@datagrok/bio 1.8.2 → 1.9.0

package/package.json

@@ -5,7 +5,7 @@
     "name": "Leonid Stolbov",
     "email": "lstolbov@datagrok.ai"
   },
-  "version": "1.8.2",
+  "version": "1.9.0",
   "description": "Bio is a [package](https://datagrok.ai/help/develop/develop#packages) for the [Datagrok](https://datagrok.ai) platform",
   "repository": {
     "type": "git",
@@ -14,8 +14,8 @@
   },
   "dependencies": {
     "@biowasm/aioli": ">=2.4.0",
-    "@datagrok-libraries/bio": "^3.1.0",
-    "@datagrok-libraries/ml": "^3.1.0",
+    "@datagrok-libraries/bio": "^3.1.1",
+    "@datagrok-libraries/ml": "^4.0.0",
     "@datagrok-libraries/utils": "^1.6.2",
     "cash-dom": "latest",
     "datagrok-api": "^1.5.5",

package/src/package.ts

@@ -15,7 +15,7 @@ import {Aminoacids} from '@datagrok-libraries/bio/src/aminoacids';
 import {getEmbeddingColsNames, sequenceSpace} from './utils/sequence-space';
 import {AvailableMetrics} from '@datagrok-libraries/ml/src/typed-metrics';
 import {getActivityCliffs} from '@datagrok-libraries/ml/src/viewers/activity-cliffs';
-import {sequenceGetSimilarities, drawTooltip} from './utils/sequence-activity-cliffs';
+import {drawSequences, sequenceGetSimilarities} from './utils/sequence-activity-cliffs';
 import {createJsonMonomerLibFromSdf, encodeMonomers, getMolfilesFromSeq, HELM_CORE_LIB_FILENAME} from './utils/utils';
 import {getMacroMol} from './utils/atomic-works';
 import {MacromoleculeSequenceCellRenderer} from './utils/cell-renderer';
@@ -142,7 +142,7 @@ export async function activityCliffs(df: DG.DataFrame, macroMolecule: DG.Column,
     tags,
     sequenceSpace,
     sequenceGetSimilarities,
-    drawTooltip,
+    drawSequences,
     (options as any)[methodName]);
     return sp;
 }

package/src/utils/cell-renderer.ts

@@ -6,9 +6,9 @@ import {UnknownSeqPalette, UnknownSeqPalettes} from '@datagrok-libraries/bio/src
 import {SplitterFunc, WebLogo} from '@datagrok-libraries/bio/src/viewers/web-logo';
 import {SeqPalette} from '@datagrok-libraries/bio/src/seq-palettes';
 import * as ui from 'datagrok-api/ui';
+import {printLeftOrCentered} from '@datagrok-libraries/bio/src/utils/cell-renderer';
 
 const undefinedColor = 'rgb(100,100,100)';
-const grayColor = '#808080';
 
 function getPalleteByType(paletteType: string): SeqPalette {
   switch (paletteType) {
@@ -44,81 +44,6 @@ export function processSequence(subParts: string[]): [string[], boolean] {
 }
 
