@datagrok/bio 2.25.9 → 2.25.10

package/src/tests/sequence-space-utils.ts

@@ -1,7 +1,7 @@
 import * as DG from 'datagrok-api/dg';
 import * as grok from 'datagrok-api/grok';
 
-import {expect} from '@datagrok-libraries/utils/src/test';
+import {expect} from '@datagrok-libraries/test/src/test';
 import {MmDistanceFunctionsNames} from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
 import {BYPASS_LARGE_DATA_WARNING} from '@datagrok-libraries/ml/src/functionEditors/consts';
 import {DimReductionMethods} from '@datagrok-libraries/ml/src/multi-column-dimensionality-reduction/types';

package/src/tests/similarity-diversity-tests.ts

@@ -1,7 +1,7 @@
 import * as DG from 'datagrok-api/dg';
 import * as grok from 'datagrok-api/grok';
 
-import {category, test, expect, awaitCheck, delay} from '@datagrok-libraries/utils/src/test';
+import {category, test, expect, awaitCheck, delay} from '@datagrok-libraries/test/src/test';
 import {SequenceSimilarityViewer} from '../analysis/sequence-similarity-viewer';
 import {SequenceDiversityViewer} from '../analysis/sequence-diversity-viewer';
 

package/src/tests/splitters-test.ts

@@ -4,7 +4,7 @@ import * as DG from 'datagrok-api/dg';
 
 import wu from 'wu';
 
-import {after, before, category, test, expect, expectArray} from '@datagrok-libraries/utils/src/test';
+import {after, before, category, test, expect, expectArray} from '@datagrok-libraries/test/src/test';
 import {TAGS as bioTAGS, splitterAsFasta} from '@datagrok-libraries/bio/src/utils/macromolecule';
 import {splitterAsHelm} from '@datagrok-libraries/bio/src/utils/macromolecule/utils';
 import {ISeqSplitted} from '@datagrok-libraries/bio/src/utils/macromolecule/types';

package/src/tests/substructure-filters-tests.ts

@@ -7,7 +7,7 @@ import * as DG from 'datagrok-api/dg';
 import $ from 'cash-dom';
 import wu from 'wu';
 
-import {after, before, category, test, expect, delay, testEvent, awaitCheck} from '@datagrok-libraries/utils/src/test';
+import {after, before, category, test, expect, delay, testEvent, awaitCheck} from '@datagrok-libraries/test/src/test';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {
   getUserLibSettings, setUserLibSettings

package/src/tests/to-atomic-level-tests.ts

@@ -5,7 +5,7 @@ import * as DG from 'datagrok-api/dg';
 
 import wu from 'wu';
 
-import {before, after, category, test, expectArray, expect} from '@datagrok-libraries/utils/src/test';
+import {before, after, category, test, expectArray, expect} from '@datagrok-libraries/test/src/test';
 import {RDModule} from '@datagrok-libraries/chem-meta/src/rdkit-api';
 import {_toAtomicLevel} from '@datagrok-libraries/bio/src/monomer-works/to-atomic-level';
 import {IMonomerLib} from '@datagrok-libraries/bio/src/types/monomer-library';

package/src/tests/to-atomic-level-ui-tests.ts

@@ -1,7 +1,7 @@
 import * as DG from 'datagrok-api/dg';
 import * as grok from 'datagrok-api/grok';
 
-import {after, before, category, expect, expectArray, test} from '@datagrok-libraries/utils/src/test';
+import {after, before, category, expect, expectArray, test} from '@datagrok-libraries/test/src/test';
 import {IMonomerLib} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {sequenceToMolfile} from '../utils/sequence-to-mol';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/types/monomer-library';

package/src/tests/utils/detectors-utils.ts

@@ -2,7 +2,7 @@ import * as DG from 'datagrok-api/dg';
 import * as grok from 'datagrok-api/grok';
 
 import {ALIGNMENT, NOTATION, TAGS as bioTAGS} from '@datagrok-libraries/bio/src/utils/macromolecule';
-import {expect} from '@datagrok-libraries/utils/src/test';
+import {expect} from '@datagrok-libraries/test/src/test';
 import {ISeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
 
 export type DetectorTestData = { [testName: string]: { csv: string, neg?: string[], pos?: { [colName: string]: PosCol } } };

package/src/tests/utils/sequences-generators.ts

@@ -3,7 +3,7 @@ import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
 import {ALIGNMENT, ALPHABET, NOTATION, TAGS as bioTAGS} from '@datagrok-libraries/bio/src/utils/macromolecule';
-import {expect} from '@datagrok-libraries/utils/src/test';
+import {expect} from '@datagrok-libraries/test/src/test';
 
 import {awaitGrid} from '../utils';
 

package/src/tests/utils.ts

@@ -1,7 +1,7 @@
 import * as DG from 'datagrok-api/dg';
 import * as grok from 'datagrok-api/grok';
 
