@datagrok/bio 1.5.8 → 1.5.9

package/files/samples/testHelm.csv

@@ -0,0 +1,6 @@
+ID,Test type,HELM string,Valid?,Mol Weight,Mol Formula,SMILES
+RNA,Simple RNA ,RNA1{R(U)P.R(T)P.R(G)P.R(C)P.R(A)}$$$$,yes,1543.98,C48H61N17O34P4,[H]OCC1OC(N2C=CC(=O)NC2=O)C(O)C1OP(=O)(O)OCC3OC(N4C=C(C(=O)NC4=O)C)C(O)C3OP(=O)(O)OCC5OC(N6C=NC=7C(=O)NC(=NC76)N)C(O)C5OP(=O)(O)OCC8OC(N9C=CC(=NC9=O)N)C(O)C8OP(=O)(O)OCC%10OC(N%11C=NC=%12C(=NC=NC%12%11)N)C(O)C%10O[H] 
+Different arrangements of dots,Only dots beween the backbone monomers,RNA1{P.R(U)P.R(T)}$$$$,yes,644.37,C19H26N4O17P2,OP(O)(OC[C@H]1O[C@@H](N(C2=O)C=CC(N2)=O)[C@H](O)[C@@H]1OP(O)(OC[C@H]3O[C@@H](N(C4=O)C=C(C)C(N4)=O)[C@H](O)[C@@H]3O[H])=O)=O
+Different arrangements of dots,Dot after the branch,RNA1{P.R(U).P.R(T)}$$$$,yes,644.37,C19H26N4O17P2,OP(O)(OC[C@H]1O[C@@H](N(C2=O)C=CC(N2)=O)[C@H](O)[C@@H]1OP(O)(OC[C@H]3O[C@@H](N(C4=O)C=C(C)C(N4)=O)[C@H](O)[C@@H]3O[H])=O)=O
+Hydrogen bonding,RNA with hydrogen bonding,"RNA1{R(A)P.R(C)P.R(G)P}|RNA2{P.R(C)P.R(G)P.R(T)}$RNA1,RNA2,2:pair-9:pair|RNA1,RNA2,5:pair-6:pair|RNA1,RNA2,8:pair-3:pair$$$",yes,1986.2,C58H77N23O44P6,NA
+Hydrogen bonding,Shorter RNA with H bonding,"RNA1{R(U)P.R(T)P}|RNA2{P.R(A)P.R(A)}$RNA1,RNA2,2:pair-6:pair|RNA1,RNA2,5:pair-3:pair$$$",yes,1320.8,C39H52N14O30P4,NA

package/package.json

@@ -2,7 +2,7 @@
   "name": "@datagrok/bio",
   "beta": false,
   "friendlyName": "Bio",
-  "version": "1.5.8",
+  "version": "1.5.9",
   "description": "Bio is a [package](https://datagrok.ai/help/develop/develop#packages) for the [Datagrok](https://datagrok.ai) platform",
   "repository": {
     "type": "git",

package/src/tests/detectors-test.ts

@@ -105,9 +105,11 @@ MWRSWY-CKHP
     fastaCsv = 'fastaCsv',
     fastaFasta = 'fastaFasta',
     msaComplex = 'msaComplex',
-    idCsv = 'idCsv',
-    sarSmallCsv = 'sarSmallCsv',
     helmCsv = 'helmCsv',
+    testIdCsv = 'testIdCsv',
+    testSmilesCsv = 'testSmilesCsv',
+    testHelmCsv = 'testHelmCsv',
+    testDemogCsv = 'testDemogCsv',
   }
 
