@datagrok/bio 2.0.11 → 2.0.12
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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@@ -5,7 +5,7 @@
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"name": "Leonid Stolbov",
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"email": "lstolbov@datagrok.ai"
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},
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"version": "2.0.
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"version": "2.0.12",
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"description": "Bio is a [package](https://datagrok.ai/help/develop/develop#packages) for the [Datagrok](https://datagrok.ai) platform",
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"repository": {
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"type": "git",
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@@ -2,7 +2,7 @@ import {after, before, category, test, expect, delay} from '@datagrok-libraries/
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import * as DG from 'datagrok-api/dg';
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import {readDataframe} from './utils';
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import * as grok from 'datagrok-api/grok';
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import {
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import {_testSequenceSpaceReturnsResult} from './sequence-space-utils';
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category('sequenceSpace', async () => {
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let testFastaDf: DG.DataFrame;
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@@ -13,7 +13,7 @@ category('sequenceSpace', async () => {
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before(async () => {
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testFastaDf = await readDataframe('samples/sample_FASTA.csv');
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testFastaTableView = grok.shell.addTableView(testFastaDf);
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testHelmWithEmptyRows = await readDataframe('
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testHelmWithEmptyRows = await readDataframe('data/sample_HELM_empty_vals.csv');
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testHelmWithEmptyRowsTableView = grok.shell.addTableView(testHelmWithEmptyRows);
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});
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@@ -335,11 +335,12 @@ function createDifferenceCanvas(
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h: number): HTMLCanvasElement {
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const canvas = document.createElement('canvas');
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const context = canvas.getContext('2d')!;
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context.font = '12px monospace';
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const width1 = context.measureText(processSequence([amino1]).join('')).width;
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const width2 = context.measureText(processSequence([amino2]).join('')).width;
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const width = Math.max(width1, width2);
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canvas.height = h;
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canvas.width = width +
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canvas.width = width + 4;
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context.font = '12px monospace';
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context.textBaseline = 'top';
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printLeftOrCentered(0, y - shift, width, h, context, amino1, color1, 0, true);
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@@ -0,0 +1,374 @@
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<html><head><meta charset="utf-8"/><title>Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=7770371320b2. Commit f955a7eb.</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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margin: 0;
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padding: 0;
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color: #333;
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}
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body {
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padding: 2rem 1rem;
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font-size: 0.85rem;
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}
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#jesthtml-content {
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margin: 0 auto;
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max-width: 70rem;
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}
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header {
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display: flex;
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align-items: center;
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}
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#title {
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margin: 0;
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flex-grow: 1;
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}
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#logo {
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height: 4rem;
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}
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#timestamp {
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color: #777;
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margin-top: 0.5rem;
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}
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/** SUMMARY */
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#summary {
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color: #333;
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margin: 2rem 0;
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display: flex;
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font-family: monospace;
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font-size: 1rem;
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}
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#summary > div {
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margin-right: 2rem;
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background: #eee;
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padding: 1rem;
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min-width: 15rem;
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}
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#summary > div:last-child {
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margin-right: 0;
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}
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@media only screen and (max-width: 720px) {
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#summary {
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flex-direction: column;
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}
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#summary > div {
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margin-right: 0;
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margin-top: 2rem;
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}
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#summary > div:first-child {
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margin-top: 0;
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}
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}
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.summary-total {
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font-weight: bold;
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margin-bottom: 0.5rem;
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}
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.summary-passed {
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color: #4f8a10;
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border-left: 0.4rem solid #4f8a10;
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padding-left: 0.5rem;
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}
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.summary-failed,
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.summary-obsolete-snapshots {
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color: #d8000c;
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border-left: 0.4rem solid #d8000c;
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padding-left: 0.5rem;
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}
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.summary-pending {
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color: #9f6000;
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border-left: 0.4rem solid #9f6000;
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padding-left: 0.5rem;
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}
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.summary-empty {
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color: #999;
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border-left: 0.4rem solid #999;
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}
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.test-result {
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padding: 1rem;
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margin-bottom: 0.25rem;
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}
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.test-result:last-child {
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border: 0;
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}
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.test-result.passed {
