@datagrok/bio 2.1.1 → 2.1.4

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.
Files changed (12) hide show
  1. package/detectors.js +37 -11
  2. package/dist/package-test.js +97 -39
  3. package/dist/package.js +33 -18
  4. package/dist/vendors-node_modules_datagrok-libraries_ml_src_workers_dimensionality-reducer_js.js +3 -3
  5. package/package.json +5 -5
  6. package/src/package.ts +4 -1
  7. package/src/tests/checkInputColumn-tests.ts +1 -1
  8. package/src/tests/detectors-test.ts +18 -18
  9. package/src/tests/lib-tests.ts +30 -0
  10. package/src/tests/renderers-test.ts +6 -1
  11. package/src/tests/splitters-test.ts +6 -1
  12. package/{test-Bio-3afbd4014fa1-8c5a0df5.html → test-Bio-62cc009524f3-db2d0836.html} +98 -100
package/package.json CHANGED
@@ -5,7 +5,7 @@
5
5
  "name": "Leonid Stolbov",
6
6
  "email": "lstolbov@datagrok.ai"
7
7
  },
8
- "version": "2.1.1",
8
+ "version": "2.1.4",
9
9
  "description": "Bio is a [package](https://datagrok.ai/help/develop/develop#packages) for the [Datagrok](https://datagrok.ai) platform",
10
10
  "repository": {
11
11
  "type": "git",
@@ -14,12 +14,12 @@
14
14
  },
15
15
  "dependencies": {
16
16
  "@biowasm/aioli": "^3.1.0",
17
- "@datagrok-libraries/bio": "^5.9.13",
17
+ "@datagrok-libraries/bio": "^5.9.15",
18
18
  "@datagrok-libraries/chem-meta": "1.0.1",
19
19
  "@datagrok-libraries/ml": "^6.2.2",
20
- "@datagrok-libraries/utils": "^1.14.1",
20
+ "@datagrok-libraries/utils": "^1.15.5",
21
21
  "cash-dom": "^8.0.0",
22
- "datagrok-api": "^1.8.1",
22
+ "datagrok-api": "^1.8.2",
23
23
  "dayjs": "^1.11.4",
24
24
  "openchemlib": "6.0.1",
25
25
  "rxjs": "^6.5.5",
@@ -47,7 +47,7 @@
47
47
  "webpack-cli": "^4.6.0"
48
48
  },
49
49
  "grokDependencies": {
50
- "@datagrok/chem": "1.3.19",
50
+ "@datagrok/chem": "latest",
51
51
  "@datagrok/helm": "latest"
52
52
  },
53
53
  "scripts": {
package/src/package.ts CHANGED
@@ -44,6 +44,7 @@ import {Monomer, IMonomerLib, MonomerWorks, MonomerLib, readLibrary,
44
44
 
45
45
  const STORAGE_NAME = 'Libraries';
46
46
  const LIB_PATH = 'System:AppData/Bio/libraries';
47
+ const LIBS_PATH = 'libraries/';
47
48
 
48
49
  let monomerLib: IMonomerLib | null = null;
49
50
  export let hydrophobPalette: SeqPaletteCustom | null = null;
@@ -90,6 +91,8 @@ export async function initBio() {
90
91
 
91
92
  async function loadLibraries() {
92
93
  let uploadedLibraries: string[] = Object.values(await grok.dapi.userDataStorage.get(STORAGE_NAME, true));
94
+ if (uploadedLibraries.length == 0 && monomerLib == null)
95
+ monomerLib = new MonomerLib({});
93
96
  for (let i = 0; i < uploadedLibraries.length; ++i)
94
97
  await monomerManager(uploadedLibraries[i]);
95
98
  }
@@ -127,7 +130,7 @@ export async function libraryPanel(seqColumn: DG.Column): Promise<DG.Widget> {
127
130
  //@ts-ignore
128
131
  let filesButton: HTMLButtonElement = ui.button('Manage', manageFiles);
129
132
  let divInputs: HTMLDivElement = ui.div();
130
- let librariesList: string[] = (await _package.files.list(`${LIB_PATH}`, false, '')).map(it => it.fileName);
133
+ let librariesList: string[] = (await _package.files.list(`${LIBS_PATH}`, false, '')).map(it => it.fileName);
131
134
  let uploadedLibraries: string[] = Object.values(await grok.dapi.userDataStorage.get(STORAGE_NAME, true));
132
135
  for (let i = 0; i < uploadedLibraries.length; ++i) {
133
136
  let libraryName: string = uploadedLibraries[i];
package/src/tests/checkInputColumn-tests.ts CHANGED
@@ -40,7 +40,7 @@ seq4`;
40
40
  const col: DG.Column = df.getCol('seq');
41
41
  col.semType = DG.SEMTYPE.MACROMOLECULE;
42
42
  col.setTag(DG.TAGS.UNITS, bio.NOTATION.HELM);
43
- col.setTag(bio.TAGS.alphabetSize, '11');
43
+ // col.setTag(bio.TAGS.alphabetSize, '11');
44
44
  col.setTag(bio.TAGS.alphabetIsMultichar, 'true');
45
45
 
