@datagrok/bio 2.4.2 → 2.4.3

package/package.json

@@ -5,7 +5,7 @@
     "name": "Leonid Stolbov",
     "email": "lstolbov@datagrok.ai"
   },
-  "version": "2.4.2",
+  "version": "2.4.3",
   "description": "Bioinformatics support (import/export of sequences, conversion, visualization, analysis). [See more](https://github.com/datagrok-ai/public/blob/master/packages/Bio/README.md) for details.",
   "repository": {
     "type": "git",

package/src/package-test.ts

@@ -5,6 +5,7 @@ import {runTests, TestContext, tests} from '@datagrok-libraries/utils/src/test';
 import './tests/_first-tests';
 import './tests/Palettes-test';
 import './tests/detectors-tests';
+import './tests/detectors-weak-and-likely-tests';
 import './tests/detectors-benchmark-tests';
 import './tests/msa-tests';
 import './tests/splitters-test';

package/src/tests/detectors-weak-and-likely-tests.ts

@@ -0,0 +1,129 @@
+import * as grok from 'datagrok-api/grok';
+import * as ui from 'datagrok-api/ui';
+import * as DG from 'datagrok-api/dg';
+
+import {after, before, category, test, expect, expectObject} from '@datagrok-libraries/utils/src/test';
+import {ALIGNMENT, ALPHABET, NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
+import {_testNeg, _testPos} from './detectors-tests';
+import {DfReaderFunc} from './types';
+
+
+category('detectors:weak-and-likely', () => {
+  const enum csvTests {
+    fastaDnaWeak1 = 'fastaDnaWeak1',
+    fastaDnaWeak1LikelyName = 'fastaDnaWeak1LikelyName',
+
+    fastaRnaWeak1 = 'fastaRnaWeak1',
+    fastaRnaWeak1LikelyName = 'fastaRnaWeak1LikelyName',
+
+    fastaPtWeak1 = 'fastaPtWeak1',
+    fastaPtWeak1LikelyName = 'fastaPtWeak1LikelyName',
+
+    fastaUn1 = 'fastaUn1',
+    fastaUn1LikelyName = 'fastaUn1LikelyName',
+    fastaUnMsa1LikelyName = 'fastaUnMsa1LikelyName',
+  }
+
+  const csvData: { [name: string]: string } = {
+    [csvTests.fastaDnaWeak1]: `id,colName
+1,TTTTT
+2,TTTTT
+3,TTTTT
+4,TTTTT
+`,
+    [csvTests.fastaDnaWeak1LikelyName]: `id,seq
+1,TTTTT
+2,TTTTT
+3,TTTTT
+4,TTTTT
+`,
+    [csvTests.fastaRnaWeak1]: `id,colName
+1,UUUUU
+2,UUUUU
+3,UUUUU
+4,UUUUU
+`,
+    [csvTests.fastaRnaWeak1LikelyName]: `id,seq
+1,UUUUU
+2,UUUUU
+3,UUUUU
+4,UUUUU
+`,
+    [csvTests.fastaPtWeak1]: `id,colName
+1,SLSLSPGK
+2,SLSLSPGK
+3,SLSLSPGK
+4,SLSLSPGK
+`,
+    [csvTests.fastaPtWeak1LikelyName]: `id,seq
+1,SLSLSPGK
+2,SLSLSPGK
+3,SLSLSPGK
+4,SLSLSPGK
+`,
+    [csvTests.fastaUn1]: `id,colName
+1,word
+2,other
+3,some
+4,another
+`,
+    [csvTests.fastaUn1LikelyName]: `id,seq
+1,word
+2,other
+3,some
+4,another
+`,
+    [csvTests.fastaUnMsa1LikelyName]: `id,seq
+1,word
+2,male
+3,bare
+4,core
+`,
+  };
+
+  const readCsv: (key: csvTests) => DfReaderFunc = (key: keyof typeof csvData) => {
+    return async () => {
+      // Always recreate test data frame from CSV for reproducible detector behavior in tests.
+      const csv: string = csvData[key];
+      const df: DG.DataFrame = DG.DataFrame.fromCsv(csv);
+      await grok.data.detectSemanticTypes(df);
+      return df;
+    };
+  };
+
+  test(csvTests.fastaDnaWeak1, async () => {
+    await _testNeg(readCsv(csvTests.fastaDnaWeak1), 'colName');
+  });
+  test(csvTests.fastaDnaWeak1LikelyName, async () => {
+    await _testPos(readCsv(csvTests.fastaDnaWeak1LikelyName), 'seq',
+      NOTATION.FASTA, ALIGNMENT.SEQ_MSA, ALPHABET.DNA, 4, false);
+  });
+
+  test(csvTests.fastaRnaWeak1, async () => {
+    await _testNeg(readCsv(csvTests.fastaRnaWeak1), 'colName');
+  });
+  test(csvTests.fastaRnaWeak1LikelyName, async () => {
+    await _testPos(readCsv(csvTests.fastaRnaWeak1LikelyName), 'seq',
+      NOTATION.FASTA, ALIGNMENT.SEQ_MSA, ALPHABET.RNA, 4, false);
+  });
+
+  test(csvTests.fastaPtWeak1, async () => {
+    await _testNeg(readCsv(csvTests.fastaPtWeak1), 'colName');
+  });
+  test(csvTests.fastaPtWeak1LikelyName, async () => {
+    await _testPos(readCsv(csvTests.fastaPtWeak1LikelyName), 'seq',
+      NOTATION.FASTA, ALIGNMENT.SEQ_MSA, ALPHABET.PT, 20, false);
+  });
+
+  test(csvTests.fastaUn1, async () => {
+    await _testNeg(readCsv(csvTests.fastaUn1), 'colName');
+  });
+  test(csvTests.fastaUn1LikelyName, async () => {
+    await _testPos(readCsv(csvTests.fastaUn1LikelyName), 'seq',
+      NOTATION.FASTA, ALIGNMENT.SEQ, ALPHABET.UN, 11, false);
+  });
+  test(csvTests.fastaUnMsa1LikelyName, async () => {
+    await _testPos(readCsv(csvTests.fastaUnMsa1LikelyName), 'seq',
+      NOTATION.FASTA, ALIGNMENT.SEQ_MSA, ALPHABET.UN, 10, false);
+  });
+});

package/tsconfig.json

@@ -6,7 +6,7 @@
     // "incremental": true,                         /* Enable incremental compilation */
     "target": "es6",                                /* Specify ECMAScript target version: 'ES3' (default), 'ES5', 'ES2015', 'ES2016', 'ES2017', 'ES2018', 'ES2019', 'ES2020', or 'ESNEXT'. */
     "module": "es2020",                             /* Specify module code generation: 'none', 'commonjs', 'amd', 'system', 'umd', 'es2015', 'es2020', or 'ESNext'. */
-    "lib": ["es2020", "dom", "ES2021.String"],      /* Specify library files to be included in the compilation. */
+    "lib": ["ES2022", "dom"],      /* Specify library files to be included in the compilation. */
     // "allowJs": true,                             /* Allow javascript files to be compiled. */
     // "checkJs": true,                             /* Report errors in .js files. */
     // "jsx": "preserve",                           /* Specify JSX code generation: 'preserve', 'react-native', 'react', 'react-jsx' or 'react-jsxdev'. */