instanceof DG.Column, 'Shell object never changed', 2000);
|
|
59
|
-
await awaitCheck(() => accrodionInit, 'Accordion never finished initializing', 2000);
|
|
60
|
-
await awaitCheck(() => overlayInit, 'Overlay never finished initializing', 2000);
|
|
50
|
+
await delay(500);
|
|
61
51
|
});
|
|
62
52
|
|
|
63
53
|
test('Tooltip', async () => {
|
|
@@ -107,18 +97,9 @@ category('Viewers: Most Potent Residues', () => {
|
|
|
107
97
|
if (tempModel === null)
|
|
108
98
|
throw new Error('Model is null');
|
|
109
99
|
model = tempModel;
|
|
110
|
-
let overlayInit = false;
|
|
111
|
-
model._analysisView!.grid.onAfterDrawOverlay.subscribe(() => overlayInit = true);
|
|
112
|
-
|
|
113
100
|
mprViewer = model.findViewer(VIEWER_TYPE.MOST_POTENT_RESIDUES) as MostPotentResidues;
|
|
114
101
|
|
|
115
|
-
|
|
116
|
-
let accrodionInit = false;
|
|
117
|
-
grok.events.onAccordionConstructed.subscribe((_) => accrodionInit = true);
|
|
118
|
-
await awaitCheck(() => model!.df.currentRowIdx === 0, 'Grid cell never finished initializing', 2000);
|
|
119
|
-
await awaitCheck(() => grok.shell.o instanceof DG.Column, 'Shell object never changed', 2000);
|
|
120
|
-
await awaitCheck(() => accrodionInit, 'Accordion never finished initializing', 2000);
|
|
121
|
-
await awaitCheck(() => overlayInit, 'Overlay never finished initializing', 2000);
|
|
102
|
+
await delay(500);
|
|
122
103
|
});
|
|
123
104
|
|
|
124
105
|
test('Tooltip', async () => {
|
|
@@ -152,18 +133,10 @@ category('Viewers: Logo Summary Table', () => {
|
|
|
152
133
|
if (tempModel === null)
|
|
153
134
|
throw new Error('Model is null');
|
|
154
135
|
model = tempModel;
|
|
155
|
-
let overlayInit = false;
|
|
156
|
-
model._analysisView!.grid.onAfterDrawOverlay.subscribe(() => overlayInit = true);
|
|
157
136
|
|
|
158
137
|
lstViewer = model.findViewer(VIEWER_TYPE.LOGO_SUMMARY_TABLE) as LogoSummaryTable;
|
|
159
138
|
|
|
160
|
-
|
|
161
|
-
let accrodionInit = false;
|
|
162
|
-
grok.events.onAccordionConstructed.subscribe((_) => accrodionInit = true);
|
|
163
|
-
await awaitCheck(() => model!.df.currentRowIdx === 0, 'Grid cell never finished initializing', 2000);
|
|
164
|
-
await awaitCheck(() => grok.shell.o instanceof DG.Column, 'Shell object never changed', 2000);
|
|
165
|
-
await awaitCheck(() => accrodionInit, 'Accordion never finished initializing', 2000);
|
|
166
|
-
await awaitCheck(() => overlayInit, 'Overlay never finished initializing', 2000);
|
|
139
|
+
await delay(500);
|
|
167
140
|
});
|
|
168
141
|
|
|
169
142
|
test('Properties', async () => {
|
package/src/tests/widgets.ts
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
import * as grok from 'datagrok-api/grok';
|
|
2
2
|
import * as DG from 'datagrok-api/dg';
|
|
3
3
|
|
|
4
|
-
import {category, test, before, expect,
|
|
4
|
+
import {category, test, before, expect, delay} from '@datagrok-libraries/utils/src/test';
|
|
5
5
|
import {_package} from '../package-test';
|
|
6
6
|
import {CLUSTER_TYPE, PeptidesModel, VIEWER_TYPE} from '../model';
|
|
7
7
|
import {scaleActivity} from '../utils/misc';
|
|