46
46
  const [res, msg]: [boolean, string] = checkInputColumn(
package/src/tests/detectors-test.ts CHANGED
@@ -130,24 +130,24 @@ MWRSWY-CKHP
130
130
  }
131
131
 
132
132
  const samples: { [key: string]: string } = {
133
- 'fastaCsv': 'System:AppData/Bio/samples/sample_FASTA.csv',
134
- 'fastaFasta': 'System:AppData/Bio/data/sample_FASTA.fasta',
135
- 'fastaPtCsv': 'System:AppData/Bio/data/sample_FASTA_PT.csv',
136
- 'msaComplex': 'System:AppData/Bio/samples/sample_MSA.csv',
137
- 'helmCsv': 'System:AppData/Bio/samples/sample_HELM.csv',
138
- 'peptidesComplex': 'System:AppData/Bio/tests/peptides_complex_msa.csv',
139
- 'peptidesSimple': 'System:AppData/Bio/tests/peptides_simple_msa.csv',
140
- 'testDemogCsv': 'System:AppData/Bio/tests/testDemog.csv',
141
- 'testHelmCsv': 'System:AppData/Bio/tests/testHelm.csv',
142
- 'testIdCsv': 'System:AppData/Bio/tests/testId.csv',
143
- 'testSmilesCsv': 'System:AppData/Bio/tests/testSmiles.csv',
144
- 'testSmiles2Csv': 'System:AppData/Bio/tests/testSmiles2.csv',
145
- 'testActivityCliffsCsv': 'System:AppData/Bio/tests/testActivityCliffs.csv', // smiles
146
- 'testCerealCsv': 'System:AppData/Bio/tests/testCereal.csv',
147
- 'testSpgi100': 'System:AppData/Bio/tests/testSpgi100.csv',
148
- 'testUnichemSources': 'System:AppData/Bio/tests/testUnichemSources.csv',
149
- 'testDmvOffices': 'System:AppData/Bio/tests/testDmvOffices.csv',
150
- 'testAlertCollection': 'System:AppData/Bio/tests/testAlertCollection.csv',
133
+ [Samples.fastaFasta]: 'System:AppData/Bio/data/sample_FASTA.fasta',
134
+ [Samples.fastaPtCsv]: 'System:AppData/Bio/data/sample_FASTA_PT.csv',
135
+ [Samples.msaComplex]: 'System:AppData/Bio/samples/sample_MSA.csv',
136
+ [Samples.fastaCsv]: 'System:AppData/Bio/samples/sample_FASTA.csv',
137
+ [Samples.helmCsv]: 'System:AppData/Bio/samples/sample_HELM.csv',
138
+ [Samples.peptidesComplex]: 'System:AppData/Bio/tests/peptides_complex_msa.csv',
139
+ [Samples.peptidesSimple]: 'System:AppData/Bio/tests/peptides_simple_msa.csv',
140
+ [Samples.testDemogCsv]: 'System:AppData/Bio/tests/testDemog.csv',
141
+ [Samples.testHelmCsv]: 'System:AppData/Bio/tests/testHelm.csv',
142
+ [Samples.testIdCsv]: 'System:AppData/Bio/tests/testId.csv',
143
+ [Samples.testSmilesCsv]: 'System:AppData/Bio/tests/testSmiles.csv',
144
+ [Samples.testSmiles2Csv]: 'System:AppData/Bio/tests/testSmiles2.csv',
145
+ [Samples.testActivityCliffsCsv]: 'System:AppData/Bio/tests/testActivityCliffs.csv', // smiles
146
+ [Samples.testCerealCsv]: 'System:AppData/Bio/tests/testCereal.csv',
147
+ [Samples.testSpgi100]: 'System:AppData/Bio/tests/testSpgi100.csv',
148
+ [Samples.testUnichemSources]: 'System:AppData/Bio/tests/testUnichemSources.csv',
149
+ [Samples.testDmvOffices]: 'System:AppData/Bio/tests/testDmvOffices.csv',
150
+ [Samples.testAlertCollection]: 'System:AppData/Bio/tests/testAlertCollection.csv',
151
151
  };
152
152
 
