@datagrok/bio 1.7.5 → 1.7.6

package/files/tests/testCereal.csv

@@ -0,0 +1,78 @@
+cereal_name,Calories,Carbohydrates,Fat,Fiber,Potassium,Protein,Sodium,Sugar,Vitamins/Minerals
+Mueslix_Crispy_Blend,160,17,2,3,160,3,150,13,25
+"Muesli_Raisins,_Dates,_&_Almonds",150,16,3,3,170,4,95,11,25
+"Muesli_Raisins,_Peaches,_&_Pecans",150,16,3,3,170,4,150,11,25
+Just_Right_Fruit_&_Nut,140,20,1,2,95,3,170,9,100
+Nutri-Grain_Almond-Raisin,140,21,2,3,130,3,220,7,25
+Total_Raisin_Bran,140,15,1,4,230,3,190,14,100
+Basic_4,130,18,2,2,100,3,210,8,25
+Oatmeal_Raisin_Crisp,130,null,2,null,120,3,170,10,25
+100%_Natural_Bran,120,8,5,2,135,3,15,8,0
+Cap'n'Crunch,120,12,2,0,35,1,220,12,25
+Cinnamon_Toast_Crunch,120,13,3,0,45,1,210,9,25
+"Fruit_&_Fibre_Dates,_Walnuts,_and_Oats",120,12,2,5,200,3,160,10,25
+Fruitful_Bran,120,14,0,5,190,3,240,12,25
+Great_Grains_Pecan,120,13,3,3,100,3,75,4,25
+Honey_Graham_Ohs,120,12,2,1,45,1,220,11,25
+Nut&Honey_Crunch,120,15,1,0,40,2,190,9,25
+Post_Nat._Raisin_Bran,120,11,1,6,260,3,200,14,25
+Raisin_Bran,120,14,1,5,240,3,210,12,25
+Almond_Delight,110,14,2,1,-1,2,200,8,25
+Apple_Cinnamon_Cheerios,110,null,2,null,70,2,180,10,25
+Apple_Jacks,110,11,0,1,30,2,125,14,25
+Cheerios,110,17,2,2,105,6,290,1,25
+Clusters,110,13,2,2,105,3,140,7,25
+Cocoa_Puffs,110,12,1,0,55,1,180,13,25
+Corn_Chex,110,22,0,0,25,2,280,3,25
+Corn_Pops,110,13,0,1,20,1,90,12,25
+Count_Chocula,110,12,1,0,65,1,180,13,25
+Cracklin'_Oat_Bran,110,10,3,4,160,3,140,7,25
+Crispix,110,21,0,1,30,2,220,3,25
+Froot_Loops,110,11,1,1,30,2,125,13,25
+Frosted_Flakes,110,14,0,1,25,1,200,11,25
+Fruity_Pebbles,110,13,1,0,25,1,135,12,25
+Golden_Grahams,110,15,1,0,45,1,280,9,25
+Grape-Nuts,110,17,0,3,90,3,170,3,25
+Honey-comb,110,14,0,0,35,1,180,11,25
+Honey_Nut_Cheerios,110,null,1,null,90,3,250,10,25
+Just_Right_Crunchy__Nuggets,110,17,1,1,60,2,170,6,100
+Kix,110,21,1,0,40,2,260,3,25
+Lucky_Charms,110,12,1,0,55,2,180,12,25
+Rice_Chex,110,23,0,0,30,1,240,2,25
+Rice_Krispies,110,22,0,0,35,2,290,3,25
+Smacks,110,9,1,1,40,2,70,15,25
+Special_K,110,16,0,1,55,6,230,3,25
+Total_Corn_Flakes,110,21,1,0,35,2,200,3,100
+Triples,110,21,1,0,60,2,250,3,25
+Trix,110,13,1,0,25,1,140,12,25
+Wheaties_Honey_Gold,110,16,1,1,60,2,200,8,25
+Corn_Flakes,100,21,0,1,35,2,290,2,25
+Cream_of_Wheat_(Quick),100,21,0,1,-1,3,80,0,0
+Crispy_Wheat_&_Raisins,100,11,1,2,120,2,140,10,25
+Double_Chex,100,18,0,1,80,2,190,5,25
+Frosted_Mini-Wheats,100,14,0,3,100,3,0,7,25
+Golden_Crisp,100,11,0,0,40,2,45,15,25
+Grape_Nuts_Flakes,100,15,1,3,85,3,140,5,25
+Life,100,12,2,2,95,4,150,6,25
+Maypo,100,16,1,0,95,4,0,3,25
+Multi-Grain_Cheerios,100,15,1,2,90,2,220,6,25
+Product_19,100,20,0,1,45,3,320,3,100
+Quaker_Oat_Squares,100,14,1,2,110,4,135,6,25
+Quaker_Oatmeal,100,-1,2,null,110,5,0,-1,0
+Raisin_Nut_Bran,100,null,2,null,140,3,140,8,25
+Total_Whole_Grain,100,16,1,3,110,3,200,3,100
+Wheat_Chex,100,17,1,3,115,3,230,3,25
+Wheaties,100,17,1,3,110,3,200,3,25
+Bran_Chex,90,15,1,4,125,2,200,6,25
+Bran_Flakes,90,13,0,5,190,3,210,5,25
+Nutri-grain_Wheat,90,18,0,3,90,3,170,2,25
+Raisin_Squares,90,15,0,2,110,2,0,6,25
+Shredded_Wheat_'n'Bran,90,19,0,4,140,3,0,0,0
+Shredded_Wheat_spoon_size,90,20,0,3,120,3,0,0,0
+Strawberry_Fruit_Wheats,90,15,0,3,90,2,15,5,25
+Shredded_Wheat,80,16,0,3,95,2,0,0,0
+100%_Bran,70,5,1,10,280,4,130,6,25
+All-Bran,70,7,1,9,320,4,260,5,25
+All-Bran_with_Extra_Fiber,50,8,0,14,330,4,140,0,25
+Puffed_Rice,50,13,0,0,15,1,0,0,0
+Puffed_Wheat,50,10,0,1,50,2,0,0,0