-import {delay, expect, testEvent} from '@datagrok-libraries/utils/src/test';
+import {delay, expect, testEvent} from '@datagrok-libraries/test/src/test';
 import {asRenderer, IRenderer, isRenderer} from '@datagrok-libraries/bio/src/types/renderer';
 
 import {_package} from '../package-test';

package/src/tests/viewers.ts

@@ -2,7 +2,7 @@ import * as DG from 'datagrok-api/dg';
 import * as grok from 'datagrok-api/grok';
 //import * as ui from 'datagrok-api/ui';
 
-import {category, test, testViewer} from '@datagrok-libraries/utils/src/test';
+import {category, test, testViewer} from '@datagrok-libraries/test/src/test';
 import {readDataframe} from './utils';
 
 

package/src/utils/detect-macromolecule-probe.ts

@@ -4,7 +4,7 @@ import * as DG from 'datagrok-api/dg';
 
 
 import {_package} from '../package';
-import {delay} from '@datagrok-libraries/utils/src/test';
+import {delay} from '@datagrok-libraries/test/src/test';
 
 type IDetectorReport = { categoriesSample: any[], rejectReason: string };
 

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

@@ -4,7 +4,7 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {delay} from '@datagrok-libraries/utils/src/test';
+import {delay} from '@datagrok-libraries/test/src/test';
 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 {
@@ -103,7 +103,7 @@ export class MonomerLibManager implements IMonomerLibHelper {
   private _monomerLibProviders: IMonomerLibProvider[] | null = null;
   public async getProviders(): Promise<IMonomerLibProvider[]> {
     if (this._monomerLibProviders == null) {
-      const providerFuncs = DG.Func.find({tags: ['monomer-lib-provider']});
+      const providerFuncs = DG.Func.find({meta: {role: 'monomer-lib-provider'}});
       this._monomerLibProviders = await Promise.all(providerFuncs.map(async (func) => {
         return (await func.apply({})) as IMonomerLibProvider;
       }));

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

@@ -64,7 +64,7 @@ export class MonomerLibBase implements IMonomerLibBase {
   }
 
   getMonomerSymbolsByType(polymerType: PolymerType): string[] {
-    const res = Object.keys(this._monomers[polymerType]);
+    const res = Object.keys(this._monomers[polymerType] ?? {});
     if (this._smilesMonomerCache[polymerType])
       res.push(...Object.keys(this._smilesMonomerCache[polymerType]));
     return res;
@@ -130,7 +130,7 @@ export class MonomerLibBase implements IMonomerLibBase {
   }
 
   getMonomer(polymerType: PolymerType | null, argMonomerSymbol: string): Monomer | null {
-    const logPrefix = `Bio: MonomerLib.getMonomer()`;
+    // const logPrefix = `Bio: MonomerLib.getMonomer()`;
     // Adjust RNA's 'R' for ribose to 'r' and 'P' for phosphate to 'p' for case-sensitive monomer names.
     // There are uppercase 'R' and 'P' at RNA samples in test data 'helm2.csv' but lowercase in HELMCoreLibrary.json
     let monomerSymbol = argMonomerSymbol;
@@ -142,7 +142,7 @@ export class MonomerLibBase implements IMonomerLibBase {
     let res: Monomer | null = null;
 