153
153
  const _samplesDfs: { [key: string]: Promise<DG.DataFrame> } = {};
package/src/tests/lib-tests.ts ADDED
@@ -0,0 +1,30 @@
1
+ /* Do not change these import lines to match external modules in webpack configuration */
2
+ import * as grok from 'datagrok-api/grok';
3
+ import * as ui from 'datagrok-api/ui';
4
+ import * as DG from 'datagrok-api/dg';
5
+
6
+ import {category, expectArray, test} from '@datagrok-libraries/utils/src/test';
7
+ import {FastaFileHandler} from '@datagrok-libraries/bio/src/utils/fasta-handler';
8
+ import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
9
+
10
+ category('monomer lib', () => {
11
+ // test('monomerManager', async() => {
12
+ // const df: DG.DataFrame = DG.DataFrame.fromCsv(await _package.files.readAsText('tests/test.csv'));
13
+ // grok.shell.addTableView(df);
14
+ // await grok.functions.call('Helm:monomerManager', {value: 'HELMCoreLibrary.json'});
15
+ // const checkName = '2-Chloroadenine';
16
+ // let flag = false;
17
+ // const types = Object.keys(org.helm.webeditor.monomerTypeList());
18
+ // const monomers: any = [];
19
+ // for (var i = 0; i < types.length; i++) {
20
+ // //@ts-ignore
21
+ // monomers.push(new scil.helm.Monomers.getMonomerSet(types[i]));
22
+ // Object.keys(monomers[i]).forEach(k => {
23
+ // if (monomers[i][k].n == checkName){
24
+ // flag = true;
25
+ // }
26
+ // });
27
+ // }
28
+ // expect(flag, true);
29
+ // });
30
+ });
package/src/tests/renderers-test.ts CHANGED
@@ -8,15 +8,20 @@ import {importFasta, multipleSequenceAlignmentAny} from '../package';
8
8
  import {convertDo} from '../utils/convert';
9
9
  import {SEM_TYPES, TAGS} from '../utils/constants';
10
10
  import {generateLongSequence, generateManySequences, performanceTest} from './test-sequnces-generators';
11
+ import {errorToConsole} from '@datagrok-libraries/utils/src/to-console';
11
12
 
12
13
  category('renderers', () => {
13
14
  let tvList: DG.TableView[];
14
15
  let dfList: DG.DataFrame[];
15
16
 
16
17
  before(async () => {
17
- await grok.functions.call('Bio:initBio');
18
18
  tvList = [];
19
19
  dfList = [];
20
+ await grok.functions.call('Bio:initBio')
21
+ .catch((err) => {
22
+ console.error(errorToConsole(err));
23
+ throw err;
24
+ });
20
25
  });
21
26
 
22
27
  after(async () => {
package/src/tests/splitters-test.ts CHANGED
@@ -6,6 +6,7 @@ import * as bio from '@datagrok-libraries/bio';
6
6
  import {after, before, category, test, expect, expectArray, expectObject} from '@datagrok-libraries/utils/src/test';
7
7
  import * as C from '../utils/constants';
8
8
  import {splitToMonomers, _package, getHelmMonomers} from '../package';
9
+ import {errorToConsole} from '@datagrok-libraries/utils/src/to-console';
9
10
 
10
11
 
11
12
  category('splitters', () => {
@@ -13,9 +14,13 @@ category('splitters', () => {
13
14
  let dfList: DG.DataFrame[];
14
15
 
15
16
  before(async () => {
16
- await grok.functions.call('Bio:initBio');
17
17
  tvList = [];
18
18
  dfList = [];
19
+ await grok.functions.call('Bio:initBio')
20
+ .catch((err) => {
21
+ console.error(errorToConsole(err));
22
+ throw err;
23
+ });
19
24
  });
20
25
 