   const samples: { [key: string]: string } = {
@@ -115,9 +117,11 @@ MWRSWY-CKHP
     'fastaCsv': 'System:AppData/Bio/samples/sample_FASTA.csv',
     'fastaFasta': 'System:AppData/Bio/samples/sample_FASTA.fasta',
     'msaComplex': 'System:AppData/Bio/samples/sample_MSA.csv',
-    'idCsv': 'System:AppData/Bio/samples/id.csv',
-    'sarSmallCsv': 'System:AppData/Bio/samples/sar-small.csv',
     'helmCsv': 'System:AppData/Bio/samples/sample_HELM.csv',
+    'testDemogCsv': 'System:AppData/Bio/samples/testDemog.csv',
+    'testIdCsv': 'System:AppData/Bio/samples/id.csv',
+    'testHelmCsv': 'System:AppData/Bio/samples/testHelm.csv',
+    'testSmilesCsv': 'System:AppData/Bio/samples/testSmiles.csv',
   };
 
   const _samplesDfs: { [key: string]: Promise<DG.DataFrame> } = {};
@@ -238,11 +242,11 @@ MWRSWY-CKHP
   });
 
   test('samplesIdCsvNegativeID', async () => {
-    await _testNeg(readSamples(Samples.idCsv), 'ID');
+    await _testNeg(readSamples(Samples.testIdCsv), 'ID');
   });
 
   test('samplesSarSmallCsvNegativeSmiles', async () => {
-    await _testNeg(readSamples(Samples.sarSmallCsv), 'smiles');
+    await _testNeg(readSamples(Samples.testSmilesCsv), 'smiles');
   });
 
   test('samplesHelmCsvHELM', async () => {
@@ -252,6 +256,38 @@ MWRSWY-CKHP
   test('samplesHelmCsvNegativeActivity', async () => {
     await _testNeg(readSamples(Samples.helmCsv), 'Activity');
   });
+
+  // sample_testHelm.csb
+  // columns: ID,Test type,HELM string,Valid?,Mol Weight,Mol Formula,SMILES
+  test('samplesTestHelmNegativeID', async () => {
+    await _testNeg(readSamples(Samples.testHelmCsv), 'ID');
+  });
+  test('samplesTestHelmNegativeTestType', async () => {
+    await _testNeg(readSamples(Samples.testHelmCsv), 'Test type');
+  });
+  test('samplesTestHelmPositiveHelmString', async () => {
+    await _testPos(readSamples(Samples.testHelmCsv), 'HELM string', 'HELM');
+  });
+  test('samplesTestHelmNegativeValid', async () => {
+    await _testNeg(readSamples(Samples.testHelmCsv), 'Valid?');
+  });
+  test('samplesTestHelmNegativeMolWeight', async () => {
+    await _testNeg(readSamples(Samples.testHelmCsv), 'Mol Weight');
+  });
+  test('samplesTestHelmNegativeMolFormula', async () => {
+    await _testNeg(readSamples(Samples.testHelmCsv), 'Mol Formula');
+  });
+  test('samplesTestHelmNegativeSmiles', async () => {
+    await _testNeg(readSamples(Samples.testHelmCsv), 'Smiles');
+  });
+
+  test('samplesTestDemogNegativeAll', async () => {
+    const dfFunc: DfReaderFunc = readSamples(Samples.testDemogCsv);
+    const df: DG.DataFrame = await dfFunc();
+
+    for (const col of df.columns.toList())
+      await _testNeg(dfFunc, col.name);
+  });
 });
 
 export async function _testNeg(readDf: DfReaderFunc, colName: string) {

package/src/utils/cell-renderer.ts

@@ -9,7 +9,7 @@ import {SplitterFunc, WebLogo} from "@datagrok-libraries/bio/src/viewers/web-log
 import {SeqPalette} from "@datagrok-libraries/bio/src/seq-palettes";
 import * as ui from 'datagrok-api/ui';
 
