@datagrok/bio 1.7.2 → 1.7.5

package/src/utils/convert.ts

@@ -1,6 +1,13 @@
 import * as DG from 'datagrok-api/dg';
 import * as ui from 'datagrok-api/ui';
-import {NotationConverter, NOTATION} from './notation-converter';
+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 +29,35 @@ 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-ac96da52.html → test-Bio-34f75e5127b8-0507068d.html}

@@ -1,4 +1,4 @@
-<html><head><meta charset="utf-8"/><title>Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=34f75e5127b8. Commit ac96da52.</title><style type="text/css">html,
+<html><head><meta charset="utf-8"/><title>Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=34f75e5127b8. Commit 0507068d.</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 ac96da52.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-07-13 09:24:48</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">110.354s</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.
+</style></head><body><div id="jesthtml-content"><header><h1 id="title">Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=34f75e5127b8. Commit 0507068d.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-07-14 14:09:37</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">110.386s</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 Runtime._execModule (/home/runner/work/public/public/packages/Bio/node_modules/jest-runtime/build/index.js:1646:24)

package/src/tests/splitter-test.ts

@@ -1,22 +0,0 @@
-import {after, before, category, test, expect, expectObject} from '@datagrok-libraries/utils/src/test';
-
-import * as grok from 'datagrok-api/grok';
-import * as ui from 'datagrok-api/ui';
-import * as DG from 'datagrok-api/dg';
-import {WebLogo, SplitterFunc} from '@datagrok-libraries/bio/src/viewers/web-logo';
-
-category('splitter', () => {
-  const helm1 = 'PEPTIDE1{meI.hHis.Aca.N.T.dE.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.dV.E.N.D-Orn.D-aThr.Phe_4Me}$$$';
-  const helm2 = 'PEPTIDE1{meI.hHis.Hcy.Q.T.W.Q.Phe_4NH2.D-Tyr_Et.Tyr_ab-dehydroMe.dV.E.N.N.meK}$$$';
-
-  test('helm1', async () => { await _testHelmSplitter(helm1); });
-  test('helm2', async () => { await _testHelmSplitter(helm2); });
-});
-
-export async function _testHelmSplitter(txt: string) {
-  // const splitter: SplitterFunc = WebLogo.getSplitterAsHelm();
-  //
-  // const mList: string[] = splitter(txt);
-  // expect(mList.length, 12);
-}
-

