@datagrok/bio 1.7.13 → 1.7.16

package/package.json

@@ -2,7 +2,7 @@
   "name": "@datagrok/bio",
   "beta": false,
   "friendlyName": "Bio",
-  "version": "1.7.13",
+  "version": "1.7.16",
   "description": "Bio is a [package](https://datagrok.ai/help/develop/develop#packages) for the [Datagrok](https://datagrok.ai) platform",
   "repository": {
     "type": "git",
@@ -15,7 +15,7 @@
     "@datagrok-libraries/ml": "^3.0.0",
     "@datagrok-libraries/utils": "^1.4.0",
     "cash-dom": "latest",
-    "datagrok-api": "^1.5.1",
+    "datagrok-api": "^1.5.0",
     "dayjs": "^1.11.4",
     "openchemlib": "6.0.1",
     "rxjs": "^6.5.5",
@@ -40,16 +40,16 @@
     "link-bio": "npm link @datagrok-libraries/bio",
     "link-ml": "npm link @datagrok-libraries/ml",
     "link-all": "npm link datagrok-api @datagrok-libraries/utils @datagrok-libraries/bio @datagrok-libraries/ml",
-    "debug-sequences1": "grok publish --rebuild",
-    "release-sequences1": "grok publish --rebuild --release",
+    "debug-sequences1": "grok publish",
+    "release-sequences1": "grok publish --release",
     "build-sequences1": "webpack",
     "debug-local": "grok publish local",
     "release-local": "grok publish local --release",
     "build": "webpack",
-    "debug-sequences1-public": "grok publish public --rebuild",
-    "release-sequences1-public": "grok publish public --rebuild --release",
-    "debug-sequences1-local": "grok publish local --rebuild",
-    "release-sequences1-local": "grok publish local --rebuild --release",
+    "debug-sequences1-public": "grok publish public",
+    "release-sequences1-public": "grok publish public --release",
+    "debug-sequences1-local": "grok publish local",
+    "release-sequences1-local": "grok publish local --release",
     "lint": "eslint \"./src/**/*.ts\"",
     "lint-fix": "eslint \"./src/**/*.ts\" --fix",
     "test": "jest",

package/setup-unlink-clean.cmd

@@ -0,0 +1,15 @@
+set package_dir=%cd%
+
+set dirs=^
+\..\..\js-api\ ^
+\..\..\libraries\utils\ ^
+\..\..\libraries\ml\ ^
+\..\..\libraries\bio\ ^
+\
+
+call npm uninstall -g datagrok-api @datagrok-libraries/utils @datagrok-libraries/ml @datagrok-libraries/bio
+
+for %%p in (%dirs%) do cd %package_dir%\%%p & rmdir /s /q node_modules
+for %%p in (%dirs%) do cd %package_dir%\%%p & rmdir /s /q dist
+
+rem for %%p in (%dirs%) do cd %package_dir%\%%p & del "package-lock.json"

package/setup.cmd

@@ -1,19 +1,15 @@
-cd ../../js-api
-call npm install
-call npm link
-cd ../libraries/utils
-call npm install
-call npm link
-call npm link datagrok-api
-cd ../libraries/ml
-call npm install
-call npm link
-call npm link @datagrok-libraries/utils
-cd ../libraries/bio
-call npm install
-call npm link
-call npm link @datagrok-libraries/utils
-cd ../../packages/Bio
-call npm install
-call npm link datagrok-api @datagrok-libraries/bio @datagrok-libraries/utils @datagrok-libraries/ml
-webpack
+call setup-unlink-clean.cmd
+
+set package_dir=%cd%
+
+set dirs=^
+\..\..\js-api\ ^
+\..\..\libraries\utils\ ^
+\..\..\libraries\ml\ ^
+\..\..\libraries\bio\ ^
+\
+
+for %%p in (%dirs%) do cd %package_dir%\%%p & call npm install
+for %%p in (%dirs%) do cd %package_dir%\%%p & call npm link
+for %%p in (%dirs%) do cd %package_dir%\%%p & call npm run link-all
+for %%p in (%dirs%) do cd %package_dir%\%%p & call npm run build

package/src/package.ts

@@ -22,6 +22,7 @@ import {MacromoleculeSequenceCellRenderer} from './utils/cell-renderer';
 import {convert} from './utils/convert';
 import {lru} from './utils/cell-renderer';
 import {representationsWidget} from './widgets/representations';
+import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
 
 //tags: init
 export async function initBio(): Promise<void> {
@@ -241,25 +242,52 @@ export async function compositionAnalysis(): Promise<void> {
   const tv = grok.shell.tv;
   const df = tv.dataFrame;
 
