@datagrok/bio 2.0.2 → 2.0.4

package/package.json

@@ -5,7 +5,7 @@
     "name": "Leonid Stolbov",
     "email": "lstolbov@datagrok.ai"
   },
-  "version": "2.0.2",
+  "version": "2.0.4",
   "description": "Bio is a [package](https://datagrok.ai/help/develop/develop#packages) for the [Datagrok](https://datagrok.ai) platform",
   "repository": {
     "type": "git",

package/src/package.ts

@@ -32,7 +32,7 @@ import {
 
 import {splitAlignedSequences} from '@datagrok-libraries/bio/src/utils/splitter';
 import * as C from './utils/constants';
-import {getFingerprints} from './calculations/fingerprints'
+import {getFingerprints} from './calculations/fingerprints';
 
 //tags: init
 export async function initBio() {
@@ -40,8 +40,8 @@ export async function initBio() {
 
 //name: fastaSequenceCellRenderer
 //tags: cellRenderer
-//meta.cellType: Sequence
-//meta.columnTags: units=fasta
+//meta.cellType: sequence
+//meta.columnTags: quality=Macromolecule, units=fasta
 //output: grid_cell_renderer result
 export function fastaSequenceCellRenderer(): MacromoleculeSequenceCellRenderer {
   return new MacromoleculeSequenceCellRenderer();
@@ -49,8 +49,8 @@ export function fastaSequenceCellRenderer(): MacromoleculeSequenceCellRenderer {
 
 //name: separatorSequenceCellRenderer
 //tags: cellRenderer
-//meta.cellType: Sequence
-//meta.columnTags: units=separator
+//meta.cellType: sequence
+//meta.columnTags: quality=Macromolecule, units=fasta
 //output: grid_cell_renderer result
 export function separatorSequenceCellRenderer(): MacromoleculeSequenceCellRenderer {
   return new MacromoleculeSequenceCellRenderer();
@@ -138,7 +138,7 @@ export function vdRegionViewer() {
 //input: dataframe table [Input data table]
 //input: column macroMolecule {semType: Macromolecule}
 //input: column activities
-//input: double similarity = 90 [Similarity cutoff]
+//input: double similarity = 80 [Similarity cutoff]
 //input: string methodName { choices:["UMAP", "t-SNE", "SPE"] }
 export async function activityCliffs(df: DG.DataFrame, macroMolecule: DG.Column, activities: DG.Column,
   similarity: number, methodName: string): Promise<DG.Viewer | undefined> {
@@ -379,6 +379,7 @@ export function monomerCellRenderer(): MonomerCellRenderer {
 //name: MacromoleculeDifferenceCellRenderer
 //tags: cellRenderer
 //meta.cellType: MacromoleculeDifference
+//meta.columnTags: quality=MacromoleculeDifference
 //output: grid_cell_renderer result
 export function macromoleculeDifferenceCellRenderer(): MacromoleculeDifferenceCellRenderer {
   return new MacromoleculeDifferenceCellRenderer();
@@ -463,7 +464,7 @@ export function getHelmMonomers(seqCol: DG.Column<string>): string[] {
 export async function macromoleculesFingerprints(mcol: DG.Column): Promise<Uint8Array[]> {
   grok.functions.call('Chem:getRdKitModule');
   const monomers = getHelmMonomers(mcol);
-  const mols = await grok.functions.call('HELM:getMolFiles', {mcol : mcol});
+  const mols = await grok.functions.call('HELM:getMolFiles', {mcol: mcol});
 
   return getFingerprints(mols.toList(), monomers);
 }

package/src/tests/renderers-test.ts

@@ -114,7 +114,7 @@ category('renderers', () => {
     const tw = grok.shell.addTableView(df);
     await delay(100);
     const renderer = tw.dataFrame.col('SequencesDiff')?.getTag(DG.TAGS.CELL_RENDERER);
-    if (renderer !== 'MacromoleculeDifferenceCR')
+    if (renderer !== 'MacromoleculeDifference') // this is value of MacromoleculeDifferenceCR.cellType
       throw new Error(`Units 'separator', separator '/' and semType 'MacromoleculeDifference' have been ` +
         `manually set on column but after df aws added as table view renderer has been reset to '${renderer}'`);
   }

package/src/tests/splitters-test.ts

@@ -8,6 +8,20 @@ import {splitToMonomers, _package} from '../package';
 import * as C from '../utils/constants';
 
