@datagrok/bio 2.25.14 → 2.25.15

package/files/monomer-collections/Canonical AAs.json

@@ -0,0 +1,27 @@
+{
+  "monomerSymbols": [
+    "A",
+    "C",
+    "D",
+    "E",
+    "F",
+    "G",
+    "H",
+    "I",
+    "K",
+    "L",
+    "M",
+    "N",
+    "P",
+    "Q",
+    "R",
+    "S",
+    "T",
+    "V",
+    "W",
+    "Y"
+  ],
+  "description": "Canonical amino acids collection",
+  "updatedBy": "rizhi",
+  "updatedOn": "2026-01-01T12:00:00Z"
+}

package/package.json

@@ -5,7 +5,7 @@
     "name": "Davit Rizhinashvili",
     "email": "drizhinashvili@datagrok.ai"
   },
-  "version": "2.25.14",
+  "version": "2.25.15",
   "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": "^5.61.6",
+    "@datagrok-libraries/bio": "^5.62.0",
     "@datagrok-libraries/chem-meta": "^1.2.9",
     "@datagrok-libraries/math": "^1.2.6",
     "@datagrok-libraries/ml": "^6.10.9",

package/src/utils/monomer-lib/lib-manager.ts

@@ -5,7 +5,7 @@ import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
 import {ILogger} from '@datagrok-libraries/bio/src/utils/logger';
-import {DEFAULT_FILES_LIB_PROVIDER_NAME, findProviderWithLibraryName, IMonomerLib, IMonomerSet} from '@datagrok-libraries/bio/src/types/monomer-library';
+import {DEFAULT_FILES_LIB_PROVIDER_NAME, findProviderWithLibraryName, IMonomerLib, IMonomerSet, MonomerCollection} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {
   getUserLibSettings, setUserLibSettings,
 } from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
@@ -19,6 +19,7 @@ import {_package} from '../../package';
 import {IMonomerLibHelper, IMonomerLibProvider} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {merge, Observable, Subject} from 'rxjs';
 import {MonomerLibFromFilesProvider} from './library-file-manager/monomers-lib-provider';
+const MONOMER_COLLECTION_STORAGE_PATH = 'System:AppData/Bio/monomer-collections/';
 
 type MonomerLibWindowType = Window & { $monomerLibHelperPromise?: Promise<MonomerLibManager> };
 declare const window: MonomerLibWindowType;
@@ -409,6 +410,39 @@ export class MonomerLibManager implements IMonomerLibHelper {
     }
   }
 
+  async listMonomerCollections(): Promise<string[]> {
+    // these are provider less functions. coleections will be in files storage in txt format
+    const collections = (await grok.dapi.files.list(MONOMER_COLLECTION_STORAGE_PATH))
+      .filter((file) => file.extension === 'json' || file.name.endsWith('.json'));
+    return collections.map((file) => file.name);
+  }
+
+  async deleteMonomerCollection(collectionName: string): Promise<void> {
+    if (!collectionName.endsWith('.json'))
+      collectionName += '.json';
+    if (await grok.dapi.files.exists(MONOMER_COLLECTION_STORAGE_PATH + collectionName))
+      await grok.dapi.files.delete(MONOMER_COLLECTION_STORAGE_PATH + collectionName);
+  }
+
+  async readMonomerCollection(collectionName: string): Promise<MonomerCollection> {
+    if (!collectionName.endsWith('.json'))
+      collectionName += '.json';
+    const file = await grok.dapi.files.readAsText(MONOMER_COLLECTION_STORAGE_PATH + collectionName);
+    return JSON.parse(file) as MonomerCollection;
+  }
+
+  async addOrUpdateMonomerCollection(collectionName: string, monomerSymbols: string[], desc?: string): Promise<void> {
+    if (!collectionName.endsWith('.json'))
+      collectionName += '.json';
+    const content = JSON.stringify({
+      description: desc,
+      monomerSymbols: monomerSymbols,
+      updatedBy: DG.User.current().login,
+      updatedOn: new Date().toISOString(),
+    } satisfies MonomerCollection, null, 2);
+    await grok.dapi.files.writeAsText(MONOMER_COLLECTION_STORAGE_PATH + collectionName, content);
+  }
+
   // -- Instance singleton --
   public static async getInstance(): Promise<MonomerLibManager> {
     let res = window.$monomerLibHelperPromise;

package/src/utils/monomer-lib/monomer-manager/monomer-manager.ts

@@ -255,6 +255,58 @@ export class MonomerManager implements IMonomerManager {
     }
   }
 