package/package.json

@@ -2,7 +2,7 @@
   "name": "@datagrok/bio",
   "beta": false,
   "friendlyName": "Bio",
-  "version": "1.7.5",
+  "version": "1.7.6",
   "description": "Bio is a [package](https://datagrok.ai/help/develop/develop#packages) for the [Datagrok](https://datagrok.ai) platform",
   "repository": {
     "type": "git",

package/src/__jest__/remote.test.ts

@@ -16,15 +16,30 @@ beforeAll(async () => {
 }, P_START_TIMEOUT);
 
 afterAll(async () => {
-  await browser.close();
+  await browser?.close();
+});
+
+expect.extend({
+  checkOutput(received, expected, context) {
+    if (received === expected) {
+      return {
+        message: () => context,
+        pass: true
+      };
+    } else {
+      return {
+        message: () => context,
+        pass: false
+      };
+    }
+  }
 });
 
 it('TEST', async () => {
-  const targetPackage: string = process.env.TARGET_PACKAGE ?? 'Bio';
+  const targetPackage:string = process.env.TARGET_PACKAGE ?? 'Bio';
   console.log(`Testing ${targetPackage} package`);
 
-  //console.log(require('root-require')('package.json').version);
-  const r = await page.evaluate((targetPackage): Promise<object> => {
+  const r = await page.evaluate((targetPackage):Promise<object> => {
     return new Promise<object>((resolve, reject) => {
       (<any>window).grok.functions.eval(targetPackage + ':test()').then((df: any) => {
         const cStatus = df.columns.byName('success');
@@ -32,23 +47,22 @@ it('TEST', async () => {
         const cCat = df.columns.byName('category');
         const cName = df.columns.byName('name');
         let failed = false;
-        let report = '';
+        let passReport = '';
+        let failReport = '';
         for (let i = 0; i < df.rowCount; i++) {
-          if (!cStatus.get(i)) {
-            report += `${cCat.get(i)}.${cName.get(i)}: ${cMessage.get(i)}\n`;
+          if (cStatus.get(i)) {
+            passReport += `Test result : ${targetPackage}.${cCat.get(i)}.${cName.get(i)} : ${cMessage.get(i)}\n`;
+          } else {
             failed = true;
+            failReport += `Test result : ${targetPackage}.${cCat.get(i)}.${cName.get(i)} : ${cMessage.get(i)}\n`;
           }
         }
-        resolve({report, failed});
+        resolve({failReport, passReport, failed});
       }).catch((e: any) => reject(e));
     });
   }, targetPackage);
   // @ts-ignore
-  console.log(r.report);
+  console.log(r.passReport);
   // @ts-ignore
-  expect(r.failed).toBe(false);
+  expect(r.failed).checkOutput(false, r.failReport);
 }, 100000);
-
-// it('WebLogo.getAlphabetSimilarity', () => {
-//
-// });