21
26
  after(async () => {
package/{test-Bio-3afbd4014fa1-8c5a0df5.html → test-Bio-62cc009524f3-db2d0836.html} RENAMED
@@ -1,4 +1,4 @@
1
- <html><head><meta charset="utf-8"/><title>Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=3afbd4014fa1. Commit 8c5a0df5.</title><style type="text/css">html,
1
+ <html><head><meta charset="utf-8"/><title>Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=62cc009524f3. Commit db2d0836.</title><style type="text/css">html,
2
2
  body {
3
3
  font-family: Arial, Helvetica, sans-serif;
4
4
  font-size: 1rem;
@@ -229,17 +229,10 @@ header {
229
229
  font-size: 1rem;
230
230
  padding: 0 0.5rem;
231
231
  }
232
- </style></head><body><div id="jesthtml-content"><header><h1 id="title">Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=3afbd4014fa1. Commit 8c5a0df5.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-11-08 13:09:19</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">28.64s</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">19.009s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: Test result : Failed : 180 : Bio.splitters.splitToMonomers : TypeError: Cannot read properties of undefined (reading 'push')
233
- Test result : Failed : 0 : Bio.splitters.init : TypeError: Cannot read properties of undefined (reading 'forEach')
234
- Test result : Failed : 0 : Bio.splitters.init : TypeError: Cannot read properties of null (reading 'getMonomerMolsByType')
235
- Test result : Failed : 311 : Bio.renderers.rendererMacromoleculeFasta : TypeError: Cannot read properties of undefined (reading 'push')
236
- Test result : Failed : 184 : Bio.renderers.rendererMacromoleculeSeparator : TypeError: Cannot read properties of undefined (reading 'push')
237
- Test result : Failed : 54 : Bio.renderers.rendererMacromoleculeDifference : TypeError: Cannot read properties of undefined (reading 'push')
238
- Test result : Failed : 311 : Bio.renderers.afterMsa : TypeError: Cannot read properties of undefined (reading 'push')
239
- Test result : Failed : 186 : Bio.renderers.afterConvert : TypeError: Cannot read properties of undefined (reading 'push')
240
- Test result : Failed : 58 : Bio.renderers.selectRendererBySemType : TypeError: Cannot read properties of undefined (reading 'push')
241
- Test result : Failed : 0 : Bio.renderers.init : TypeError: Cannot read properties of undefined (reading 'forEach')
242
- Test result : Failed : 0 : Bio.renderers.init : TypeError: Cannot read properties of null (reading 'getMonomerMolsByType')
232
+ </style></head><body><div id="jesthtml-content"><header><h1 id="title">Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=62cc009524f3. Commit db2d0836.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-11-14 13:45:35</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">32.136s</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">21.674s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: Test result : Failed : 122 : Bio.detectors.samplesTestAlertCollectionNegativeSmarts : Error: Negative test detected semType='Macromolecule', units='separator'.
233
+ Test result : Failed : 0 : Bio.splitters.init : TypeError: Cannot convert undefined or null to object
234
+ Test result : Failed : 0 : Bio.renderers.init : TypeError: Cannot convert undefined or null to object
235
+ Test result : Failed : 1449 : Bio.substructureFilters.helm : Error: Expected "2", got "0"
243
236
 
