@datagrok/bio 1.7.3 → 1.7.6

package/src/utils/convert.ts

@@ -1,7 +1,14 @@
 import * as DG from 'datagrok-api/dg';
 import * as ui from 'datagrok-api/ui';
+import * as grok from 'datagrok-api/grok';
+
+import {Subscription} from 'rxjs';
 import {NotationConverter, NOTATION} from '@datagrok-libraries/bio/src/utils/notation-converter';
 
+
+let convertDialog: DG.Dialog | null = null;
+let convertDialogSubs: Subscription[] = [];
+
 /**
  * Converts notations of a Macromolecule column
  *
@@ -22,19 +29,37 @@ export function convert(col: DG.Column): void {
 
   const separatorInput = ui.choiceInput('Choose separator', separatorArray[0], separatorArray);
 
-  ui.dialog('Convert sequence notation')
-    .add(ui.div([
-      ui.h1('Current notation: ' + current),
-      targetNotationInput.root,
-      // TODO: conditional separator input
-      separatorInput.root
-    ]))
-    .onOK(() => {
-      //TODO: create new converted column
-      const targetNotation = targetNotationInput.value as NOTATION;
-      const separator = separatorInput.value!;
-      const newColumn = converter.convert(targetNotation, separator);
-      col.dataFrame.columns.add(newColumn);
-    })
-    .show();
+  if (convertDialog == null) {
+    convertDialog = ui.dialog('Convert sequence notation')
+      .add(ui.div([
+        ui.h1('Current notation: ' + current),
+        targetNotationInput.root,
+        // TODO: conditional separator input
+        separatorInput.root
+      ]))
+      .onOK(async () => {
+        const targetNotation = targetNotationInput.value as NOTATION;
+        const separator: string | null = separatorInput.value;
+
+        await convertDo(col, targetNotation, separator);
+      })
+      .show();
+
+    convertDialogSubs.push(convertDialog.onClose.subscribe((value) => {
+      convertDialogSubs.forEach((s) => { s.unsubscribe(); });
+      convertDialogSubs = [];
+      convertDialog = null;
+    }));
+  }
+}
+
+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);
+  await grok.data.detectSemanticTypes(srcCol.dataFrame);
+  return newColumn;
 }
+

package/src/utils/utils.ts

@@ -1,6 +1,7 @@
 import * as DG from 'datagrok-api/dg';
 import {WebLogo, SplitterFunc} from '@datagrok-libraries/bio/src/viewers/web-logo';
 import * as grok from 'datagrok-api/grok';
+import { CAP_GROUP_NAME, CAP_GROUP_SMILES, jsonSdfMonomerLibDict, MONOMER_SYMBOL, RGROUP_ALTER_ID, RGROUP_FIELD, RGROUP_LABEL, SDF_MONOMER_NAME } from '../const';
 
 export const HELM_CORE_LIB_FILENAME = '/samples/HELMCoreLibrary.json';
 export const HELM_CORE_LIB_MONOMER_SYMBOL = 'symbol';
@@ -43,3 +44,37 @@ export function createMomomersMolDict(lib: any[]): { [key: string]: string | any
   });
   return dict;
 }
+
+
+export function createJsonMonomerLibFromSdf(table: DG.DataFrame): any {
+  const resultLib = [];
+  for (let i = 0; i < table.rowCount; i++) {
+    const monomer: { [key: string]: string | any } = {};
+    Object.keys(jsonSdfMonomerLibDict).forEach(key => {
+      if (key === MONOMER_SYMBOL) {
+        const monomerSymbol = table.get(jsonSdfMonomerLibDict[key], i);
+        monomer[key] = monomerSymbol === '.' ? table.get(SDF_MONOMER_NAME, i) : monomerSymbol;
+      } else if (key === RGROUP_FIELD) {
+        const rgroups = table.get(jsonSdfMonomerLibDict[key], i).split('\n');
+        const jsonRgroups: any[] = [];
+        rgroups.forEach((g: string) => {
+          const rgroup: { [key: string]: string | any } = {};
+          const altAtom = g.substring(g.lastIndexOf("]") + 1);
+          let radicalNum = g.match(/\[R(\d+)\]/)![1];
+          rgroup[CAP_GROUP_SMILES] = altAtom === 'H' ? `[*:${radicalNum}][H]` : `O[*:${radicalNum}]`;
+          rgroup[RGROUP_ALTER_ID] = altAtom === 'H' ? `R${radicalNum}-H` : `R${radicalNum}-OH`;
+          rgroup[CAP_GROUP_NAME] = altAtom === 'H' ? `H` : `OH`;
+          rgroup[RGROUP_LABEL] = `R${radicalNum}`;
+          jsonRgroups.push(rgroup);
+        })
+        monomer[key] = jsonRgroups;
+      } else {
+        if((jsonSdfMonomerLibDict as { [key: string]: string | any })[key]) {
+          monomer[key] = table.get((jsonSdfMonomerLibDict as { [key: string]: string | any })[key], i);
+        }
+      }
+    })
+    resultLib.push(monomer);
+  }
+  return resultLib;
+}

package/{test-Bio-34f75e5127b8-303cfb72.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 303cfb72.</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 303cfb72.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-07-13 14:53:02</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">110.084s</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">100.002s</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>