 category('splitters', () => {
+  let tvList: DG.TableView[];
+  let dfList: DG.DataFrame[];
+
+  before(async () => {
+    await grok.functions.call('Bio:initBio');
+    tvList = [];
+    dfList = [];
+  });
+
+  after(async () => {
+    dfList.forEach((df: DG.DataFrame) => { grok.shell.closeTable(df); });
+    tvList.forEach((tv: DG.TableView) => tv.close());
+  });
+
   const helm1 = 'PEPTIDE1{meI.hHis.Aca.N.T.dE.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.dV.E.N.D-Orn.D-aThr.Phe_4Me}$$$';
 
   const helm2 = 'PEPTIDE1{meI.hHis.Hcy.Q.T.W.Q.Phe_4NH2.D-Tyr_Et.Tyr_ab-dehydroMe.dV.E.N.N.meK}$$$';
@@ -63,6 +77,13 @@ category('splitters', () => {
       seqCol.semType = semType;
     seqCol.setTag(C.TAGS.ALIGNED, C.MSA);
 
+    const tv: DG.TableView = grok.shell.addTableView(df);
+    // call to calculate 'cell.renderer' tag
+    await grok.data.detectSemanticTypes(df);
+
+    dfList.push(df);
+    tvList.push(tv);
+
     splitToMonomers(seqCol);
     expect(df.columns.names().includes('17'), true);
   });

package/test-Bio-c5a05867bf79-52614433.html

@@ -1,261 +0,0 @@
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-</style></head><body><div id="jesthtml-content"><header><h1 id="title">Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=c5a05867bf79. Commit 52614433.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-09-14 15:22:41</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">8.856s</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">0s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: Unknown server alias. Please add it to /home/runner/.grok/config.yaml
-    at getDevKey (/home/runner/work/public/public/packages/Bio/src/__jest__/test-node.ts:48:13)
-    at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/Bio/src/__jest__/test-node.ts:57:15)
-    at Generator.next (&lt;anonymous&gt;)
-    at /home/runner/work/public/public/packages/Bio/src/__jest__/test-node.ts:31:71
-    at new Promise (&lt;anonymous&gt;)
-    at Object.&lt;anonymous&gt;.__awaiter (/home/runner/work/public/public/packages/Bio/src/__jest__/test-node.ts:27:12)
-    at Object.getBrowserPage (/home/runner/work/public/public/packages/Bio/src/__jest__/test-node.ts:94:12)
-    at /home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:13:27
-    at Generator.next (&lt;anonymous&gt;)
-    at /home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:34:71
-    at new Promise (&lt;anonymous&gt;)
-    at Object.&lt;anonymous&gt;.__awaiter (/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:30:12)
-    at /home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:12:22
-    at Promise.then.completed (/home/runner/work/public/public/packages/Bio/node_modules/jest-circus/build/utils.js:391:28)
-    at new Promise (&lt;anonymous&gt;)
-    at callAsyncCircusFn (/home/runner/work/public/public/packages/Bio/node_modules/jest-circus/build/utils.js:316:10)
-    at _callCircusHook (/home/runner/work/public/public/packages/Bio/node_modules/jest-circus/build/run.js:181:40)
-    at _runTestsForDescribeBlock (/home/runner/work/public/public/packages/Bio/node_modules/jest-circus/build/run.js:47:7)
-    at run (/home/runner/work/public/public/packages/Bio/node_modules/jest-circus/build/run.js:25:3)
-    at runAndTransformResultsToJestFormat (/home/runner/work/public/public/packages/Bio/node_modules/jest-circus/build/legacy-code-todo-rewrite/jestAdapterInit.js:170:21)
-    at jestAdapter (/home/runner/work/public/public/packages/Bio/node_modules/jest-circus/build/legacy-code-todo-rewrite/jestAdapter.js:82:19)
-    at runTestInternal (/home/runner/work/public/public/packages/Bio/node_modules/jest-runner/build/runTest.js:389:16)
-    at runTest (/home/runner/work/public/public/packages/Bio/node_modules/jest-runner/build/runTest.js:475:34)
-    at TestRunner.runTests (/home/runner/work/public/public/packages/Bio/node_modules/jest-runner/build/index.js:101:12)
-    at TestScheduler.scheduleTests (/home/runner/work/public/public/packages/Bio/node_modules/@jest/core/build/TestScheduler.js:333:13)
-    at runJest (/home/runner/work/public/public/packages/Bio/node_modules/@jest/core/build/runJest.js:404:19)
-    at _run10000 (/home/runner/work/public/public/packages/Bio/node_modules/@jest/core/build/cli/index.js:320:7)
-    at runCLI (/home/runner/work/public/public/packages/Bio/node_modules/@jest/core/build/cli/index.js:173:3)
-    at Object.run (/home/runner/work/public/public/packages/Bio/node_modules/jest-cli/build/cli/index.js:155:37)</pre></div></div></div></div></div></body></html>