 
-/**
- * A function that prints a string aligned to left or centered.
- *
- * @param {number} x x coordinate.
- * @param {number} y y coordinate.
- * @param {number} w Width.
- * @param {number} h Height.
- * @param {CanvasRenderingContext2D} g Canvas rendering context.
- * @param {string} s String to print.
- * @param {string} [color=undefinedColor] String color.
- * @param {number} [pivot=0] Pirvot.
- * @param {boolean} [left=false] Is left aligned.
- * @param {number} [transparencyRate=0.0] Transparency rate where 1.0 is fully transparent
- * @param {string} [separator=''] Is separator for sequence.
- * @param {boolean} [last=false] Is checker if element last or not.
- * @return {number} x coordinate to start printing at.
- */
-export function printLeftOrCentered(
-  x: number, y: number, w: number, h: number,
-  g: CanvasRenderingContext2D, s: string, color = undefinedColor,
-  pivot: number = 0, left = false, transparencyRate: number = 1.0,
-  separator: string = '', last: boolean = false, drawStyle: string = 'classic', maxWord: any = {}, maxWordIdx: number = 0, gridCell: any = {}): number {
-  g.textAlign = 'start';
-  const colorPart = s.substring(0);
-  let grayPart = last ? '' : separator;
-  if (drawStyle === 'msa') {
-    grayPart = '';
-  }
-
-  let textSize: any = g.measureText(colorPart + grayPart);
-  const indent = 5;
-
-  let maxColorTextSize = g.measureText(colorPart).width;
-  let colorTextSize = g.measureText(colorPart).width;
-  const dy = (textSize.fontBoundingBoxAscent + textSize.fontBoundingBoxDescent) / 2;
-  textSize = textSize.width;
-  if (drawStyle === 'msa') {
-    maxColorTextSize = maxWord[maxWordIdx];
-    textSize = maxWord[maxWordIdx];
-    if (maxColorTextSize > maxWord) {
-      maxWord[maxWordIdx] = maxColorTextSize;
-      gridCell.cell.column.temp = maxWord;
-    }
-    if (maxWordIdx > (maxWord['bio-maxIndex'] ?? 0)) {
-      maxWord['bio-maxIndex'] = maxWordIdx;
-      gridCell.cell.column.temp = maxWord;
-    }
-  }
-
-  function draw(dx1: number, dx2: number): void {
-    g.fillStyle = color;
-    g.globalAlpha = transparencyRate;
-    if (drawStyle === 'classic') {
-      g.fillText(colorPart, x + dx1, y + dy);
-      g.fillStyle = grayColor;
-      g.fillText(grayPart, x + dx2, y + dy);
-    }
-    if (drawStyle === 'msa') {
-      g.fillStyle = color;
-      g.fillText(colorPart, x + dx1 + ((maxWord[maxWordIdx] - colorTextSize) / 2), y + dy);
-    }
-  }
-
-  if (left || textSize > w) {
-    draw(indent, indent + maxColorTextSize);
-    return x + maxColorTextSize + g.measureText(grayPart).width;
-
-  } else {
-    const dx = (w - textSize) / 2;
-    draw(dx, dx + maxColorTextSize);
-    return x + dx + maxColorTextSize;
-  }
-}
-
-
 export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
   get name(): string { return 'sequence'; }
 
@@ -344,9 +269,8 @@ export class MacromoleculeDifferenceCellRenderer extends DG.GridCellRenderer {
     // 28 is the height of the two substitutions on top of each other + space
     const updatedY = Math.max(y, y + (h - 28) / 2);
 
-    let palette: SeqPalette = UnknownSeqPalettes.Color;
-    if (units != 'HELM')
-      palette = getPalleteByType(units.substring(units.length - 2));
+    let palette: SeqPalette = units == 'HELM' ? UnknownSeqPalettes.Color :
+      getPalleteByType(gridCell.tableColumn!.tags[C.TAGS.ALPHABET]);
 
     const vShift = 7;
     for (let i = 0; i < subParts1.length; i++) {

package/src/utils/sequence-activity-cliffs.ts

@@ -1,4 +1,4 @@
-import {IDrawTooltipParams} from '@datagrok-libraries/ml/src/viewers/activity-cliffs';
+import {ITooltipAndPanelParams} from '@datagrok-libraries/ml/src/viewers/activity-cliffs';
 import * as DG from 'datagrok-api/dg';
 import * as ui from 'datagrok-api/ui';
 import {getSimilarityFromDistance} from '@datagrok-libraries/utils/src/similarity-metrics';
@@ -12,25 +12,9 @@ export async function sequenceGetSimilarities(col: DG.Column, seq: string): Prom
   return DG.Column.fromList(DG.COLUMN_TYPE.FLOAT, 'distances', distances);
 }
 
-export function drawTooltip(params: IDrawTooltipParams) {
-  params.tooltips[params.line.id] = ui.divH([]);
-  const columnNames = ui.divV([
-    ui.divText('sequense'),
-    ui.divText(params.activity.name),
-  ]);
-  columnNames.style.fontWeight = 'bold';
-  columnNames.style.display = 'flex';
-  columnNames.style.justifyContent = 'space-between';
-  params.tooltips[params.line.id].append(columnNames);
-  params.line.mols.forEach((mol: number) => {
-    const seq = ui.divText(params.df.get(params.seqCol.name, mol));
-    const activity = ui.divText(params.df.get(params.activity.name, mol).toFixed(2));
-    activity.style.display = 'flex';
-    activity.style.justifyContent = 'left';
-    activity.style.paddingLeft = '30px';
-    params.tooltips[params.line.id].append(ui.divV([
-      seq,
-      activity,
-    ], {style: {paddingLeft: '5px'}}));
+export function drawSequences(params: ITooltipAndPanelParams) {
+  params.line.mols.forEach((mol: number, index: number) => {
+    ui.empty(params.hosts[index]);
+    params.hosts[index].append(ui.divText(params.seqCol.get(mol)));
   });
 }