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background-color: #dff2bf;
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color: #4f8a10;
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}
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.test-result.failed {
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background-color: #ffbaba;
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color: #d8000c;
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}
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.test-result.pending {
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background-color: #ffdf61;
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color: #9f6000;
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}
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.test-info {
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display: flex;
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justify-content: space-between;
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}
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.test-suitename {
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width: 20%;
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text-align: left;
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font-weight: bold;
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word-break: break-word;
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}
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.test-title {
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width: 40%;
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text-align: left;
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font-style: italic;
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}
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.test-status {
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width: 20%;
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text-align: right;
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}
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.test-duration {
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width: 10%;
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text-align: right;
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font-size: 0.75rem;
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}
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.failureMessages {
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padding: 0 1rem;
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margin-top: 1rem;
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border-top: 1px dashed #d8000c;
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}
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.failureMessages.suiteFailure {
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border-top: none;
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}
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.failureMsg {
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white-space: pre-wrap;
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white-space: -moz-pre-wrap;
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white-space: -pre-wrap;
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white-space: -o-pre-wrap;
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word-wrap: break-word;
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}
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.suite-container {
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margin-bottom: 2rem;
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}
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.suite-info {
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padding: 1rem;
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background-color: #eee;
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color: #777;
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display: flex;
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align-items: center;
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margin-bottom: 0.25rem;
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}
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.suite-info .suite-path {
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word-break: break-all;
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flex-grow: 1;
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font-family: monospace;
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font-size: 1rem;
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}
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.suite-info .suite-time {
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margin-left: 0.5rem;
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padding: 0.2rem 0.3rem;
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font-size: 0.75rem;
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}
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.suite-info .suite-time.warn {
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background-color: #d8000c;
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color: #fff;
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}
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/* CONSOLE LOGS */
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.suite-consolelog {
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margin-bottom: 0.25rem;
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padding: 1rem;
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background-color: #efefef;
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}
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.suite-consolelog-header {
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font-weight: bold;
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}
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.suite-consolelog-item {
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padding: 0.5rem;
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}
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.suite-consolelog-item pre {
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margin: 0.5rem 0;
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white-space: pre-wrap;
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white-space: -moz-pre-wrap;
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white-space: -pre-wrap;
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white-space: -o-pre-wrap;
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word-wrap: break-word;
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}
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.suite-consolelog-item-origin {
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color: #777;
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font-weight: bold;
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}
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.suite-consolelog-item-message {
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color: #000;
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font-size: 1rem;
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padding: 0 0.5rem;
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}
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/* OBSOLETE SNAPSHOTS */
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.suite-obsolete-snapshots {
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margin-bottom: 0.25rem;
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padding: 1rem;
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background-color: #ffbaba;
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color: #d8000c;
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}
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.suite-obsolete-snapshots-header {
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font-weight: bold;
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}
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.suite-obsolete-snapshots-item {
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padding: 0.5rem;
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}
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.suite-obsolete-snapshots-item pre {
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margin: 0.5rem 0;
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white-space: pre-wrap;
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white-space: -moz-pre-wrap;
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white-space: -pre-wrap;
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word-wrap: break-word;
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}
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.suite-obsolete-snapshots-item-message {
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color: #000;
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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">Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=7770371320b2. Commit f955a7eb.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-09-20 08:18:04</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/Bio/src/__jest__/remote.test.ts</div><div class="suite-time warn">39.844s</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">25.009s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: Test result : Failed : 247 : Bio.renderers.afterMsa : Request failed with status 502: Bad Gateway
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Test result : Failed : 11 : Bio.renderers.afterConvert : Request failed with status 502: Bad Gateway
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Test result : Failed : 187 : Bio.renderers.setRendererManually : Error: Tag 'cell.renderer' has been manually set to 'MacromoleculeDifference' for column but after df was added as table, tag 'cell.renderer' has reset to 'sequence' instead of manual 'MacromoleculeDifference'.