package/src/const.ts

@@ -3,23 +3,23 @@ import * as grok from 'datagrok-api/grok';
 import * as DG from 'datagrok-api/dg';
 
 export const jsonSdfMonomerLibDict = {
-    "monomerType": null, 
-    "smiles": null, 
-    "name": "MonomerName", 
-    "author": null, 
-    "molfile": "molecule", 
-    "naturalAnalog": "MonomerNaturalAnalogCode", 
-    "rgroups": "MonomerCaps",
-    "createDate": null, 
-    "id": null, 
-    "polymerType": "MonomerType", 
-    "symbol": "MonomerCode"
-}
+  'monomerType': null,
+  'smiles': null,
+  'name': 'MonomerName',
+  'author': null,
+  'molfile': 'molecule',
+  'naturalAnalog': 'MonomerNaturalAnalogCode',
+  'rgroups': 'MonomerCaps',
+  'createDate': null,
+  'id': null,
+  'polymerType': 'MonomerType',
+  'symbol': 'MonomerCode'
+};
 
-export const RGROUP_FIELD = "rgroups";
-export const CAP_GROUP_SMILES = "capGroupSmiles";
-export const RGROUP_ALTER_ID = "alternateId";
-export const CAP_GROUP_NAME = "capGroupName";
-export const RGROUP_LABEL = "label";
-export const MONOMER_SYMBOL = "symbol";
-export const SDF_MONOMER_NAME = "MonomerName";
+export const RGROUP_FIELD = 'rgroups';
+export const CAP_GROUP_SMILES = 'capGroupSmiles';
+export const RGROUP_ALTER_ID = 'alternateId';
+export const CAP_GROUP_NAME = 'capGroupName';
+export const RGROUP_LABEL = 'label';
+export const MONOMER_SYMBOL = 'symbol';
+export const SDF_MONOMER_NAME = 'MonomerName';

package/src/package.ts

@@ -252,7 +252,7 @@ export async function compositionAnalysis(): Promise<void> {
 //name: sdfToJsonLib
 //input: dataframe table
 export async function sdfToJsonLib(table: DG.DataFrame) {
-  const jsonMonomerLibrary = createJsonMonomerLibFromSdf(table);   
+  const jsonMonomerLibrary = createJsonMonomerLibFromSdf(table);
 }
 
 // helper function for importFasta

package/src/tests/convert-test.ts

@@ -83,7 +83,7 @@ MKP---SEYV
 
     separatorGaps: `seq
 F/W//P/H//E/Y
-//Y/N/R/Q/W/Y/V//
+/Y/N/R/Q/W/Y/V/
 M/K/P////S/E/Y/V
 `,
 
@@ -133,6 +133,7 @@ PEPTIDE1{M.K.P.*.*.*.S.E.Y.V}$$$
   }
 
   // FASTA tests
+  // fasta -> separator
   test('testFastaPtToSeparator', async () => {
     await _testConvert(Samples.fastaPt, converter(NOTATION.SEPARATOR, '-'), Samples.separatorPt);
   });
@@ -142,7 +143,11 @@ PEPTIDE1{M.K.P.*.*.*.S.E.Y.V}$$$
   test('testFastaRnaToSeparator', async () => {
     await _testConvert(Samples.fastaRna, converter(NOTATION.SEPARATOR, '*'), Samples.separatorRna);
   });
+  test('testFastaGapsToSeparator', async () => {
+    await _testConvert(Samples.fastaGaps, converter(NOTATION.SEPARATOR, '/'), Samples.separatorGaps);
+  });
 