package/test-Bio-d4ef1f35c295-90ae719f.html

@@ -0,0 +1,245 @@
+<html><head><meta charset="utf-8"/><title>Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=d4ef1f35c295. Commit 90ae719f.</title><style type="text/css">html,
+body {
+  font-family: Arial, Helvetica, sans-serif;
+  font-size: 1rem;
+  margin: 0;
+  padding: 0;
+  color: #333;
+}
+body {
+  padding: 2rem 1rem;
+  font-size: 0.85rem;
+}
+#jesthtml-content {
+  margin: 0 auto;
+  max-width: 70rem;
+}
+header {
+  display: flex;
+  align-items: center;
+}
+#title {
+  margin: 0;
+  flex-grow: 1;
+}
+#logo {
+  height: 4rem;
+}
+#timestamp {
+  color: #777;
+  margin-top: 0.5rem;
+}
+
+/** SUMMARY */
+#summary {
+  color: #333;
+  margin: 2rem 0;
+  display: flex;
+  font-family: monospace;
+  font-size: 1rem;
+}
+#summary > div {
+  margin-right: 2rem;
+  background: #eee;
+  padding: 1rem;
+  min-width: 15rem;
+}
+#summary > div:last-child {
+  margin-right: 0;
+}
+@media only screen and (max-width: 720px) {
+  #summary {
+    flex-direction: column;
+  }
+  #summary > div {
+    margin-right: 0;
+    margin-top: 2rem;
+  }
+  #summary > div:first-child {
+    margin-top: 0;
+  }
+}
+
+.summary-total {
+  font-weight: bold;
+  margin-bottom: 0.5rem;
+}
+.summary-passed {
+  color: #4f8a10;
+  border-left: 0.4rem solid #4f8a10;
+  padding-left: 0.5rem;
+}
+.summary-failed,
+.summary-obsolete-snapshots {
+  color: #d8000c;
+  border-left: 0.4rem solid #d8000c;
+  padding-left: 0.5rem;
+}
+.summary-pending {
+  color: #9f6000;
+  border-left: 0.4rem solid #9f6000;
+  padding-left: 0.5rem;
+}
+.summary-empty {
+  color: #999;
+  border-left: 0.4rem solid #999;
+}
+
+.test-result {
+  padding: 1rem;
+  margin-bottom: 0.25rem;
+}
+.test-result:last-child {
+  border: 0;
+}
+.test-result.passed {
+  background-color: #dff2bf;
+  color: #4f8a10;
+}
+.test-result.failed {
+  background-color: #ffbaba;
+  color: #d8000c;
+}
+.test-result.pending {
+  background-color: #ffdf61;
+  color: #9f6000;
+}
+
+.test-info {
+  display: flex;
+  justify-content: space-between;
+}
+.test-suitename {
+  width: 20%;
+  text-align: left;
+  font-weight: bold;
+  word-break: break-word;
+}
+.test-title {
+  width: 40%;
+  text-align: left;
+  font-style: italic;
+}
+.test-status {
+  width: 20%;
+  text-align: right;
+}
+.test-duration {
+  width: 10%;
+  text-align: right;
+  font-size: 0.75rem;
+}
+
+.failureMessages {
+  padding: 0 1rem;
+  margin-top: 1rem;
+  border-top: 1px dashed #d8000c;
+}
+.failureMessages.suiteFailure {
+  border-top: none;
+}
+.failureMsg {
+  white-space: pre-wrap;
+  white-space: -moz-pre-wrap;
+  white-space: -pre-wrap;
+  white-space: -o-pre-wrap;
+  word-wrap: break-word;
+}
+
+.suite-container {
+  margin-bottom: 2rem;
+}
+.suite-info {
+  padding: 1rem;
+  background-color: #eee;
+  color: #777;
+  display: flex;
+  align-items: center;
+  margin-bottom: 0.25rem;
+}
+.suite-info .suite-path {
+  word-break: break-all;
+  flex-grow: 1;
+  font-family: monospace;
+  font-size: 1rem;
+}
+.suite-info .suite-time {
+  margin-left: 0.5rem;
+  padding: 0.2rem 0.3rem;
+  font-size: 0.75rem;
+}
+.suite-info .suite-time.warn {
+  background-color: #d8000c;