-const lru = new DG.LruCache<any, any>(); 
+const lru = new DG.LruCache<any, any>();
 
 function getPalleteByType(paletteType: string): SeqPalette  {
   switch (paletteType) {
@@ -127,9 +127,6 @@ function renderSequense(
 }
 
 export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
-  constructor() {
-    super();
-  }
 
   get name(): string {return 'macromoleculeSequence';}
 
@@ -162,7 +159,7 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
       let host = ui.div([], { style: { width: `${w}px`, height: `${h}px`}});
       host.setAttribute('dataformat', 'helm');
       host.setAttribute('data', gridCell.cell.value);
-      
+      gridCell.element = host;
       //@ts-ignore
       var canvas = new JSDraw2.Editor(host, { width: w, height: h, skin: "w8", viewonly: true });
       var formula = canvas.getFormula(true);
@@ -186,28 +183,28 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
       g.font = '12px monospace';
       g.textBaseline = 'top';
       const s: string = cell.value ?? '';
-  
+
       //TODO: can this be replaced/merged with splitSequence?
       const units = gridCell.cell.column.getTag(DG.TAGS.UNITS);
-  
+
       const palette = getPalleteByType(paletteType);
-  
+
       const separator = gridCell.cell.column.getTag('separator') ?? '';
       const splitterFunc: SplitterFunc = WebLogo.getSplitter(units, gridCell.cell.column.getTag('separator') );// splitter,
-  
+
       const subParts:string[] =  splitterFunc(cell.value);
       console.log(subParts);
-  
+
       const textSize = g.measureText(subParts.join(''));
       let x1 = Math.max(x, x + (w - textSize.width) / 2);
-  
+
       subParts.forEach((amino, index) => {
         let [color, outerAmino,, pivot] = ChemPalette.getColorAAPivot(amino);
         color = palette.get(amino);
         g.fillStyle = ChemPalette.undefinedColor;
         x1 = printLeftOrCentered(x1, y, w, h, g, amino, color, pivot, true, false, 1.0, separator);
       });
-  
+
       g.restore();
     }
   }

package/{test-Bio-34f75e5127b8-c4c5a3dc.html → test-Bio-34f75e5127b8-b47d4664.html}

@@ -1,4 +1,4 @@
-<html><head><meta charset="utf-8"/><title>Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=34f75e5127b8. Commit c4c5a3dc.</title><style type="text/css">html,
+<html><head><meta charset="utf-8"/><title>Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=34f75e5127b8. Commit b47d4664.</title><style type="text/css">html,
 body {
   font-family: Arial, Helvetica, sans-serif;
   font-size: 1rem;
@@ -229,7 +229,7 @@ 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 c4c5a3dc.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-07-11 10:13:14</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">94.078s</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">84.418s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: expect(received).toBe(expected) // Object.is equality
+</style></head><body><div id="jesthtml-content"><header><h1 id="title">Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=34f75e5127b8. Commit b47d4664.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-07-11 12:49:26</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">107.855s</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">98.311s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: expect(received).toBe(expected) // Object.is equality
 
 Expected: false
 Received: true
@@ -249,7 +249,8 @@ Received: true
     at new Promise (&lt;anonymous&gt;)</pre><pre class="suite-consolelog-item-message">Testing Bio package</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:47:11
     at Generator.next (&lt;anonymous&gt;)
     at fulfilled (/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:31:58)
-    at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">MSA.is_correct: TypeError: Cannot read properties of undefined (reading 'split')
+    at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">detectors.samplesIdCsvNegativeID: Operation caused an exception (FileSystemException: Cannot open file, path = '/home/grok/data/prod/packages/data/Bio/samples/id.csv' (OS Error: No such file or directory, errno = 2))
+MSA.is_correct: TypeError: Cannot read properties of undefined (reading 'split')
 sequenceSpace.sequenceSpaceOpens: TypeError: Cannot read properties of undefined (reading 'col')
 sequenceSpace.init: Operation caused an exception (FileSystemException: Cannot open file, path = '/home/grok/data/prod/packages/data/Bio/sample_FASTA.csv' (OS Error: No such file or directory, errno = 2))
 activityCliffs.activityCliffsOpen: TypeError: Cannot read properties of undefined (reading 'columns')