244
237
  at /home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:70:20
245
238
  at Generator.next (&lt;anonymous&gt;)
@@ -259,108 +252,114 @@ Test result : Failed : 0 : Bio.renderers.init : TypeError: Cannot read propertie
259
252
  at Generator.next (&lt;anonymous&gt;)
260
253
  at fulfilled (/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:31:58)
261
254
  at runMicrotasks (&lt;anonymous&gt;)
262
- at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Test result : Success : 0 : Bio.Palettes.testPaletteN : OK
263
- Test result : Success : 1 : Bio.Palettes.testPaletteAA : OK
264
- Test result : Success : 0 : Bio.Palettes.testPalettePtMe : OK
265
- Test result : Success : 83 : Bio.detectors.NegativeEmpty : OK
266
- Test result : Success : 15 : Bio.detectors.Negative1 : OK
267
- Test result : Success : 27 : Bio.detectors.Negative2 : OK
268
- Test result : Success : 18 : Bio.detectors.Negative3 : OK
269
- Test result : Success : 372 : Bio.detectors.NegativeSmiles : OK
270
- Test result : Success : 27 : Bio.detectors.Dna1 : OK
271
- Test result : Success : 16 : Bio.detectors.Rna1 : OK
272
- Test result : Success : 8 : Bio.detectors.AA1 : OK
273
- Test result : Success : 16 : Bio.detectors.MsaDna1 : OK
274
- Test result : Success : 13 : Bio.detectors.MsaAA1 : OK
275
- Test result : Success : 28 : Bio.detectors.SepDna : OK
276
- Test result : Success : 24 : Bio.detectors.SepRna : OK
277
- Test result : Success : 26 : Bio.detectors.SepPt : OK
278
- Test result : Success : 9 : Bio.detectors.SepUn1 : OK
279
- Test result : Success : 7 : Bio.detectors.SepUn2 : OK
255
+ at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Test result : Success : 1 : Bio.Palettes.testPaletteN : OK
256
+ Test result : Success : 0 : Bio.Palettes.testPaletteAA : OK
257
+ Test result : Success : 1 : Bio.Palettes.testPalettePtMe : OK
258
+ Test result : Success : 116 : Bio.detectors.NegativeEmpty : OK
259
+ Test result : Success : 36 : Bio.detectors.Negative1 : OK
260
+ Test result : Success : 76 : Bio.detectors.Negative2 : OK
261
+ Test result : Success : 15 : Bio.detectors.Negative3 : OK
262
+ Test result : Success : 490 : Bio.detectors.NegativeSmiles : OK
263
+ Test result : Success : 31 : Bio.detectors.Dna1 : OK
264
+ Test result : Success : 18 : Bio.detectors.Rna1 : OK
265
+ Test result : Success : 19 : Bio.detectors.AA1 : OK
266
+ Test result : Success : 39 : Bio.detectors.MsaDna1 : OK
267
+ Test result : Success : 9 : Bio.detectors.MsaAA1 : OK
268
+ Test result : Success : 29 : Bio.detectors.SepDna : OK
269
+ Test result : Success : 12 : Bio.detectors.SepRna : OK
270
+ Test result : Success : 21 : Bio.detectors.SepPt : OK
271
+ Test result : Success : 27 : Bio.detectors.SepUn1 : OK
272
+ Test result : Success : 22 : Bio.detectors.SepUn2 : OK
280
273
  Test result : Success : 19 : Bio.detectors.SepMsaN1 : OK
281
- Test result : Success : 425 : Bio.detectors.SamplesFastaCsvPt : OK
282
- Test result : Success : 4 : Bio.detectors.SamplesFastaCsvNegativeEntry : OK
283
- Test result : Success : 16 : Bio.detectors.SamplesFastaCsvNegativeLength : OK
284
- Test result : Success : 78 : Bio.detectors.SamplesFastaCsvNegativeUniProtKB : OK
285
- Test result : Success : 195 : Bio.detectors.SamplesFastaFastaPt : OK
286
- Test result : Success : 636 : Bio.detectors.samplesPeptidesComplexNegativeID : OK
287
- Test result : Success : 7 : Bio.detectors.SamplesPeptidesComplexNegativeMeasured : OK
288
- Test result : Success : 94 : Bio.detectors.SamplesPeptidesComplexNegativeValue : OK
289
- Test result : Success : 189 : Bio.detectors.samplesMsaComplexUn : OK
290
- Test result : Success : 39 : Bio.detectors.samplesMsaComplexNegativeActivity : OK
291
- Test result : Success : 128 : Bio.detectors.samplesIdCsvNegativeID : OK
292
- Test result : Success : 142 : Bio.detectors.samplesSarSmallCsvNegativeSmiles : OK
293
- Test result : Success : 140 : Bio.detectors.samplesHelmCsvHELM : OK
274
+ Test result : Success : 503 : Bio.detectors.SamplesFastaCsvPt : OK
275
+ Test result : Success : 9 : Bio.detectors.SamplesFastaCsvNegativeEntry : OK
276
+ Test result : Success : 5 : Bio.detectors.SamplesFastaCsvNegativeLength : OK
277
+ Test result : Success : 96 : Bio.detectors.SamplesFastaCsvNegativeUniProtKB : OK
278
+ Test result : Success : 161 : Bio.detectors.SamplesFastaFastaPt : OK
279
+ Test result : Success : 1043 : Bio.detectors.samplesPeptidesComplexNegativeID : OK