-  const col: DG.Column | null = WebLogo.pickUpSeqCol2(df);
-  if (!col) {
+  const colList: DG.Column[] = df.columns.toList().filter((col) => {
+    if (col.semType != DG.SEMTYPE.MACROMOLECULE)
+      return false;
+
+    const colUH = new UnitsHandler(col);
+    // TODO: prevent for cyclic, branched or multiple chains in Helm
+    return true;
+  });
+
+  const handler = async (col: DG.Column) => {
+    if (!checkInputColumn(col, 'Composition'))
+      return;
+
+    const wlViewer = tv.addViewer('WebLogo', {sequenceColumnName: col.name});
+    grok.shell.tv.dockManager.dock(wlViewer, DG.DOCK_TYPE.DOWN, null, 'Composition analysis', 0.25);
+  };
+
+  let col: DG.Column | null = null;
+  if (colList.length == 0) {
     grok.shell.error('Current table does not contain sequences');
     return;
+  } else if (colList.length > 1) {
+    const colListNames: string [] = colList.map((col) => col.name);
+    const colInput: DG.InputBase = ui.choiceInput('Column', colListNames[0], colListNames);
+    ui.dialog({
+      title: 'R-Groups Analysis',
+      helpUrl: '/help/domains/bio/macromolecules.md#composition-analysis'
+    })
+      .add(ui.div([
+        colInput,
+      ]))
+      .onOK(async () => {
+        const col: DG.Column | null = colList.find((col) => col.name == colInput.value) ?? null;
+
+        if (col)
+          await handler(col);
+      })
+      .show();
+  } else {
+    col = colList[0];
   }
 
-  if (!checkInputColumn(col, 'Composition'))
+  if (!col)
     return;
 
-  const allowedNotations: string[] = ['fasta', 'separator'];
-  const units = col.getTag(DG.TAGS.UNITS);
-  if (!allowedNotations.some((n) => units.toUpperCase().startsWith(n.toUpperCase()))) {
-    grok.shell.warning('Composition analysis is allowed for ' +
-      `notation${allowedNotations.length > 1 ? 's' : ''} ${allowedNotations.map((n) => `"${n}"`).join(', ')}.`);
-    return;
-  }
-
-  const wlViewer = tv.addViewer('WebLogo', {sequenceColumnName: col.name});
-  grok.shell.tv.dockManager.dock(wlViewer, DG.DOCK_TYPE.DOWN, null, 'Composition analysis', 0.25);
+  await handler(col);
 }
 
 //top-menu: Bio | Sdf to Json lib...
@@ -287,7 +315,7 @@ function parseMacromolecule(
 export async function peptideMolecule(macroMolecule: DG.Cell): Promise<DG.Widget> {
   const monomersLibFile = await _package.files.readAsText(HELM_CORE_LIB_FILENAME);
   const monomersLibObject: any[] = JSON.parse(monomersLibFile);
-  
+
   return representationsWidget(macroMolecule, monomersLibObject);
 }
 

package/src/tests/detectors-test.ts

@@ -14,6 +14,13 @@ category('detectors', () => {
 2
 3`;
 
+  const csvDfEmpty: string = `id,col1
+1,
+2,
+3,
+4,
+5,`;
+
   const csvDf2: string = `col1
 4
 5
@@ -179,6 +186,7 @@ MWRSWY-CKHP
     };
   };
 
+  test('NegativeEmpty', async () => {await _testNeg(readCsv('csvDfEmpty', csvDfEmpty), 'col1'); });
   test('Negative1', async () => { await _testNeg(readCsv('csvDf1', csvDf1), 'col1'); });
   test('Negative2', async () => { await _testNeg(readCsv('csvDf2', csvDf2), 'col1'); });
   test('Negative3', async () => { await _testNeg(readCsv('csvDf3', csvDf3), 'col1'); });

package/{test-Bio-34f75e5127b8-781e9df9.html → test-Bio-4f0c8bae6479-dda97945.html}

@@ -1,4 +1,4 @@
-<html><head><meta charset="utf-8"/><title>Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=34f75e5127b8. Commit 781e9df9.</title><style type="text/css">html,
+<html><head><meta charset="utf-8"/><title>Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=4f0c8bae6479. Commit dda97945.</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 781e9df9.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-07-27 13:06:16</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">213.765s</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">199.116s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: Test result : Bio.MSA.is_correct : TypeError: Cannot read properties of undefined (reading 'split')
+</style></head><body><div id="jesthtml-content"><header><h1 id="title">Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=4f0c8bae6479. Commit dda97945.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-07-28 11:23:15</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">220.921s</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">200.288s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: Test result : Bio.MSA.is_correct : TypeError: Cannot read properties of undefined (reading 'split')
 Test result : Bio.activityCliffs.activityCliffsOpen : Error: Expected "105 cliffs", got "2362 cliffs"
 
     at /home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:67:20
@@ -263,6 +263,7 @@ Test result : Bio.WebLogo.monomerToText.longMonomerComplexFirstPartShort : OK
 Test result : Bio.WebLogo.monomerToText.longMonomerComplexFirstPartLong56 : OK
 Test result : Bio.Palettes.testPaletteN : OK
 Test result : Bio.Palettes.testPaletteAA : OK
+Test result : Bio.detectors.NegativeEmpty : OK
 Test result : Bio.detectors.Negative1 : OK
 Test result : Bio.detectors.Negative2 : OK
 Test result : Bio.detectors.Negative3 : OK