+  async createNewMonomersCollectionDialog(monomerSymbols: string[]) {
+    const existingCollections = (await this.monomerLibManamger.listMonomerCollections()).map((name) => name.toLowerCase());
+    const nameInput = ui.input.string('Collection Name', {tooltipText: 'Name of the monomer collection, should be unique', placeholder: 'Enter collection name', nullable: false});
+    const descriptionInput = ui.input.string('Description', {tooltipText: 'Description of the monomer collection', placeholder: 'Enter collection description', nullable: true});
+    const d = ui.dialog('Create New Monomer Collection')
+      .add(nameInput)
+      .add(descriptionInput)
+      .addButton('Add', async () => {
+        if (!nameInput.value || !nameInput.value.trim()) {
+          grok.shell.warning('Collection name cannot be empty');
+          return;
+        }
+        const saveAction = async (symbols: string[]) => {
+          await this.monomerLibManamger.addOrUpdateMonomerCollection(nameInput.value!, symbols, descriptionInput.value ?? undefined);
+          grok.shell.info(`Collection ${nameInput.value} saved successfully`);
+        };
+        if (existingCollections.includes(nameInput.value!.toLowerCase()) || existingCollections.includes(nameInput.value!.toLowerCase() + '.json')) {
+          const confD = ui.dialog('Collection already exists')
+            .add(ui.divText(`A collection with the name ${nameInput.value} already exists. Do you want to merge or overwrite it?`));
+          confD.addButton('Merge', async () => {
+            const existingCollection = await this.monomerLibManamger.readMonomerCollection(nameInput.value!);
+            const mergedSymbols = Array.from(new Set([...(existingCollection.monomerSymbols ?? []), ...monomerSymbols]));
+            try {
+              await saveAction(mergedSymbols);
+            } catch (e) {
+              grok.shell.error('Error merging monomer collection');
+              console.error(e);
+            }
+            confD.close();
+          });
+          confD.addButton('Overwrite', async () => {
+            try {
+              await saveAction(monomerSymbols);
+            } catch (e) {
+              grok.shell.error('Error overwriting monomer collection');
+              console.error(e);
+            }
+            confD.close();
+          });
+          confD.show();
+        } else {
+          try {
+            await saveAction(monomerSymbols);
+          } catch (e) {
+            grok.shell.error('Error creating monomer collection');
+            console.error(e);
+          }
+        }
+        d.close();
+      }).show();
+  }
+
   async createNewLibDialog(monomers?: Monomer[]) {
     const monomerLibs = await this.monomerLibManamger.getAvaliableLibraryNames();
     const libNameInput = ui.input.string('Library Name', {
@@ -321,26 +373,36 @@ export class MonomerManager implements IMonomerManager {
           args.context.tableView.id !== (this.tv!.id ?? '') || !args.item || !args.item.isTableCell || (args.item.tableRowIndex ?? -1) < 0)
           return;
         const rowIdx = args.item.tableRowIndex;
-        args.menu.item('Edit Monomer', async () => {
+        const menu = args.menu as DG.Menu;
+        menu.item('Edit Monomer', async () => {
           await this.editMonomer(this.tv!.dataFrame.rows.get(rowIdx));
         });
 
-        args.menu.item('Fix all monomers', () => {
+        menu.item('Fix all monomers', () => {
           this.fixAllMonomers();
         });
         if (this.tv!.dataFrame.selection.trueCount > 0) {
-          args.menu.item('Remove Selected Monomers', async () => {
+          const group = menu.group('Selected Monomers');
+          group.item('Remove', async () => {
             const monomers = await Promise.all(Array.from(this.tv!.dataFrame.selection.getSelectedIndexes())
               .map((r) => monomerFromDfRow(this.tv!.dataFrame.rows.get(r))));
             this._newMonomerForm.removeMonomers(monomers, this.libInput.value!);
           });
-          args.menu.item('Selection To New Library', async () => {
+          group.item('Create Library', async () => {
             const monomers = await Promise.all(Array.from(this.tv!.dataFrame.selection.getSelectedIndexes())
               .map((r) => monomerFromDfRow(this.tv!.dataFrame.rows.get(r))));
             this.createNewLibDialog(monomers);
           });
+          group.item('Create Collection', async () => {
+            const monomerSymbols = Array.from(this.tv!.dataFrame.selection.getSelectedIndexes())
+              .map((r) => this.tv!.dataFrame.col(MONOMER_DF_COLUMN_NAMES.SYMBOL)!.get(r) as string)
+              .filter((s): s is string => !!s && s.trim().length > 0);
+            if (monomerSymbols.length === 0)
+              return grok.shell.warning('No valid monomer symbols found in selection');
+            this.createNewMonomersCollectionDialog(monomerSymbols);
+          });
         } else {
-          args.menu.item('Remove Monomer', async () => {
+          menu.item('Remove Monomer', async () => {
             const monomer = await monomerFromDfRow(this.tv!.dataFrame.rows.get(rowIdx));
             this._newMonomerForm.removeMonomers([monomer], this.libInput.value!);
           });