@datagrok/bio 2.25.0 → 2.25.1

package/package.json

@@ -5,7 +5,7 @@
     "name": "Davit Rizhinashvili",
     "email": "drizhinashvili@datagrok.ai"
   },
-  "version": "2.25.0",
+  "version": "2.25.1",
   "description": "Bioinformatics support (import/export of sequences, conversion, visualization, analysis). [See more](https://github.com/datagrok-ai/public/blob/master/packages/Bio/README.md) for details.",
   "repository": {
     "type": "git",
@@ -44,7 +44,7 @@
   ],
   "dependencies": {
     "@biowasm/aioli": "^3.1.0",
-    "@datagrok-libraries/bio": "^5.61.0",
+    "@datagrok-libraries/bio": "^5.61.1",
     "@datagrok-libraries/chem-meta": "^1.2.9",
     "@datagrok-libraries/math": "^1.2.6",
     "@datagrok-libraries/ml": "^6.10.6",

package/src/utils/monomer-lib/library-file-manager/ui.ts

@@ -5,7 +5,7 @@ import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
 import $ from 'cash-dom';
-import {Subject} from 'rxjs';
+import {Subject, Subscription} from 'rxjs';
 
 import {
   getUserLibSettings, setUserLibSettings
@@ -67,10 +67,12 @@ class MonomerLibraryManagerWidget {
     instance._widget = await instance.createWidget();
   }
 
+  private _fileUploadSubscription: Subscription | null = null;
   private async createWidget() {
     const content = await this.getWidgetContent();
     const monomerLibHelper = await getMonomerLibHelper();
-    // eslint-disable-next-line rxjs/no-ignored-subscription
+    this._fileUploadSubscription?.unsubscribe();
+    this._fileUploadSubscription =
     monomerLibHelper.fileUploadRequested.subscribe(
       () => this.promptToAddLibraryFiles()
     );
@@ -92,14 +94,29 @@ class MonomerLibraryManagerWidget {
       accept: '.json',
       open: async (selectedFile) => {
         const doAdd = async (provider: IMonomerLibProvider) => {
-          const content = await selectedFile.text();
           const name = selectedFile.name;
+          const existingLibs = await provider.listLibraries();
+          // chech if library already exists
+          if (existingLibs.includes(name)) {
+            const confirm = await new Promise<boolean>((resolve) => {
+              ui.dialog('Confirm Library Update')
+                .add(ui.divText(`Library '${name}' already exists. Do you want to overwrite it?`))
+                .onOK(() => resolve(true))
+                .onCancel(() => resolve(false))
+                .show();
+            });
+            if (!confirm)
+              return;
+          }
+
+          const content = await selectedFile.text();
           const progressIndicator = DG.TaskBarProgressIndicator.create(`Adding ${name} as a monomer library`);
           try {
             await provider.addOrUpdateLibraryString(name, content);
           // this.eventManager.updateLibrarySelectionStatus(name, true);
           } catch (e) {
             grok.shell.error(`File ${name} is not a valid monomer library, verify it is aligned to HELM JSON schema.`);
+            console.error(e);
           } finally {
             progressIndicator.close();
           }
@@ -122,7 +139,7 @@ class MonomerLibraryManagerWidget {
           .onOK(async () => {
             const provider = providers.find((p) => p.name === providersInput.value)!; // should not be null
             await doAdd(provider);
-          });
+          }).show();
       },
     });
   }

package/src/utils/seq-helper/seq-handler.ts

@@ -1049,21 +1049,30 @@ function joinToHelm(srcSS: ISeqSplitted, wrappers: string[], isDnaOrRna: boolean
 }
 
 function joinToBiln(srcSS: ISeqSplitted): string {
+  const needsSquareBrackets = (cm: string | null) => {
+    return cm && (cm.includes('-') || cm.includes('*') || cm.includes('[R'));
+  };
+
   if (!srcSS.graphInfo || !((srcSS.graphInfo.connections?.length ?? 0) > 0)) {
     const resOMList: string[] = new Array<string>(srcSS.length);
     for (let posIdx: number = 0; posIdx < srcSS.length; ++posIdx) {
-      resOMList[posIdx] = srcSS.getCanonical(posIdx);
-      if (resOMList[posIdx]?.includes('-')) // Biln uses '-' as a separator, need to enclose in []
-        resOMList[posIdx] = `[${resOMList[posIdx]}]`;
+      const canonical = srcSS.getCanonical(posIdx);
+      if (needsSquareBrackets(canonical)) // Biln uses '-' as a separator, need to enclose in []. also there might be smiles in there, where Rs are represented as '*' or R
+        resOMList[posIdx] = `[${canonical}]`;
+      else
+        resOMList[posIdx] = canonical;
     }
     return resOMList.join('-'); // Biln uses '-' as a separator
   } else { // conversion happens only if there is a graph info
     const disjointSequenceIdxs = srcSS.graphInfo.disjointSeqStarts;
     const allSeqParts = new Array<string>(srcSS.length);
     for (let posIdx = 0; posIdx < srcSS.length; ++posIdx) {
-      allSeqParts[posIdx] = srcSS.getCanonical(posIdx);
-      if (allSeqParts[posIdx]?.includes('-')) // Biln uses '-' as a separator, need to enclose in []
-        allSeqParts[posIdx] = `[${allSeqParts[posIdx]}]`;
+      const canonical = srcSS.getCanonical(posIdx);
+      // allSeqParts[posIdx] = srcSS.getCanonical(posIdx);
+      if (needsSquareBrackets(canonical)) // Biln uses '-' as a separator, need to enclose in []
+        allSeqParts[posIdx] = `[${canonical}]`;
+      else
+        allSeqParts[posIdx] = canonical;
     }
     for (let i = 0; i < srcSS.graphInfo.connections.length; i++) {
       const conn: ISeqConnection = srcSS.graphInfo.connections[i];