@datagrok/bio 1.7.21 → 1.7.24

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Files changed (18) hide show
  1. package/detectors.js +24 -12
  2. package/dist/package-test.js +415 -59
  3. package/dist/package.js +206 -58
  4. package/files/tests/testAlertCollection.csv +1252 -0
  5. package/package.json +8 -5
  6. package/src/__jest__/remote.test.ts +2 -2
  7. package/src/package-test.ts +1 -0
  8. package/src/package.ts +27 -12
  9. package/src/tests/WebLogo-positions-test.ts +78 -6
  10. package/src/tests/WebLogo-test.ts +1 -0
  11. package/src/tests/detectors-test.ts +9 -0
  12. package/src/tests/fasta-handler-test.ts +141 -0
  13. package/src/utils/cell-renderer.ts +77 -29
  14. package/src/utils/constants.ts +3 -4
  15. package/src/utils/sequence-activity-cliffs.ts +1 -1
  16. package/src/viewers/vd-regions-viewer.ts +17 -0
  17. package/test-Bio-4f0c8bae6479-367602e1.html +358 -0
  18. package/test-Bio-4f0c8bae6479-9ad1eb12.html +0 -346
package/src/viewers/vd-regions-viewer.ts CHANGED
@@ -50,6 +50,9 @@ export class VdRegionsViewer extends DG.JsViewer {
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  public chains: string[];
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  public sequenceColumnNamePostfix: string;
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+ public skipEmptyPositions: boolean;
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+
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+
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  public get df(): DG.DataFrame {
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  return this.dataFrame;
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  }
@@ -72,6 +75,8 @@ export class VdRegionsViewer extends DG.JsViewer {
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  this.chains = this.stringList('chains', ['Heavy', 'Light'],
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  {choices: ['Heavy', 'Light']});
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  this.sequenceColumnNamePostfix = this.string('sequenceColumnNamePostfix', 'chain sequence');
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+
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+ this.skipEmptyPositions = this.bool('skipEmptyPositions', false);
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  }
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  public async init() {
@@ -119,6 +124,17 @@ export class VdRegionsViewer extends DG.JsViewer {
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  break;
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  case 'sequenceColumnNamePostfix':
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  break;
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+ case 'skipEmptyPositions':
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+ // for (let orderI = 0; orderI < this.logos.length; orderI++) {
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+ // for (let chainI = 0; chainI < this.chains.length; chainI++) {
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+ // const chain: string = this.chains[chainI];
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+ // this.logos[orderI][chain].setOptions({skipEmptyPositions: this.skipEmptyPositions});
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+ // }
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+ // }
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+ // this.calcSize();
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+ await this.destroyView();
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+ await this.buildView();
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+ break;
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  }
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  }
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  }
@@ -188,6 +204,7 @@ export class VdRegionsViewer extends DG.JsViewer {
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  startPositionName: region!.positionStartName,
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  endPositionName: region!.positionEndName,
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  fixWidth: true,
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+ skipEmptyPositions: this.skipEmptyPositions,
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  })) as unknown as WebLogo;
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  }
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  // WebLogo creation fires onRootSizeChanged event even before control being added to this.logos
package/test-Bio-4f0c8bae6479-367602e1.html ADDED
@@ -0,0 +1,358 @@
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+ <html><head><meta charset="utf-8"/><title>Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=4f0c8bae6479. Commit 367602e1.</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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+
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+ /** SUMMARY */
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+ #summary {
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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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+ #summary {
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+ }
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+ #summary > div {
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+ margin-top: 2rem;
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+ .summary-total {
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+ font-weight: bold;
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+ }
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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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+ color: #9f6000;
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+ border-left: 0.4rem solid #9f6000;
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+ padding-left: 0.5rem;
