@datagrok/sequence-translator 1.0.2 → 1.0.3
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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@@ -1,7 +1,7 @@
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{
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"name": "@datagrok/sequence-translator",
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"friendlyName": "Sequence Translator",
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"version": "1.0.
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"version": "1.0.3",
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"description": "SequenceTranslator is a [package](https://datagrok.ai/help/develop/develop#packages) for the [Datagrok](https://datagrok.ai) platform, used to translate [oligonucleotide](https://en.wikipedia.org/wiki/Oligonucleotide) sequences between [different representations](https://github.com/datagrok-ai/public/tree/master/packages/SequenceTranslator#sequence-representations).",
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"repository": {
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"type": "git",
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package/src/package.ts
CHANGED
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@@ -10,6 +10,7 @@ import {sequenceToSmiles, sequenceToMolV3000} from './structures-works/from-mono
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import {convertSequence, undefinedInputSequence, isValidSequence, getFormat} from
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'./structures-works/sequence-codes-tools';
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import {map, COL_NAMES, MODIFICATIONS} from './structures-works/map';
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import {siRnaAxolabsToGcrs} from './structures-works/converters';
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import {SALTS_CSV} from './salts';
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import {USERS_CSV} from './users';
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import {ICDS} from './ICDs';
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@@ -216,10 +217,12 @@ export function sequenceTranslator(): void {
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'SDF': saveSenseAntiSense(),
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});
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$(codesTablesDiv).hide();
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const v = grok.shell.newView('Sequence Translator', [tabControl]);
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v.box = true;
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const switchInput = ui.switchInput('Codes',
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const switchInput = ui.switchInput('Codes', false, (v: boolean) => (v) ?
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$(codesTablesDiv).show() :
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$(codesTablesDiv).hide(),
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);
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@@ -306,9 +309,26 @@ function molecularWeight(sequence: string, weightsObj: {[index: string]: number}
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//tags: autostart
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export function autostartOligoSdFileSubscription() {
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let alreadyAdded = false;
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grok.events.onViewAdded.subscribe((v: any) => {
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if (v.type == 'TableView'
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if (v.type == 'TableView') {
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if (v.dataFrame.columns.contains(COL_NAMES.TYPE))
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oligoSdFile(v.dataFrame);
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grok.events.onContextMenu.subscribe((args) => {
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for (const col of v.dataFrame.columns) {
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if (!alreadyAdded && DG.Detector.sampleCategories(col, (s) => /^[fsACGUacgu]{6,}$/.test(s))) {
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alreadyAdded = true;
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args.args.menu.item('Convert to GCRS', () => {
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const seqCol = args.args.context.table.currentCol;
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args.args.context.table.columns.addNewString(seqCol.name + ' to GCRS').init((i: number) => {
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return siRnaAxolabsToGcrs(seqCol.get(i));
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});
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});
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break;
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};
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}
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});
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}
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});
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}
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@@ -366,7 +386,7 @@ export function oligoSdFile(table: DG.DataFrame) {
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ui.button('Save SD file', () => saveTableAsSdFile(addColumnsPressed ? newDf : table)),
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);
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const view = grok.shell.getTableView(table.name)
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const view = grok.shell.getTableView(table.name);
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view.table!.col(COL_NAMES.TYPE)!.setTag(DG.TAGS.CHOICES, '["AS", "SS", "Duplex"]');
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view.table!.col(COL_NAMES.OWNER)!.setTag(DG.TAGS.CHOICES, stringifyItems(usersDf.columns.byIndex(0).toList()));
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@@ -1,4 +1,4 @@
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<html><head><meta charset="utf-8"/><title>SequenceTranslator Test Report. Datagrok version datagrok/datagrok:latest SHA=
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<html><head><meta charset="utf-8"/><title>SequenceTranslator Test Report. Datagrok version datagrok/datagrok:latest SHA=46784acc64a5. Commit c67dd897.</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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@@ -229,7 +229,7 @@ header {
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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">SequenceTranslator Test Report. Datagrok version datagrok/datagrok:latest SHA=
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</style></head><body><div id="jesthtml-content"><header><h1 id="title">SequenceTranslator Test Report. Datagrok version datagrok/datagrok:latest SHA=46784acc64a5. Commit c67dd897.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-07-07 17:11:12</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/SequenceTranslator/src/__jest__/remote.test.ts</div><div class="suite-time warn">10.531s</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">0.564s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: Evaluation failed: Unable to find JS function "test"
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at ExecutionContext._evaluateInternal (/home/runner/work/public/public/packages/SequenceTranslator/node_modules/puppeteer/src/common/ExecutionContext.ts:273:13)
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at processTicksAndRejections (internal/process/task_queues.js:97:5)
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at ExecutionContext.evaluate (/home/runner/work/public/public/packages/SequenceTranslator/node_modules/puppeteer/src/common/ExecutionContext.ts:140:12)</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/SequenceTranslator/src/__jest__/test-node.ts:62:11)
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