+  color: #fff;
+}
+
+/* CONSOLE LOGS */
+.suite-consolelog {
+  margin-bottom: 0.25rem;
+  padding: 1rem;
+  background-color: #efefef;
+}
+.suite-consolelog-header {
+  font-weight: bold;
+}
+.suite-consolelog-item {
+  padding: 0.5rem;
+}
+.suite-consolelog-item pre {
+  margin: 0.5rem 0;
+  white-space: pre-wrap;
+  white-space: -moz-pre-wrap;
+  white-space: -pre-wrap;
+  white-space: -o-pre-wrap;
+  word-wrap: break-word;
+}
+.suite-consolelog-item-origin {
+  color: #777;
+  font-weight: bold;
+}
+.suite-consolelog-item-message {
+  color: #000;
+  font-size: 1rem;
+  padding: 0 0.5rem;
+}
+
+/* OBSOLETE SNAPSHOTS */
+.suite-obsolete-snapshots {
+  margin-bottom: 0.25rem;
+  padding: 1rem;
+  background-color: #ffbaba;
+  color: #d8000c;
+}
+.suite-obsolete-snapshots-header {
+  font-weight: bold;
+}
+.suite-obsolete-snapshots-item {
+  padding: 0.5rem;
+}
+.suite-obsolete-snapshots-item pre {
+  margin: 0.5rem 0;
+  white-space: pre-wrap;
+  white-space: -moz-pre-wrap;
+  white-space: -pre-wrap;
+  white-space: -o-pre-wrap;
+  word-wrap: break-word;
+}
+.suite-obsolete-snapshots-item-message {
+  color: #000;
+  font-size: 1rem;
+  padding: 0 0.5rem;
+}
+</style></head><body><div id="jesthtml-content"><header><h1 id="title">Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=d4ef1f35c295. Commit 90ae719f.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-08-29 04:53:14</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">1813.741s</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">0.001s</div></div><div class="failureMessages"> <pre class="failureMsg">TimeoutError: waiting for selector `.grok-preloader` failed: timeout 1800000ms exceeded
+    at new WaitTask (/home/runner/work/public/public/packages/Bio/node_modules/puppeteer/src/common/DOMWorld.ts:813:28)
+    at DOMWorld.waitForSelectorInPage (/home/runner/work/public/public/packages/Bio/node_modules/puppeteer/src/common/DOMWorld.ts:656:22)
+    at Object.internalHandler.waitFor (/home/runner/work/public/public/packages/Bio/node_modules/puppeteer/src/common/QueryHandler.ts:78:19)
+    at DOMWorld.waitForSelector (/home/runner/work/public/public/packages/Bio/node_modules/puppeteer/src/common/DOMWorld.ts:511:25)
+    at Frame.waitForSelector (/home/runner/work/public/public/packages/Bio/node_modules/puppeteer/src/common/FrameManager.ts:1290:47)
+    at Page.waitForSelector (/home/runner/work/public/public/packages/Bio/node_modules/puppeteer/src/common/Page.ts:3222:29)
+    at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/Bio/src/__jest__/test-node.ts:79:16)
+    at Generator.next (&lt;anonymous&gt;)
+    at fulfilled (/home/runner/work/public/public/packages/Bio/src/__jest__/test-node.ts:28:58)
+    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.&lt;anonymous&gt; (/home/runner/work/public/public/packages/Bio/src/__jest__/test-node.ts:63:11)
+    at Generator.next (&lt;anonymous&gt;)
+    at fulfilled (/home/runner/work/public/public/packages/Bio/src/__jest__/test-node.ts:28:58)
+    at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Using web root: http://localhost:8080</pre></div></div></div></div></body></html>