     if (!polymerType) {
-      _package.logger.warning(`${logPrefix} symbol '${argMonomerSymbol}', polymerType not specified.`);
+      // _package.logger.warning(`${logPrefix} symbol '${argMonomerSymbol}', polymerType not specified.`);
       // Assume any polymer type
       for (const [_polymerType, dict] of Object.entries(this._monomers)) {
         res = dict[monomerSymbol];
@@ -154,6 +154,8 @@ export class MonomerLibBase implements IMonomerLibBase {
         monomerSymbol = this._smilesMonomerCache[polymerType][monomerSymbol];
       const dict = this._monomers[polymerType];
       res = dict?.[monomerSymbol] ?? null;
+      if (!res)
+        return this.getMonomer(null, monomerSymbol); // fallback to search without polymer type
     }
     return res;
   }
@@ -252,6 +254,8 @@ export class MonomerLibBase implements IMonomerLibBase {
             .replace(/_/g, ' ')
             .replace(/-/g, ' ')
             .replace(/([a-z])([a-z])([A-Z])/g, '$1$2 $3');
+          if (monomer.polymerType)
+            res.append(ui.divText(monomer.polymerType, {style: {fontStyle: 'italic'}}));
           res.append(ui.divText(source));
         }
       }

package/src/utils/multiple-sequence-alignment-ui.ts

@@ -6,7 +6,7 @@ import * as DG from 'datagrok-api/dg';
 import * as ui from 'datagrok-api/ui';
 
 import {ColumnInputOptions} from '@datagrok-libraries/utils/src/type-declarations';
-import {delay} from '@datagrok-libraries/utils/src/test';
+import {delay} from '@datagrok-libraries/test/src/test';
 import {ALPHABET, NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
 import {ISeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
 

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

@@ -149,8 +149,7 @@ export class SeqHandler implements ISeqHandler {
 
     const stats = getStats(categoriesSample, 3, (s) => s.split(this.separator!));
     let invalidateRequired = false;
-
-    const refinerList = DG.Func.find({tags: ['notationRefiner']});
+    const refinerList = DG.Func.find({meta: {role: 'notationRefiner'}});
 
     for (const refineFuncFind of refinerList) {
       try {
@@ -773,14 +772,25 @@ export class SeqHandler implements ISeqHandler {
   public convert(tgtNotation: NOTATION, tgtSeparator?: string): DG.Column<string> {
     // Get joiner from the source column units handler (this) knowing about the source sequence.
     // For example, converting DNA Helm to fasta requires removing the r(X)p decoration.
-    const joiner: JoinerFunc = this.getJoiner({notation: tgtNotation, separator: tgtSeparator});
-    const newColumn = this.getNewColumn(tgtNotation, tgtSeparator);
-    // assign the values to the newly created empty column
-    newColumn.init((rowIdx: number) => {
-      const srcSS = this.getSplitted(rowIdx);
-      return joiner(srcSS);
-    });
-    return newColumn;
+    if (!this.isCustom() || tgtNotation !== NOTATION.HELM) {
+      const joiner: JoinerFunc = this.getJoiner({notation: tgtNotation, separator: tgtSeparator});
+      const newColumn = this.getNewColumn(tgtNotation, tgtSeparator);
+      // assign the values to the newly created empty column
+      newColumn.init((rowIdx: number) => {
+        const srcSS = this.getSplitted(rowIdx);
+        return joiner(srcSS);
+      });
+      return newColumn;
+    } else {
+      if (!this.notationProvider || !this.notationProvider.getHelm)
+        throw new Error('Notation provider with getHelm function is required for custom notation conversion.');
+      const newColumn = this.getNewColumn(tgtNotation, tgtSeparator);
+      newColumn.init((rowIdx: number) => {
+        const srcSeq = this.column.get(rowIdx);
+        return this.notationProvider!.getHelm(srcSeq, {});
+      });
+      return newColumn;
+    }
   }
 
   /**
@@ -932,6 +942,8 @@ export class SeqHandler implements ISeqHandler {
 
   private convertToHelm(src: string): string {
     if (this.notation == NOTATION.HELM) return src;
+    if (this.isCustom() && this.notationProvider?.getHelm)
+      return this.notationProvider.getHelm(src, {});
 
     const wrappers = this.getHelmWrappers();
 

package/src/utils/split-to-monomers.ts

@@ -2,7 +2,7 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {delay} from '@datagrok-libraries/utils/src/test';
+import {delay} from '@datagrok-libraries/test/src/test';
 import {checkInputColumnUI} from './check-input-column';
 import {splitAlignedSequences} from '@datagrok-libraries/bio/src/utils/splitter';
 import * as C from './constants';

package/src/viewers/vd-regions-viewer.ts

@@ -4,7 +4,7 @@ import * as DG from 'datagrok-api/dg';
 
 import {fromEvent, Observable, Subject, Unsubscribable} from 'rxjs';
 
