@datagrok/bio 2.16.9 → 2.17.1

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Files changed (26) hide show
  1. package/CHANGELOG.md +11 -0
  2. package/css/monomer-manager.css +4 -0
  3. package/dist/package-test.js +2 -2
  4. package/dist/package-test.js.map +1 -1
  5. package/dist/package.js +2 -2
  6. package/dist/package.js.map +1 -1
  7. package/dockerfiles/container.json +6 -0
  8. package/files/tests/peptides_with_random_motif_1600.csv +1601 -0
  9. package/package.json +5 -5
  10. package/src/package.ts +6 -5
  11. package/src/tests/activity-cliffs-tests.ts +1 -1
  12. package/src/tests/msa-tests.ts +3 -5
  13. package/src/tests/pepsea-tests.ts +0 -5
  14. package/src/tests/renderers-test.ts +6 -1
  15. package/src/tests/sequence-space-test.ts +1 -1
  16. package/src/tests/substructure-filters-tests.ts +13 -5
  17. package/src/tests/utils.ts +0 -2
  18. package/src/utils/cell-renderer-custom.ts +3 -1
  19. package/src/utils/cell-renderer.ts +62 -14
  20. package/src/utils/monomer-lib/library-file-manager/style.css +2 -0
  21. package/src/utils/monomer-lib/library-file-manager/ui.ts +5 -2
  22. package/src/utils/monomer-lib/monomer-manager/duplicate-monomer-manager.ts +6 -6
  23. package/src/utils/monomer-lib/monomer-manager/monomer-manager.ts +32 -7
  24. package/src/utils/multiple-sequence-alignment-ui.ts +0 -3
  25. package/src/utils/pepsea.ts +0 -3
  26. package/src/utils/docker.ts +0 -52
package/src/utils/docker.ts DELETED
@@ -1,52 +0,0 @@
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- import * as grok from 'datagrok-api/grok';
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- import * as ui from 'datagrok-api/ui';
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- import * as DG from 'datagrok-api/dg';
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-
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- import {delay} from '@datagrok-libraries/utils/src/test';
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-
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- import {Pepsea} from './pepsea';
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-
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- /** Waits if container is not started
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- * @param {number} ms - time to wait in milliseconds */
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- export async function awaitContainerStart(ms: number = 60000): Promise<void> {
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- const dc = await Pepsea.getDockerContainer();
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- await startDockerContainer(dc, ms);
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- }
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-
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- export async function startDockerContainer(argDc: DG.DockerContainer, timeout: number = 60000): Promise<void> {
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- // argDc contains current container status
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- let dc: DG.DockerContainer | null = argDc;
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- let end: boolean = false;
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- for (let i = 0; i < timeout / 200; ++i) {
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- if (dc === null) dc = await grok.dapi.docker.dockerContainers.find(argDc.id);
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-
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- if (isStarted(dc)) {
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- end = true;
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- break;
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- }
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-
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- switch (dc.status) {
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- case 'stopped': {
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- // TODO: Use the new dockerContainers API
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- await grok.dapi.docker.dockerContainers.run(dc.id);
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- break;
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- }
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- case 'pending change':
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- case 'changing': {
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- // skip to wait
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- break;
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- }
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- case 'error': {
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- throw new Error('Docker container error state.');
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- }
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- }
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- dc = null;
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- await delay(200);
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- }
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- if (!end) throw new Error('Docker container start timeout.');
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- // this.dc = await grok.dapi.docker.dockerContainers.find(dcId);
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- }
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-
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- export function isStarted(dc: DG.DockerContainer): boolean {
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- return dc.status === 'checking' || dc.status === 'started';
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- }