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at /home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:68:20
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at Generator.next (<anonymous>)
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at fulfilled (/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:31:58)
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at runMicrotasks (<anonymous>)
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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/Bio/src/__jest__/test-node.ts:63:11)
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at Generator.next (<anonymous>)
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at fulfilled (/home/runner/work/public/public/packages/Bio/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/Bio/src/__jest__/remote.test.ts:40:11
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at Generator.next (<anonymous>)
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at /home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:34:71
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at new Promise (<anonymous>)
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at Object.<anonymous>.__awaiter (/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:30:12)
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at Object.<anonymous> (/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:38:23)
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at Promise.then.completed (/home/runner/work/public/public/packages/Bio/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 Bio package</pre></div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin"> at /home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:66:11
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at Generator.next (<anonymous>)
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at fulfilled (/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:31:58)
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at runMicrotasks (<anonymous>)
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at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Test result : Success : 11 : Bio.WebLogo.testGetStats : OK
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Test result : Success : 1 : Bio.WebLogo.testGetAlphabetSimilarity : OK
|
|
256
|
+
Test result : Success : 5 : Bio.WebLogo.testPickupPaletteN1 : OK
|
|
257
|
+
Test result : Success : 2 : Bio.WebLogo.testPickupPaletteN1e : OK
|
|
258
|
+
Test result : Success : 7 : Bio.WebLogo.testPickupPaletteAA1 : OK
|
|
259
|
+
Test result : Success : 2 : Bio.WebLogo.testPickupPaletteX : OK
|
|
260
|
+
Test result : Success : 0 : Bio.WebLogo.monomerToText.longMonomerSingle : OK
|
|
261
|
+
Test result : Success : 0 : Bio.WebLogo.monomerToText.longMonomerShort : OK
|
|
262
|
+
Test result : Success : 0 : Bio.WebLogo.monomerToText.longMonomerLong56 : OK
|
|
263
|
+
Test result : Success : 1 : Bio.WebLogo.monomerToText.longMonomerComplexFirstPartShort : OK
|
|
264
|
+
Test result : Success : 0 : Bio.WebLogo.monomerToText.longMonomerComplexFirstPartLong56 : OK
|
|
265
|
+
Test result : Success : 1 : Bio.Palettes.testPaletteN : OK
|
|
266
|
+
Test result : Success : 0 : Bio.Palettes.testPaletteAA : OK
|
|
267
|
+
Test result : Success : 1 : Bio.Palettes.testPalettePtMe : OK
|
|
268
|
+
Test result : Success : 78 : Bio.detectors.NegativeEmpty : OK
|
|
269
|
+
Test result : Success : 26 : Bio.detectors.Negative1 : OK
|
|
270
|
+
Test result : Success : 31 : Bio.detectors.Negative2 : OK
|
|
271
|
+
Test result : Success : 25 : Bio.detectors.Negative3 : OK
|
|
272
|
+
Test result : Success : 22 : Bio.detectors.NegativeSmiles : OK
|
|
273
|
+
Test result : Success : 10 : Bio.detectors.Dna1 : OK
|
|
274
|
+
Test result : Success : 35 : Bio.detectors.Rna1 : OK
|
|
275
|
+
Test result : Success : 43 : Bio.detectors.AA1 : OK
|
|
276
|
+
Test result : Success : 23 : Bio.detectors.MsaDna1 : OK
|
|
277
|
+
Test result : Success : 12 : Bio.detectors.MsaAA1 : OK
|
|
278
|
+
Test result : Success : 38 : Bio.detectors.SepDna : OK