@@ -36,16 +36,8 @@ category('Widgets: Settings', () => {
|
|
|
36
36
|
if (tempModel === null)
|
|
37
37
|
throw new Error('Model is null');
|
|
38
38
|
model = tempModel;
|
|
39
|
-
|
|
40
|
-
|
|
41
|
-
|
|
42
|
-
// Ensure grid finished initializing to prevent Unhandled exceptions
|
|
43
|
-
let accrodionInit = false;
|
|
44
|
-
grok.events.onAccordionConstructed.subscribe((_) => accrodionInit = true);
|
|
45
|
-
await awaitCheck(() => model!.df.currentRowIdx === 0, 'Grid cell never finished initializing', 2000);
|
|
46
|
-
await awaitCheck(() => grok.shell.o instanceof DG.Column, 'Shell object never changed', 2000);
|
|
47
|
-
await awaitCheck(() => accrodionInit, 'Accordion never finished initializing', 2000);
|
|
48
|
-
await awaitCheck(() => overlayInit, 'Overlay never finished initializing', 2000);
|
|
39
|
+
|
|
40
|
+
await delay(500);
|
|
49
41
|
});
|
|
50
42
|
|
|
51
43
|
test('UI', async () => {
|
|
@@ -87,16 +79,8 @@ category('Widgets: Distribution panel', () => {
|
|
|
87
79
|
if (tempModel === null)
|
|
88
80
|
throw new Error('Model is null');
|
|
89
81
|
model = tempModel;
|
|
90
|
-
|
|
91
|
-
|
|
92
|
-
|
|
93
|
-
// Ensure grid finished initializing to prevent Unhandled exceptions
|
|
94
|
-
let accrodionInit = false;
|
|
95
|
-
grok.events.onAccordionConstructed.subscribe((_) => accrodionInit = true);
|
|
96
|
-
await awaitCheck(() => model!.df.currentRowIdx === 0, 'Grid cell never finished initializing', 2000);
|
|
97
|
-
await awaitCheck(() => grok.shell.o instanceof DG.Column, 'Shell object never changed', 2000);
|
|
98
|
-
await awaitCheck(() => accrodionInit, 'Accordion never finished initializing', 2000);
|
|
99
|
-
await awaitCheck(() => overlayInit, 'Overlay never finished initializing', 2000);
|
|
82
|
+
|
|
83
|
+
await delay(500);
|
|
100
84
|
});
|
|
101
85
|
|
|
102
86
|
test('UI', async () => {
|
|
@@ -125,16 +109,8 @@ category('Widgets: Mutation cliffs', () => {
|
|
|
125
109
|
if (tempModel === null)
|
|
126
110
|
throw new Error('Model is null');
|
|
127
111
|
model = tempModel;
|
|
128
|
-
|
|
129
|
-
|
|
130
|
-
|
|
131
|
-
// Ensure grid finished initializing to prevent Unhandled exceptions
|
|
132
|
-
let accrodionInit = false;
|
|
133
|
-
grok.events.onAccordionConstructed.subscribe((_) => accrodionInit = true);
|
|
134
|
-
await awaitCheck(() => model!.df.currentRowIdx === 0, 'Grid cell never finished initializing', 2000);
|
|
135
|
-
await awaitCheck(() => grok.shell.o instanceof DG.Column, 'Shell object never changed', 2000);
|
|
136
|
-
await awaitCheck(() => accrodionInit, 'Accordion never finished initializing', 2000);
|
|
137
|
-
await awaitCheck(() => overlayInit, 'Overlay never finished initializing', 2000);
|
|
112
|
+
|
|
113
|
+
await delay(500);
|
|
138
114
|
});
|
|
139
115
|
|
|
140
116
|
test('UI', async () => {
|
|
@@ -163,16 +139,8 @@ category('Widgets: Actions', () => {
|
|
|
163
139
|
if (tempModel === null)
|
|
164
140
|
throw new Error('Model is null');
|
|
165
141
|
model = tempModel;
|
|
166
|
-
|
|
167
|
-
|
|
168
|
-
|
|
169
|
-
// Ensure grid finished initializing to prevent Unhandled exceptions