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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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+ padding: 1rem;
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+ }
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+ color: #d8000c;
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+ }
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+ background-color: #ffdf61;
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+ color: #9f6000;
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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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+ .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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+ width: 10%;
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+ font-size: 0.75rem;
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+ }
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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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+ word-wrap: break-word;
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+ }
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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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+ 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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+
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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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+
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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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+ white-space: -o-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=4f0c8bae6479. Commit 367602e1.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-08-05 13:35:35</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">237.34s</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">221.518s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: Test result : Failed : Bio.WebLogo-positions.allPositions : Error: Expected "12", got "0"
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+
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+ at /home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:67:20
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+ at Generator.next (&lt;anonymous&gt;)
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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 (&lt;anonymous&gt;)
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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.&lt;anonymous&gt; (/home/runner/work/public/public/packages/Bio/src/__jest__/test-node.ts:63:11)
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+ at Generator.next (&lt;anonymous&gt;)
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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 (&lt;anonymous&gt;)
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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 (&lt;anonymous&gt;)
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+ at Object.&lt;anonymous&gt;.__awaiter (/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:30:12)
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+ at Object.&lt;anonymous&gt; (/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 (&lt;anonymous&gt;)</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:65:11
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+ at Generator.next (&lt;anonymous&gt;)
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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 (&lt;anonymous&gt;)
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+ at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Test result : Success : Bio.WebLogo.testGetStats : OK
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+ Test result : Success : Bio.WebLogo.testGetAlphabetSimilarity : OK
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+ Test result : Success : Bio.WebLogo.testPickupPaletteN1 : OK
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+ Test result : Success : Bio.WebLogo.testPickupPaletteN1e : OK
256
+ Test result : Success : Bio.WebLogo.testPickupPaletteAA1 : OK
257
+ Test result : Success : Bio.WebLogo.testPickupPaletteX : OK
258
+ Test result : Success : Bio.WebLogo.monomerToText.longMonomerSingle : OK
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+ Test result : Success : Bio.WebLogo.monomerToText.longMonomerShort : OK
260
+ Test result : Success : Bio.WebLogo.monomerToText.longMonomerLong56 : OK
261
+ Test result : Success : Bio.WebLogo.monomerToText.longMonomerComplexFirstPartShort : OK
262
+ Test result : Success : Bio.WebLogo.monomerToText.longMonomerComplexFirstPartLong56 : OK
263
+ Test result : Success : Bio.Palettes.testPaletteN : OK
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+ Test result : Success : Bio.Palettes.testPaletteAA : OK
265
+ Test result : Success : Bio.detectors.NegativeEmpty : OK
266
+ Test result : Success : Bio.detectors.Negative1 : OK
267
+ Test result : Success : Bio.detectors.Negative2 : OK
268
+ Test result : Success : Bio.detectors.Negative3 : OK
269
+ Test result : Success : Bio.detectors.NegativeSmiles : OK
270
+ Test result : Success : Bio.detectors.Dna1 : OK
271
+ Test result : Success : Bio.detectors.Rna1 : OK
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+ Test result : Success : Bio.detectors.AA1 : OK
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+ Test result : Success : Bio.detectors.MsaDna1 : OK
274
+ Test result : Success : Bio.detectors.MsaAA1 : OK
275
+ Test result : Success : Bio.detectors.SepDna : OK
276
+ Test result : Success : Bio.detectors.SepRna : OK
277
+ Test result : Success : Bio.detectors.SepPt : OK
278
+ Test result : Success : Bio.detectors.SepUn1 : OK
279
+ Test result : Success : Bio.detectors.SepUn2 : OK
280
+ Test result : Success : Bio.detectors.SepMsaN1 : OK