+  // fasta -> helm
   test('testFastaPtToHelm', async () => {
     await _testConvert(Samples.fastaPt, converter(NOTATION.HELM), Samples.helmPt);
   });
@@ -152,16 +157,13 @@ PEPTIDE1{M.K.P.*.*.*.S.E.Y.V}$$$
   test('testFastaRnaToHelm', async () => {
     await _testConvert(Samples.fastaRna, converter(NOTATION.HELM), Samples.helmRna);
   });
-
-  test('testFastaGapsToSeparator', async () => {
-    await _testConvert(Samples.fastaGaps, converter(NOTATION.SEPARATOR, '/'), Samples.separatorGaps);
-  });
   test('testFastaGapsToHelm', async () => {
-    await _testConvert(Samples.fastaGaps, converter(NOTATION.SEPARATOR), Samples.helmGaps);
+    await _testConvert(Samples.fastaGaps, converter(NOTATION.HELM), Samples.helmGaps);
   });
 
 
   // SEPARATOR tests
+  // separator -> fasta
   test('testSeparatorPtToFasta', async () => {
     await _testConvert(Samples.separatorPt, converter(NOTATION.FASTA), Samples.fastaPt);
   });
@@ -171,7 +173,11 @@ PEPTIDE1{M.K.P.*.*.*.S.E.Y.V}$$$
   test('testSeparatorRnaToFasta', async () => {
     await _testConvert(Samples.separatorRna, converter(NOTATION.FASTA), Samples.fastaRna);
   });
+  test('testSeparatorGapsToFasta', async () => {
+    await _testConvert(Samples.separatorGaps, converter(NOTATION.FASTA), Samples.fastaGaps);
+  });
 
+  // separator -> helm
   test('testSeparatorPtToHelm', async () => {
     await _testConvert(Samples.separatorPt, converter(NOTATION.HELM), Samples.helmPt);
   });
@@ -181,13 +187,31 @@ PEPTIDE1{M.K.P.*.*.*.S.E.Y.V}$$$
   test('testSeparatorRnaToHelm', async () => {
     await _testConvert(Samples.separatorRna, converter(NOTATION.HELM), Samples.helmRna);
   });
-  test('testSeparatorGapsToFasta', async () => {
-    await _testConvert(Samples.separatorGaps, converter(NOTATION.FASTA), Samples.fastaGaps);
-  });
   test('testSeparatorGapsToHelm', async () => {
     await _testConvert(Samples.separatorGaps, converter(NOTATION.HELM), Samples.helmGaps);
   });
 
 
-  // HELM tests: TODO
+  // HELM tests
+  // helm -> fasta
+  test('HelmDnaToFasta', async () => {
+    await _testConvert(Samples.helmDna, converter(NOTATION.FASTA), Samples.fastaDna);
+  });
+  test('HelmRnaToFasta', async () => {
+    await _testConvert(Samples.helmRna, converter(NOTATION.FASTA), Samples.fastaRna);
+  });
+  test('HelmPtToFasta', async () => {
+    await _testConvert(Samples.helmPt, converter(NOTATION.FASTA), Samples.fastaPt);
+  });
+
+  // helm -> separator
+  test('HelmDnaToSeparator', async () => {
+    await _testConvert(Samples.helmDna, converter(NOTATION.SEPARATOR), Samples.separatorDna);
+  });
+  test('HelmRnaToSeparator', async () => {
+    await _testConvert(Samples.helmRna, converter(NOTATION.SEPARATOR, '*'), Samples.separatorRna);
+  });
+  test('HelmPtToSeparator', async () => {
+    await _testConvert(Samples.helmPt, converter(NOTATION.SEPARATOR, '-'), Samples.separatorPt);
+  });
 });

package/src/tests/detectors-test.ts

@@ -113,6 +113,7 @@ MWRSWY-CKHP
     testIdCsv = 'testIdCsv',
     testSmilesCsv = 'testSmilesCsv',
     testSmiles2Csv = 'testSmiles2Csv',
+    testCerealCsv = 'testCerealCsv',
   }
 