280
+ Test result : Success : 27 : Bio.detectors.SamplesPeptidesComplexNegativeMeasured : OK
281
+ Test result : Success : 15 : Bio.detectors.SamplesPeptidesComplexNegativeValue : OK
282
+ Test result : Success : 282 : Bio.detectors.samplesMsaComplexUn : OK
283
+ Test result : Success : 13 : Bio.detectors.samplesMsaComplexNegativeActivity : OK
284
+ Test result : Success : 160 : Bio.detectors.samplesIdCsvNegativeID : OK
285
+ Test result : Success : 134 : Bio.detectors.samplesSarSmallCsvNegativeSmiles : OK
286
+ Test result : Success : 142 : Bio.detectors.samplesHelmCsvHELM : OK
294
287
  Test result : Success : 5 : Bio.detectors.samplesHelmCsvNegativeActivity : OK
295
- Test result : Success : 85 : Bio.detectors.samplesTestHelmNegativeID : OK
296
- Test result : Success : 4 : Bio.detectors.samplesTestHelmNegativeTestType : OK
297
- Test result : Success : 4 : Bio.detectors.samplesTestHelmPositiveHelmString : OK
298
- Test result : Success : 3 : Bio.detectors.samplesTestHelmNegativeValid : OK
299
- Test result : Success : 4 : Bio.detectors.samplesTestHelmNegativeMolWeight : OK
300
- Test result : Success : 4 : Bio.detectors.samplesTestHelmNegativeMolFormula : OK
301
- Test result : Success : 4 : Bio.detectors.samplesTestHelmNegativeSmiles : OK
302
- Test result : Success : 459 : Bio.detectors.samplesTestDemogNegativeAll : OK
303
- Test result : Success : 214 : Bio.detectors.samplesTestSmiles2NegativeSmiles : OK
304
- Test result : Success : 122 : Bio.detectors.samplesTestActivityCliffsNegativeSmiles : OK
305
- Test result : Success : 90 : Bio.detectors.samplesFastaPtPosSequence : OK
306
- Test result : Success : 102 : Bio.detectors.samplesTestCerealNegativeCerealName : OK
307
- Test result : Success : 136 : Bio.detectors.samplesTestSpgi100NegativeStereoCategory : OK
308
- Test result : Success : 5 : Bio.detectors.samplesTestSpgi100NegativeScaffoldNames : OK
309
- Test result : Success : 7 : Bio.detectors.samplesTestSpgi100NegativePrimaryScaffoldName : OK
310
- Test result : Success : 4 : Bio.detectors.samplesTestSpgi100NegativeSampleName : OK
311
- Test result : Success : 128 : Bio.detectors.samplesTestUnichemSourcesNegativeSrcUrl : OK
312
- Test result : Success : 3 : Bio.detectors.samplesTestUnichemSourcesNegativeBaseIdUrl : OK
313
- Test result : Success : 106 : Bio.detectors.samplesTestDmvOfficesNegativeOfficeName : OK
314
- Test result : Success : 5 : Bio.detectors.samplesTestDmvOfficesNegativeCity : OK
315
- Test result : Success : 116 : Bio.detectors.samplesTestAlertCollectionNegativeSmarts : OK
316
- Test result : Success : 1104 : Bio.MSA.isCorrect : OK
317
- Test result : Success : 134 : Bio.MSA.isCorrectLong : OK
318
- Test result : Success : 920 : Bio.sequenceSpace.sequenceSpaceOpens : OK
319
- Test result : Success : 498 : Bio.sequenceSpace.sequenceSpaceWithEmptyRows : OK
320
- Test result : Success : 730 : Bio.activityCliffs.activityCliffsOpens : OK
321
- Test result : Success : 793 : Bio.activityCliffs.activityCliffsWithEmptyRows : OK
288
+ Test result : Success : 96 : Bio.detectors.samplesTestHelmNegativeID : OK
289
+ Test result : Success : 11 : Bio.detectors.samplesTestHelmNegativeTestType : OK
290
+ Test result : Success : 5 : Bio.detectors.samplesTestHelmPositiveHelmString : OK
291
+ Test result : Success : 4 : Bio.detectors.samplesTestHelmNegativeValid : OK
292
+ Test result : Success : 6 : Bio.detectors.samplesTestHelmNegativeMolWeight : OK
293
+ Test result : Success : 6 : Bio.detectors.samplesTestHelmNegativeMolFormula : OK
294
+ Test result : Success : 15 : Bio.detectors.samplesTestHelmNegativeSmiles : OK
295
+ Test result : Success : 384 : Bio.detectors.samplesTestDemogNegativeAll : OK
296
+ Test result : Success : 208 : Bio.detectors.samplesTestSmiles2NegativeSmiles : OK
297
+ Test result : Success : 123 : Bio.detectors.samplesTestActivityCliffsNegativeSmiles : OK
298
+ Test result : Success : 103 : Bio.detectors.samplesFastaPtPosSequence : OK
299
+ Test result : Success : 114 : Bio.detectors.samplesTestCerealNegativeCerealName : OK
300
+ Test result : Success : 160 : Bio.detectors.samplesTestSpgi100NegativeStereoCategory : OK
301
+ Test result : Success : 6 : Bio.detectors.samplesTestSpgi100NegativeScaffoldNames : OK
302
+ Test result : Success : 5 : Bio.detectors.samplesTestSpgi100NegativePrimaryScaffoldName : OK
303
+ Test result : Success : 5 : Bio.detectors.samplesTestSpgi100NegativeSampleName : OK