-import {testEvent} from '@datagrok-libraries/utils/src/test';
+import {testEvent} from '@datagrok-libraries/test/src/test';
 import {
   IVdRegionsViewer,
   VdRegion, VdRegionType,

package/src/viewers/web-logo-viewer.ts

@@ -22,7 +22,7 @@ import {
 import {errorToConsole} from '@datagrok-libraries/utils/src/to-console';
 import {intToHtmlA} from '@datagrok-libraries/utils/src/color';
 import {ISeqSplitted} from '@datagrok-libraries/bio/src/utils/macromolecule/types';
-import {testEvent} from '@datagrok-libraries/utils/src/test';
+import {testEvent} from '@datagrok-libraries/test/src/test';
 import {PromiseSyncer} from '@datagrok-libraries/bio/src/utils/syncer';
 import {GAP_SYMBOL} from '@datagrok-libraries/bio/src/utils/macromolecule/consts';
 import {IMonomerLibBase} from '@datagrok-libraries/bio/src/types/monomer-library';

package/src/widgets/bio-substructure-filter-helm.ts

@@ -9,7 +9,7 @@ import {App, IHelmWebEditor} from '@datagrok-libraries/bio/src/helm/types';
 import {getHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
 import {ILogger} from '@datagrok-libraries/bio/src/utils/logger';
 import {errInfo} from '@datagrok-libraries/bio/src/utils/err-info';
-import {delay} from '@datagrok-libraries/utils/src/test';
+import {delay} from '@datagrok-libraries/test/src/test';
 import {ISeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
 
 import {updateDivInnerHTML} from '../utils/ui-utils';

package/src/widgets/bio-substructure-filter.ts

@@ -14,7 +14,7 @@ import wu from 'wu';
 import {Observable, Subject, Unsubscribable} from 'rxjs';
 
 import {TAGS as bioTAGS, NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
-import {delay, testEvent} from '@datagrok-libraries/utils/src/test';
+import {delay, testEvent} from '@datagrok-libraries/test/src/test';
 import {IRenderer} from '@datagrok-libraries/bio/src/types/renderer';
 import {ILogger} from '@datagrok-libraries/bio/src/utils/logger';
 import {PromiseSyncer} from '@datagrok-libraries/bio/src/utils/syncer';

package/src/widgets/to-atomic-level-widget.ts

@@ -18,12 +18,6 @@ export async function toAtomicLevelSingle(sequence: DG.SemanticValue): Promise<{
       errorText = 'Atomic level conversion requeires a sequence column';
       return {errorText, mol: ''};
     }
-    const supportedUnits: string[] = [NOTATION.FASTA, NOTATION.SEPARATOR, NOTATION.HELM, NOTATION.BILN];
-    //todo: add support for custom notations
-    if (!supportedUnits.includes(sequence.cell.column.meta.units?.toLowerCase() ?? '')) {
-      errorText = 'Unsupported sequence notation. please use Bio | Polytool | Convert';
-      return {errorText, mol: ''};
-    }
     const seqHelper = await PackageFunctions.getSeqHelper();
     const seqSh = seqHelper.getSeqHandler(sequence.cell.column);
     if (!seqSh) {
@@ -46,7 +40,7 @@ export async function toAtomicLevelSingle(sequence: DG.SemanticValue): Promise<{
       singleValCol.temp[SeqTemps.notationProvider] = sequence.cell.column.temp[SeqTemps.notationProvider];
     // helm and biln will have cyclization marks, so we need to use POM to convert them
     const seqSplitted = seqSh.getSplitted(sequence.cell.rowIndex);
-    const shouldUsePOM = (seqSplitted.graphInfo?.connections?.length ?? 0) > 0;
+    const shouldUsePOM = (seqSplitted.graphInfo?.connections?.length ?? 0) > 0 || seqSh.units === NOTATION.CUSTOM;
     const isHelmWithMultiplePolymerTypes = seqSh.isHelm() &&
       (new Set((seqSplitted.graphInfo?.polymerTypes ?? []))).size > 1;