|
|
279
|
+
Test result : Success : 25 : Bio.detectors.SepRna : OK
|
|
280
|
+
Test result : Success : 18 : Bio.detectors.SepPt : OK
|
|
281
|
+
Test result : Success : 15 : Bio.detectors.SepUn1 : OK
|
|
282
|
+
Test result : Success : 15 : Bio.detectors.SepUn2 : OK
|
|
283
|
+
Test result : Success : 7 : Bio.detectors.SepMsaN1 : OK
|
|
284
|
+
Test result : Success : 659 : Bio.detectors.SamplesFastaCsvPt : OK
|
|
285
|
+
Test result : Success : 18 : Bio.detectors.SamplesFastaCsvNegativeEntry : OK
|
|
286
|
+
Test result : Success : 23 : Bio.detectors.SamplesFastaCsvNegativeLength : OK
|
|
287
|
+
Test result : Success : 72 : Bio.detectors.SamplesFastaCsvNegativeUniProtKB : OK
|
|
288
|
+
Test result : Success : 361 : Bio.detectors.SamplesFastaFastaPt : OK
|
|
289
|
+
Test result : Success : 1082 : Bio.detectors.samplesPeptidesComplexNegativeID : OK
|
|
290
|
+
Test result : Success : 23 : Bio.detectors.SamplesPeptidesComplexNegativeMeasured : OK
|
|
291
|
+
Test result : Success : 190 : Bio.detectors.SamplesPeptidesComplexNegativeValue : OK
|
|
292
|
+
Test result : Success : 265 : Bio.detectors.samplesMsaComplexUn : OK
|
|
293
|
+
Test result : Success : 42 : Bio.detectors.samplesMsaComplexNegativeActivity : OK
|
|
294
|
+
Test result : Success : 197 : Bio.detectors.samplesIdCsvNegativeID : OK
|
|
295
|
+
Test result : Success : 263 : Bio.detectors.samplesSarSmallCsvNegativeSmiles : OK
|
|
296
|
+
Test result : Success : 220 : Bio.detectors.samplesHelmCsvHELM : OK
|
|
297
|
+
Test result : Success : 27 : Bio.detectors.samplesHelmCsvNegativeActivity : OK
|
|
298
|
+
Test result : Success : 189 : Bio.detectors.samplesTestHelmNegativeID : OK
|
|
299
|
+
Test result : Success : 13 : Bio.detectors.samplesTestHelmNegativeTestType : OK
|
|
300
|
+
Test result : Success : 8 : Bio.detectors.samplesTestHelmPositiveHelmString : OK
|
|
301
|
+
Test result : Success : 4 : Bio.detectors.samplesTestHelmNegativeValid : OK
|
|
302
|
+
Test result : Success : 4 : Bio.detectors.samplesTestHelmNegativeMolWeight : OK
|
|
303
|
+
Test result : Success : 6 : Bio.detectors.samplesTestHelmNegativeMolFormula : OK
|
|
304
|
+
Test result : Success : 8 : Bio.detectors.samplesTestHelmNegativeSmiles : OK
|
|
305
|
+
Test result : Success : 1404 : Bio.detectors.samplesTestDemogNegativeAll : OK
|
|
306
|
+
Test result : Success : 500 : Bio.detectors.samplesTestSmiles2NegativeSmiles : OK
|
|
307
|
+
Test result : Success : 170 : Bio.detectors.samplesTestActivityCliffsNegativeSmiles : OK
|
|
308
|
+
Test result : Success : 159 : Bio.detectors.samplesFastaPtPosSequence : OK
|
|
309
|
+
Test result : Success : 208 : Bio.detectors.samplesTestCerealNegativeCerealName : OK
|
|
310
|
+
Test result : Success : 357 : Bio.detectors.samplesTestSpgi100NegativeStereoCategory : OK
|
|
311
|
+
Test result : Success : 4 : Bio.detectors.samplesTestSpgi100NegativeScaffoldNames : OK
|
|
312
|
+
Test result : Success : 17 : Bio.detectors.samplesTestSpgi100NegativePrimaryScaffoldName : OK
|
|
313
|
+
Test result : Success : 5 : Bio.detectors.samplesTestSpgi100NegativeSampleName : OK
|
|
314
|
+
Test result : Success : 188 : Bio.detectors.samplesTestUnichemSourcesNegativeSrcUrl : OK
|
|
315
|
+
Test result : Success : 4 : Bio.detectors.samplesTestUnichemSourcesNegativeBaseIdUrl : OK
|
|
316
|
+
Test result : Success : 224 : Bio.detectors.samplesTestDmvOfficesNegativeOfficeName : OK
|
|
317
|
+
Test result : Success : 5 : Bio.detectors.samplesTestDmvOfficesNegativeCity : OK
|
|
318
|
+
Test result : Success : 264 : Bio.detectors.samplesTestAlertCollectionNegativeSmarts : OK
|
|
319
|
+
Test result : Success : 1215 : Bio.MSA.isCorrect : OK
|
|
320
|
+
Test result : Success : 258 : Bio.MSA.isCorrectLong : OK
|
|
321
|
+
Test result : Success : 1255 : Bio.sequenceSpace.sequenceSpaceOpens : OK
|
|
322
|
+
Test result : Success : 4489 : Bio.sequenceSpace.sequenceSpaceOpensWithEmptyRows : OK
|
|
323
|
+
Test result : Success : 926 : Bio.activityCliffs.activityCliffsOpen : OK
|
|
324
|
+
Test result : Success : 857 : Bio.activityCliffs.activityCliffsOpenWithEmptyRows : OK
|