304
+ Test result : Success : 130 : Bio.detectors.samplesTestUnichemSourcesNegativeSrcUrl : OK
305
+ Test result : Success : 4 : Bio.detectors.samplesTestUnichemSourcesNegativeBaseIdUrl : OK
306
+ Test result : Success : 123 : Bio.detectors.samplesTestDmvOfficesNegativeOfficeName : OK
307
+ Test result : Success : 11 : Bio.detectors.samplesTestDmvOfficesNegativeCity : OK
308
+ Test result : Success : 941 : Bio.MSA.isCorrect : OK
309
+ Test result : Success : 141 : Bio.MSA.isCorrectLong : OK
310
+ Test result : Success : 1146 : Bio.sequenceSpace.sequenceSpaceOpens : OK
311
+ Test result : Success : 538 : Bio.sequenceSpace.sequenceSpaceWithEmptyRows : OK
312
+ Test result : Success : 841 : Bio.activityCliffs.activityCliffsOpens : OK
313
+ Test result : Success : 849 : Bio.activityCliffs.activityCliffsWithEmptyRows : OK
322
314
  Test result : Success : 1 : Bio.splitters.fastaMulti : OK
323
315
  Test result : Success : 1 : Bio.splitters.helm1 : OK
324
316
  Test result : Success : 0 : Bio.splitters.helm2 : OK
325
317
  Test result : Success : 0 : Bio.splitters.helm3-multichar : OK
326
318
  Test result : Success : 0 : Bio.splitters.testHelm1 : OK
327
319
  Test result : Success : 1 : Bio.splitters.testHelm2 : OK
328
- Test result : Success : 1 : Bio.splitters.testHelm3 : OK
329
- Test result : Success : 1 : Bio.splitters.getHelmMonomers : OK
330
- Test result : Success : 70 : Bio.renderers.long sequence performance : OK
331
- Test result : Success : 615 : Bio.renderers.many sequence performance : OK
320
+ Test result : Success : 0 : Bio.splitters.testHelm3 : OK
321
+ Test result : Success : 314 : Bio.splitters.splitToMonomers : OK
322
+ Test result : Success : 2 : Bio.splitters.getHelmMonomers : OK
323
+ Test result : Success : 68 : Bio.renderers.long sequence performance : OK
324
+ Test result : Success : 774 : Bio.renderers.many sequence performance : OK
325
+ Test result : Success : 311 : Bio.renderers.rendererMacromoleculeFasta : OK
326
+ Test result : Success : 187 : Bio.renderers.rendererMacromoleculeSeparator : OK
327
+ Test result : Success : 62 : Bio.renderers.rendererMacromoleculeDifference : OK
328
+ Test result : Success : 351 : Bio.renderers.afterMsa : OK
329
+ Test result : Success : 236 : Bio.renderers.afterConvert : OK
330
+ Test result : Success : 176 : Bio.renderers.selectRendererBySemType : OK
332
331
  Test result : Success : 0 : Bio.renderers.setRendererManually : GROK-11212
333
332
  Test result : Success : 4 : Bio.converters.testFastaPtToSeparator : OK
334
333
  Test result : Success : 3 : Bio.converters.testFastaDnaToSeparator : OK
335
- Test result : Success : 2 : Bio.converters.testFastaRnaToSeparator : OK
334
+ Test result : Success : 3 : Bio.converters.testFastaRnaToSeparator : OK
336
335
  Test result : Success : 3 : Bio.converters.testFastaGapsToSeparator : OK
337
336
  Test result : Success : 2 : Bio.converters.testFastaPtToHelm : OK
338
- Test result : Success : 1 : Bio.converters.testFastaDnaToHelm : OK
339
- Test result : Success : 2 : Bio.converters.testFastaRnaToHelm : OK
340
- Test result : Success : 1 : Bio.converters.testFastaGapsToHelm : OK
341
- Test result : Success : 1 : Bio.converters.testSeparatorPtToFasta : OK
342
- Test result : Success : 0 : Bio.converters.testSeparatorDnaToFasta : OK
343
- Test result : Success : 1 : Bio.converters.testSeparatorRnaToFasta : OK
337
+ Test result : Success : 2 : Bio.converters.testFastaDnaToHelm : OK
338
+ Test result : Success : 1 : Bio.converters.testFastaRnaToHelm : OK
339
+ Test result : Success : 7 : Bio.converters.testFastaGapsToHelm : OK
340
+ Test result : Success : 0 : Bio.converters.testSeparatorPtToFasta : OK
341
+ Test result : Success : 1 : Bio.converters.testSeparatorDnaToFasta : OK
342
+ Test result : Success : 0 : Bio.converters.testSeparatorRnaToFasta : OK
344
343
  Test result : Success : 0 : Bio.converters.testSeparatorGapsToFasta : OK
345
344
  Test result : Success : 0 : Bio.converters.testSeparatorPtToHelm : OK
346
345
  Test result : Success : 0 : Bio.converters.testSeparatorDnaToHelm : OK
347
346
  Test result : Success : 0 : Bio.converters.testSeparatorRnaToHelm : OK
348
- Test result : Success : 1 : Bio.converters.testSeparatorGapsToHelm : OK
349
- Test result : Success : 0 : Bio.converters.testHelmDnaToFasta : OK
347
+ Test result : Success : 0 : Bio.converters.testSeparatorGapsToHelm : OK