|
|
170
|
-
let accrodionInit = false;
|
|
171
|
-
grok.events.onAccordionConstructed.subscribe((_) => accrodionInit = true);
|
|
172
|
-
await awaitCheck(() => model!.df.currentRowIdx === 0, 'Grid cell never finished initializing', 2000);
|
|
173
|
-
await awaitCheck(() => grok.shell.o instanceof DG.Column, 'Shell object never changed', 2000);
|
|
174
|
-
await awaitCheck(() => accrodionInit, 'Accordion never finished initializing', 2000);
|
|
175
|
-
await awaitCheck(() => overlayInit, 'Overlay never finished initializing', 2000);
|
|
142
|
+
|
|
143
|
+
await delay(500);
|
|
176
144
|
});
|
|
177
145
|
|
|
178
146
|
test('New view', async () => {
|
|
@@ -192,8 +160,7 @@ category('Widgets: Actions', () => {
|
|
|
192
160
|
expect(currentTable.getTag(C.TAGS.UUID), newViewId, 'Current table is expected to have the same UUID as new view');
|
|
193
161
|
expect(currentTable.rowCount, 1, 'Current table is expected to have 1 row');
|
|
194
162
|
|
|
195
|
-
await
|
|
196
|
-
|
|
163
|
+
await delay(500);
|
|
197
164
|
const currentTableModel = currentTable.temp[PeptidesModel.modelName] as PeptidesModel;
|
|
198
165
|
const lstViewer = currentTableModel.findViewer(VIEWER_TYPE.LOGO_SUMMARY_TABLE);
|
|
199
166
|
expect(lstViewer !== null, true, 'New view is expected to have Logo Summary Table viewer attached');
|
package/src/utils/misc.ts
CHANGED
|
@@ -99,3 +99,36 @@ export function prepareTableForHistogram(table: DG.DataFrame): DG.DataFrame {
|
|
|
99
99
|
DG.Column.fromList(DG.TYPE.BOOL, C.COLUMNS_NAMES.SPLIT_COL, expandedMasks),
|
|
100
100
|
]);
|
|
101
101
|
}
|
|
102
|
+
|
|
103
|
+
export function addExpandIcon(grid: DG.Grid): void {
|
|
104
|
+
const fullscreenIcon = ui.iconFA('expand-alt', () => {
|
|
105
|
+
const fullscreenGrid = grid.dataFrame.plot.grid();
|
|
106
|
+
setGridProps(fullscreenGrid);
|
|
107
|
+
fullscreenGrid.root.style.height = '100%';
|
|
108
|
+
const pairsFullscreenDialog = ui.dialog(grid.dataFrame.name);
|
|
109
|
+
pairsFullscreenDialog.add(fullscreenGrid.root);
|
|
110
|
+
pairsFullscreenDialog.showModal(true);
|
|
111
|
+
fullscreenGrid.invalidate();
|
|
112
|
+
});
|
|
113
|
+
grid.root.appendChild(fullscreenIcon);
|
|
114
|
+
fullscreenIcon.style.position = 'absolute';
|
|
115
|
+
fullscreenIcon.style.right = '0px';
|
|
116
|
+
fullscreenIcon.style.top = '0px';
|
|
117
|
+
fullscreenIcon.style.visibility = 'hidden';
|
|
118
|
+
grid.root.addEventListener('mouseenter', (_) => {
|
|
119
|
+
fullscreenIcon.style.visibility = 'visible';
|
|
120
|
+
});
|
|
121
|
+
grid.root.addEventListener('mouseleave', (_) => {
|
|
122
|
+
fullscreenIcon.style.visibility = 'hidden';
|
|
123
|
+
});
|
|
124
|
+
}
|
|
125
|
+
|
|
126
|
+
export function setGridProps(grid: DG.Grid): void {
|
|
127
|
+
grid.props.allowEdit = false;
|
|
128
|
+
grid.props.allowRowSelection = false;
|
|
129
|
+
grid.props.allowBlockSelection = false;
|
|
130
|
+
grid.props.allowColSelection = false;
|
|
131
|
+
grid.props.showRowHeader = false;
|
|
132
|
+
grid.props.showCurrentRowIndicator = false;
|
|
133
|
+
grid.root.style.width = '100%';
|
|
134
|
+
}
|