   const samples: { [key: string]: string } = {
@@ -128,6 +129,7 @@ MWRSWY-CKHP
     'testIdCsv': 'System:AppData/Bio/tests/testId.csv',
     'testSmilesCsv': 'System:AppData/Bio/tests/testSmiles.csv',
     'testSmiles2Csv': 'System:AppData/Bio/tests/testSmiles2.csv',
+    'testCerealCsv': 'System:AppData/Bio/tests/testCereal.csv',
   };
 
   const _samplesDfs: { [key: string]: Promise<DG.DataFrame> } = {};
@@ -306,6 +308,10 @@ MWRSWY-CKHP
   test('samplesFastaPtPosSequence', async () => {
     await (_testPos(readSamples(Samples.fastaPtCsv), 'sequence', 'fasta:SEQ:PT'));
   });
+
+  test('samplesTestCerealNegativeCerealName', async () => {
+    await (_testNeg(readSamples(Samples.testCerealCsv), 'cereal_name'));
+  });
 });
 
 export async function _testNeg(readDf: DfReaderFunc, colName: string) {

package/src/utils/cell-renderer.ts

@@ -219,7 +219,6 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
 
       g.restore();
       return;
-
     }
   }
 }

package/src/utils/convert.ts

@@ -46,14 +46,16 @@ export function convert(col: DG.Column): void {
       .show();
 
     convertDialogSubs.push(convertDialog.onClose.subscribe((value) => {
-      convertDialogSubs.forEach((s) => {s.unsubscribe(); });
+      convertDialogSubs.forEach((s) => { s.unsubscribe(); });
       convertDialogSubs = [];
       convertDialog = null;
     }));
   }
 }
 
-export async function convertDo(srcCol: DG.Column, targetNotation: NOTATION, separator: string | null): Promise<DG.Column> {
+export async function convertDo(
+  srcCol: DG.Column, targetNotation: NOTATION, separator: string | null
+): Promise<DG.Column> {
   const converter = new NotationConverter(srcCol);
   const newColumn = converter.convert(targetNotation, separator);
   srcCol.dataFrame.columns.add(newColumn);

package/{test-Bio-34f75e5127b8-0507068d.html → test-Bio-34f75e5127b8-c46c3f48.html}

@@ -1,4 +1,4 @@
-<html><head><meta charset="utf-8"/><title>Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=34f75e5127b8. Commit 0507068d.</title><style type="text/css">html,
+<html><head><meta charset="utf-8"/><title>Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=34f75e5127b8. Commit c46c3f48.</title><style type="text/css">html,
 body {
   font-family: Arial, Helvetica, sans-serif;
   font-size: 1rem;
@@ -229,9 +229,9 @@ header {
   font-size: 1rem;
   padding: 0 0.5rem;
 }
-</style></head><body><div id="jesthtml-content"><header><h1 id="title">Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=34f75e5127b8. Commit 0507068d.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-07-14 14:09:37</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">110.386s</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">100.001s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: thrown: "Exceeded timeout of 100000 ms for a test.
+</style></head><body><div id="jesthtml-content"><header><h1 id="title">Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=34f75e5127b8. Commit c46c3f48.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-07-15 08:43:03</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">110.047s</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">100.001s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: thrown: "Exceeded timeout of 100000 ms for a test.
 Use jest.setTimeout(newTimeout) to increase the timeout value, if this is a long-running test."
-    at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:22:1)
+    at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:38:1)
     at Runtime._execModule (/home/runner/work/public/public/packages/Bio/node_modules/jest-runtime/build/index.js:1646:24)
     at Runtime._loadModule (/home/runner/work/public/public/packages/Bio/node_modules/jest-runtime/build/index.js:1185:12)
     at Runtime.requireModule (/home/runner/work/public/public/packages/Bio/node_modules/jest-runtime/build/index.js:1009:12)
@@ -246,11 +246,11 @@ Use jest.setTimeout(newTimeout) to increase the timeout value, if this is a long
     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 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)
     at Generator.next (&lt;anonymous&gt;)
     at fulfilled (/home/runner/work/public/public/packages/Bio/src/__jest__/test-node.ts:28:58)
-    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:24:11
+    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
     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 Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:22:23)
+    at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:38:23)
     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;)</pre><pre class="suite-consolelog-item-message">Testing Bio package</pre></div></div></div></div></body></html>