348
+ Test result : Success : 1 : Bio.converters.testHelmDnaToFasta : OK
350
349
  Test result : Success : 0 : Bio.converters.testHelmRnaToFasta : OK
351
- Test result : Success : 0 : Bio.converters.testHelmPtToFasta : OK
350
+ Test result : Success : 1 : Bio.converters.testHelmPtToFasta : OK
352
351
  Test result : Success : 0 : Bio.converters.testHelmDnaToSeparator : OK
353
352
  Test result : Success : 0 : Bio.converters.testHelmRnaToSeparator : OK
354
- Test result : Success : 1 : Bio.converters.testHelmPtToSeparator : OK
355
- Test result : Success : 1 : Bio.converters.testHelmLoneRibose : OK
356
- Test result : Success : 2 : Bio.converters.testHelmLoneDeoxyribose : OK
357
- Test result : Success : 1 : Bio.converters.testHelmLonePhosphorus : OK
358
- Test result : Success : 1 : Bio.fastaFileHandler.testNormalFormatting : OK
353
+ Test result : Success : 0 : Bio.converters.testHelmPtToSeparator : OK
354
+ Test result : Success : 2 : Bio.converters.testHelmLoneRibose : OK
355
+ Test result : Success : 1 : Bio.converters.testHelmLoneDeoxyribose : OK
356
+ Test result : Success : 2 : Bio.converters.testHelmLonePhosphorus : OK
357
+ Test result : Success : 0 : Bio.fastaFileHandler.testNormalFormatting : OK
359
358
  Test result : Success : 0 : Bio.fastaFileHandler.testExtraSpaces : OK
360
359
  Test result : Success : 0 : Bio.fastaFileHandler.testExtraNewlines : OK
361
360
  Test result : Success : 0 : Bio.fastaExport.wrapSequenceSingle : OK
362
361
  Test result : Success : 0 : Bio.fastaExport.wrapSequenceMulti : OK
363
- Test result : Success : 1 : Bio.fastaExport.saveAsFastaTest1 : OK
362
+ Test result : Success : 2 : Bio.fastaExport.saveAsFastaTest1 : OK
364
363
  Test result : Success : 1 : Bio.fastaExport.saveAsFastaTest2 : OK
365
364
  Test result : Success : 1 : Bio.bio.testGetStatsHelm1 : OK
366
365
  Test result : Success : 1 : Bio.bio.testGetStatsN1 : OK
@@ -371,19 +370,18 @@ Test result : Success : 1 : Bio.bio.testPickupPaletteAA1 : OK
371
370
  Test result : Success : 1 : Bio.bio.testPickupPaletteX : OK
372
371
  Test result : Success : 0 : Bio.WebLogo.monomerToShort.longMonomerSingle : OK
373
372
  Test result : Success : 0 : Bio.WebLogo.monomerToShort.longMonomerShort : OK
374
- Test result : Success : 1 : Bio.WebLogo.monomerToShort.longMonomerLong56 : OK
375
- Test result : Success : 0 : Bio.WebLogo.monomerToShort.longMonomerComplexFirstPartShort : OK
373
+ Test result : Success : 0 : Bio.WebLogo.monomerToShort.longMonomerLong56 : OK
374
+ Test result : Success : 1 : Bio.WebLogo.monomerToShort.longMonomerComplexFirstPartShort : OK
376
375
  Test result : Success : 0 : Bio.WebLogo.monomerToShort.longMonomerComplexFirstPartLong56 : OK
377
- Test result : Success : 92 : Bio.WebLogo-positions.allPositions : OK
378
- Test result : Success : 73 : Bio.WebLogo-positions.positions with shrinkEmptyTail option true (filterd) : OK
379
- Test result : Success : 77 : Bio.WebLogo-positions.positions with skipEmptyPositions option : OK
376
+ Test result : Success : 83 : Bio.WebLogo-positions.allPositions : OK
377
+ Test result : Success : 83 : Bio.WebLogo-positions.positions with shrinkEmptyTail option true (filterd) : OK
378
+ Test result : Success : 76 : Bio.WebLogo-positions.positions with skipEmptyPositions option : OK
380
379
  Test result : Success : 3 : Bio.checkInputColumn.testMsaPos : OK
381
380
  Test result : Success : 1 : Bio.checkInputColumn.testMsaNegHelm : OK
382
381
  Test result : Success : 1 : Bio.checkInputColumn.testMsaNegUN : OK
383
382
  Test result : Success : 0 : Bio.checkInputColumn.testGetActionFunctionMeta : OK
384
- Test result : Success : 360 : Bio.similarity/diversity.similaritySearchViewer : OK
385
- Test result : Success : 214 : Bio.similarity/diversity.diversitySearchViewer : OK
386
- Test result : Success : 190 : Bio.substructureFilters.fasta : OK
387
- Test result : Success : 394 : Bio.substructureFilters.separator : OK
388
- Test result : Success : 1950 : Bio.substructureFilters.helm : OK
383
+ Test result : Success : 365 : Bio.similarity/diversity.similaritySearchViewer : OK
384
+ Test result : Success : 218 : Bio.similarity/diversity.diversitySearchViewer : OK
385
+ Test result : Success : 207 : Bio.substructureFilters.fasta : OK
386
+ Test result : Success : 396 : Bio.substructureFilters.separator : OK
389
387
  </pre></div></div></div></div></body></html>