|
325
|
+
Test result : Success : 1 : Bio.splitters.helm1 : OK
|
|
326
|
+
Test result : Success : 1 : Bio.splitters.helm2 : OK
|
|
327
|
+
Test result : Success : 1 : Bio.splitters.helm3-multichar : OK
|
|
328
|
+
Test result : Success : 0 : Bio.splitters.testHelm1 : OK
|
|
329
|
+
Test result : Success : 1 : Bio.splitters.testHelm2 : OK
|
|
330
|
+
Test result : Success : 0 : Bio.splitters.testHelm3 : OK
|
|
331
|
+
Test result : Success : 282 : Bio.splitters.splitToMonomers : OK
|
|
332
|
+
Test result : Success : 3 : Bio.splitters.getHelmMonomers : OK
|
|
333
|
+
Test result : Success : 77 : Bio.renderers.long sequence performance : OK
|
|
334
|
+
Test result : Success : 588 : Bio.renderers.many sequence performance : OK
|
|
335
|
+
Test result : Success : 333 : Bio.renderers.rendererMacromoleculeFasta : OK
|
|
336
|
+
Test result : Success : 207 : Bio.renderers.rendererMacromoleculeSeparator : OK
|
|
337
|
+
Test result : Success : 64 : Bio.renderers.rendererMacromoleculeDifference : OK
|
|
338
|
+
Test result : Success : 181 : Bio.renderers.selectRendererBySemType : OK
|
|
339
|
+
Test result : Success : 6 : Bio.converters.testFastaPtToSeparator : OK
|
|
340
|
+
Test result : Success : 4 : Bio.converters.testFastaDnaToSeparator : OK
|
|
341
|
+
Test result : Success : 13 : Bio.converters.testFastaRnaToSeparator : OK
|
|
342
|
+
Test result : Success : 4 : Bio.converters.testFastaGapsToSeparator : OK
|
|
343
|
+
Test result : Success : 3 : Bio.converters.testFastaPtToHelm : OK
|
|
344
|
+
Test result : Success : 9 : Bio.converters.testFastaDnaToHelm : OK
|
|
345
|
+
Test result : Success : 7 : Bio.converters.testFastaRnaToHelm : OK
|
|
346
|
+
Test result : Success : 1 : Bio.converters.testFastaGapsToHelm : OK
|
|
347
|
+
Test result : Success : 1 : Bio.converters.testSeparatorPtToFasta : OK
|
|
348
|
+
Test result : Success : 0 : Bio.converters.testSeparatorDnaToFasta : OK
|
|
349
|
+
Test result : Success : 0 : Bio.converters.testSeparatorRnaToFasta : OK
|
|
350
|
+
Test result : Success : 2 : Bio.converters.testSeparatorGapsToFasta : OK
|
|
351
|
+
Test result : Success : 0 : Bio.converters.testSeparatorPtToHelm : OK
|
|
352
|
+
Test result : Success : 0 : Bio.converters.testSeparatorDnaToHelm : OK
|
|
353
|
+
Test result : Success : 0 : Bio.converters.testSeparatorRnaToHelm : OK
|
|
354
|
+
Test result : Success : 1 : Bio.converters.testSeparatorGapsToHelm : OK
|
|
355
|
+
Test result : Success : 0 : Bio.converters.testHelmDnaToFasta : OK
|
|
356
|
+
Test result : Success : 0 : Bio.converters.testHelmRnaToFasta : OK
|
|
357
|
+
Test result : Success : 1 : Bio.converters.testHelmPtToFasta : OK
|
|
358
|
+
Test result : Success : 1 : Bio.converters.testHelmDnaToSeparator : OK
|
|
359
|
+
Test result : Success : 0 : Bio.converters.testHelmRnaToSeparator : OK
|
|
360
|
+
Test result : Success : 0 : Bio.converters.testHelmPtToSeparator : OK
|
|
361
|
+
Test result : Success : 2 : Bio.converters.testHelmLoneRibose : OK
|
|
362
|
+
Test result : Success : 3 : Bio.converters.testHelmLoneDeoxyribose : OK
|
|
363
|
+
Test result : Success : 2 : Bio.converters.testHelmLonePhosphorus : OK
|
|
364
|
+
Test result : Success : 0 : Bio.fastaFileHandler.testNormalFormatting : OK
|
|
365
|
+
Test result : Success : 0 : Bio.fastaFileHandler.testExtraSpaces : OK
|
|
366
|
+
Test result : Success : 0 : Bio.fastaFileHandler.testExtraNewlines : OK
|
|
367
|
+
Test result : Success : 92 : Bio.WebLogo-positions.allPositions : OK
|
|
368
|
+
Test result : Success : 106 : Bio.WebLogo-positions.positions with shrinkEmptyTail option true (filterd) : OK
|
|
369
|
+
Test result : Success : 89 : Bio.WebLogo-positions.positions with skipEmptyPositions option : OK
|
|
370
|
+
Test result : Success : 3 : Bio.checkInputColumn.testMsaPos : OK
|
|
371
|
+
Test result : Success : 2 : Bio.checkInputColumn.testMsaNegHelm : OK
|
|
372
|
+
Test result : Success : 1 : Bio.checkInputColumn.testMsaNegUN : OK
|
|
373
|
+
Test result : Success : 7 : Bio.checkInputColumn.testGetActionFunctionMeta : OK
|
|
374
|
+
</pre></div></div></div></div></body></html>
|