281
+ Test result : Success : Bio.detectors.SamplesFastaCsvPt : OK
282
+ Test result : Success : Bio.detectors.SamplesFastaCsvNegativeEntry : OK
283
+ Test result : Success : Bio.detectors.SamplesFastaCsvNegativeLength : OK
284
+ Test result : Success : Bio.detectors.SamplesFastaCsvNegativeUniProtKB : OK
285
+ Test result : Success : Bio.detectors.SamplesFastaFastaPt : OK
286
+ Test result : Success : Bio.detectors.samplesPeptidesComplexNegativeID : OK
287
+ Test result : Success : Bio.detectors.SamplesPeptidesComplexNegativeMeasured : OK
288
+ Test result : Success : Bio.detectors.SamplesPeptidesComplexNegativeValue : OK
289
+ Test result : Success : Bio.detectors.samplesMsaComplexUn : OK
290
+ Test result : Success : Bio.detectors.samplesMsaComplexNegativeActivity : OK
291
+ Test result : Success : Bio.detectors.samplesIdCsvNegativeID : OK
292
+ Test result : Success : Bio.detectors.samplesSarSmallCsvNegativeSmiles : OK
293
+ Test result : Success : Bio.detectors.samplesHelmCsvHELM : OK
294
+ Test result : Success : Bio.detectors.samplesHelmCsvNegativeActivity : OK
295
+ Test result : Success : Bio.detectors.samplesTestHelmNegativeID : OK
296
+ Test result : Success : Bio.detectors.samplesTestHelmNegativeTestType : OK
297
+ Test result : Success : Bio.detectors.samplesTestHelmPositiveHelmString : OK
298
+ Test result : Success : Bio.detectors.samplesTestHelmNegativeValid : OK
299
+ Test result : Success : Bio.detectors.samplesTestHelmNegativeMolWeight : OK
300
+ Test result : Success : Bio.detectors.samplesTestHelmNegativeMolFormula : OK
301
+ Test result : Success : Bio.detectors.samplesTestHelmNegativeSmiles : OK
302
+ Test result : Success : Bio.detectors.samplesTestDemogNegativeAll : OK
303
+ Test result : Success : Bio.detectors.samplesTestSmiles2NegativeSmiles : OK
304
+ Test result : Success : Bio.detectors.samplesTestActivityCliffsNegativeSmiles : OK
305
+ Test result : Success : Bio.detectors.samplesFastaPtPosSequence : OK
306
+ Test result : Success : Bio.detectors.samplesTestCerealNegativeCerealName : OK
307
+ Test result : Success : Bio.detectors.samplesTestSpgi100NegativeStereoCategory : OK
308
+ Test result : Success : Bio.detectors.samplesTestSpgi100NegativeScaffoldNames : OK
309
+ Test result : Success : Bio.detectors.samplesTestSpgi100NegativePrimaryScaffoldName : OK
310
+ Test result : Success : Bio.detectors.samplesTestSpgi100NegativeSampleName : OK
311
+ Test result : Success : Bio.detectors.samplesTestUnichemSourcesNegativeSrcUrl : OK
312
+ Test result : Success : Bio.detectors.samplesTestUnichemSourcesNegativeBaseIdUrl : OK
313
+ Test result : Success : Bio.detectors.samplesTestDmvOfficesNegativeOfficeName : OK
314
+ Test result : Success : Bio.detectors.samplesTestDmvOfficesNegativeCity : OK
315
+ Test result : Success : Bio.detectors.samplesTestAlertCollectionNegativeSmarts : OK
316
+ Test result : Success : Bio.MSA.isCorrect : OK
317
+ Test result : Success : Bio.MSA.isCorrectLong : OK
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+ Test result : Success : Bio.sequenceSpace.sequenceSpaceOpens : OK
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+ Test result : Success : Bio.activityCliffs.activityCliffsOpen : OK
320
+ Test result : Success : Bio.splitters.helm1 : OK
321
+ Test result : Success : Bio.splitters.helm2 : OK
322
+ Test result : Success : Bio.splitters.helm3-multichar : OK
323
+ Test result : Success : Bio.splitters.testHelm1 : OK
324
+ Test result : Success : Bio.splitters.testHelm2 : OK
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+ Test result : Success : Bio.splitters.testHelm3 : OK
326
+ Test result : Success : Bio.renderers.afterMsa : OK
327
+ Test result : Success : Bio.renderers.afterConvert : OK
328
+ Test result : Success : Bio.converters.testFastaPtToSeparator : OK
329
+ Test result : Success : Bio.converters.testFastaDnaToSeparator : OK
330
+ Test result : Success : Bio.converters.testFastaRnaToSeparator : OK
331
+ Test result : Success : Bio.converters.testFastaGapsToSeparator : OK
332
+ Test result : Success : Bio.converters.testFastaPtToHelm : OK
333
+ Test result : Success : Bio.converters.testFastaDnaToHelm : OK
334
+ Test result : Success : Bio.converters.testFastaRnaToHelm : OK
335
+ Test result : Success : Bio.converters.testFastaGapsToHelm : OK
336
+ Test result : Success : Bio.converters.testSeparatorPtToFasta : OK
337
+ Test result : Success : Bio.converters.testSeparatorDnaToFasta : OK
338
+ Test result : Success : Bio.converters.testSeparatorRnaToFasta : OK
339
+ Test result : Success : Bio.converters.testSeparatorGapsToFasta : OK
340
+ Test result : Success : Bio.converters.testSeparatorPtToHelm : OK
341
+ Test result : Success : Bio.converters.testSeparatorDnaToHelm : OK
342
+ Test result : Success : Bio.converters.testSeparatorRnaToHelm : OK
343
+ Test result : Success : Bio.converters.testSeparatorGapsToHelm : OK
344
+ Test result : Success : Bio.converters.testHelmDnaToFasta : OK
345
+ Test result : Success : Bio.converters.testHelmRnaToFasta : OK
346
+ Test result : Success : Bio.converters.testHelmPtToFasta : OK
347
+ Test result : Success : Bio.converters.testHelmDnaToSeparator : OK
348
+ Test result : Success : Bio.converters.testHelmRnaToSeparator : OK
349
+ Test result : Success : Bio.converters.testHelmPtToSeparator : OK
350
+ Test result : Success : Bio.converters.testHelmLoneRibose : OK
351
+ Test result : Success : Bio.converters.testHelmLoneDeoxyribose : OK
352
+ Test result : Success : Bio.converters.testHelmLonePhosphorus : OK
353
+ Test result : Success : Bio.fastaFileHandler.testNormalFormatting : OK
354
+ Test result : Success : Bio.fastaFileHandler.testExtraSpaces : OK
355
+ Test result : Success : Bio.fastaFileHandler.testExtraNewlines : OK
356
+ Test result : Success : Bio.WebLogo-positions.positions with shrinkEmptyTail option : OK
357
+ Test result : Success : Bio.WebLogo-positions.positions with skipEmptyPositions option : OK
358
+ </pre></div></div></div></div></body></html>