package/src/utils/notation-converter.ts

@@ -1,280 +0,0 @@
-import * as DG from 'datagrok-api/dg';
-import {WebLogo} from '@datagrok-libraries/bio/src/viewers/web-logo';
-
-/** enum type to simplify setting "user-friendly" notation if necessary */
-export const enum NOTATION {
-  FASTA = 'FASTA',
-  SEPARATOR = 'SEPARATOR',
-  HELM = 'HELM'
-}
-
-/** Class for handling conversion of notation systems in Macromolecule columns */
-export class NotationConverter {
-  private _sourceColumn: DG.Column; // the column to be converted
-  private _sourceUnits: string; // units, of the form fasta:SEQ:NT, etc.
-  private _sourceNotation: NOTATION; // current notation (without :SEQ:NT, etc.)
-  private _defaultGapSymbol: string;
-  private _defaultGapSymbolsDict = {
-    helm: '*',
-    separator: '',
-    fasta: '-',
-  };
-
-  private get sourceUnits(): string { return this._sourceUnits; }
-
-  private get sourceColumn(): DG.Column { return this._sourceColumn; }
-
-  public get sourceNotation(): NOTATION { return this._sourceNotation; }
-
-  public get defaultGapSymbol(): string { return this._defaultGapSymbol; }
-
-  public get separator(): string {
-    const separator = this.sourceColumn.getTag('separator');
-    if (separator !== null)
-      return separator;
-    else
-      throw new Error('Separator not set');
-  }
-
-  public isFasta(): boolean { return this.sourceNotation === NOTATION.FASTA; }
-
-  public isSeparator(): boolean { return this.sourceNotation === NOTATION.SEPARATOR; }
-
-  public isHelm(): boolean { return this.sourceNotation === NOTATION.HELM; }
-
-  public toFasta(targetNotation: NOTATION): boolean { return targetNotation === NOTATION.FASTA; }
-
-  public toSeparator(targetNotation: NOTATION): boolean { return targetNotation === NOTATION.SEPARATOR; }
-
-  public toHelm(targetNotation: NOTATION): boolean { return targetNotation === NOTATION.HELM; }
-
-  public isRna(): boolean { return this.sourceUnits.toLowerCase().endsWith('rna'); }
-
-  public isDna(): boolean { return this.sourceUnits.toLowerCase().endsWith('dna'); }
-
-  public isPeptide(): boolean { return this.sourceUnits.toLowerCase().endsWith('pt'); }
-
-  /** Associate notation types with the corresponding units */
-  /**
-   * @return {NOTATION}     Notation associated with the units type
-   */
-  private getSourceNotation(): NOTATION {
-    if (this.sourceUnits.toLowerCase().startsWith('fasta'))
-      return NOTATION.FASTA;
-    else if (this.sourceUnits.toLowerCase().startsWith('separator'))
-      return NOTATION.SEPARATOR;
-    else if (this.sourceUnits.toLowerCase().startsWith('helm'))
-      return NOTATION.HELM;
-    else
-      throw new Error('The column has units that do not correspond to any notation');
-  }
-
-  /**
-   * Create a new empty column of the specified notation type and the same
-   * length as sourceColumn
-   *
-   * @param {NOTATION} targetNotation
-   * @return {DG.Column}
-   */
-  private getNewColumn(targetNotation: NOTATION): DG.Column {
-    const col = this.sourceColumn;
-    const len = col.length;
-    const name = targetNotation + '(' + col.name + ')';
-    const newColName = col.dataFrame.columns.getUnusedName(name);
-    // dummy code
-    const newColumn = DG.Column.fromList('string', newColName, new Array(len).fill(''));
-    newColumn.semType = DG.SEMTYPE.MACROMOLECULE;
-    newColumn.setTag(
-      DG.TAGS.UNITS,
-      this.sourceUnits.replace(
-        this.sourceNotation.toLowerCase().toString(),
-        targetNotation.toLowerCase().toString()
-      )
-    );
-    // TODO: specify cell renderers for all cases
-    if (this.toFasta(targetNotation)) {
-      newColumn.setTag(
-        DG.TAGS.CELL_RENDERER,
-        // TODO: replace by the enumeration value
-        'Macromolecule');
-    }
-    return newColumn;
-  }
-
-  /**
-   * Convert a Macromolecule column from FASTA to SEPARATOR notation
-   *
-   * @param {string} separator  A specific separator to be used
-   * @param {string} gapSymbol  Gap symbol in FASTA, '-' by default
-   * @return {DG.Column}        A new column in SEPARATOR notation
-   */
-  private convertFastaToSeparator(separator: string, gapSymbol: string = '-'): DG.Column {
-    // a function splitting FASTA sequence into an array of monomers:
-    const splitterAsFasta = WebLogo.splitterAsFasta;
-
-    const newColumn = this.getNewColumn(NOTATION.SEPARATOR);
-    // assign the values to the newly created empty column
-    newColumn.init((idx: number) => {
-      const fastaPolymer = this.sourceColumn.get(idx);
-      const fastaMonomersArray = splitterAsFasta(fastaPolymer);
-      for (let i = 0; i < fastaMonomersArray.length; i++) {
-        if (fastaMonomersArray[i] === gapSymbol)
-          fastaMonomersArray[i] = '';
-      }
-      return fastaMonomersArray.join(separator);
-    });
-    return newColumn;
-  }
-
-  private convertToHelm(sourceGapSymbol: string | null = null) {
-    if (sourceGapSymbol === null)
-      sourceGapSymbol = this.defaultGapSymbol;
-    // A function splitting a sequence into an array of monomers according to
-    // its notation
-    const splitter = WebLogo.getSplitterForColumn(this.sourceColumn);
-
-    const prefix = (this.isDna()) ? 'DNA1{' :
-      (this.isRna()) ? 'RNA1{' :
-        (this.isPeptide()) ? 'PEPTIDE1{' :
-          'Unknown'; // this case should be handled as exceptional
-
-    if (prefix === 'Unknown')
-      throw new Error('Neither peptide, nor nucleotide');
-
-    const postfix = '}$$$';
-    const leftWrapper = (this.isDna()) ? 'D(' :
-      (this.isRna()) ? 'R(' : ''; // no wrapper for peptides
-    const rightWrapper = (this.isDna() || this.isRna()) ? ')P' : ''; // no wrapper for peptides
-
-    const newColumn = this.getNewColumn(NOTATION.HELM);
-    // assign the values to the empty column
-    newColumn.init((idx: number) => {
-      const sourcePolymer = this.sourceColumn.get(idx);
-      const sourceMonomersArray = splitter(sourcePolymer);
-      const helmArray = [prefix];
-      let firstIteration = true;
-      for (let i = 0; i < sourceMonomersArray.length; i++) {
-        const dot = firstIteration ? '' : '.';
-        let token = sourceMonomersArray[i];
-        if (token === sourceGapSymbol)
-          token = this._defaultGapSymbolsDict.helm;
-        const item = [dot, leftWrapper, token, rightWrapper];
-        helmArray.push(item.join(''));
-        firstIteration = false;
-      }
-      helmArray.push(postfix);
-      return helmArray.join('');
-    });
-    return newColumn;
-  }
-
-  private handleSeparatorItemForFasta(
-    idx: number,
-    separatorItemsArray: string[],
-    separator: string,
-    gapSymbol: string,
-    fastaMonomersArray: string[]
-  ): void {
-    const item = separatorItemsArray[idx];
-    if (item.length > 1) {
-      // the case of a multi-character monomer
-      const monomer = '[' + item + ']';
-      fastaMonomersArray.push(monomer);
-    }
-    if (item === separator) {
-      if (idx !== 0 && separatorItemsArray[idx - 1] === separator)
-        fastaMonomersArray.push(gapSymbol);
-    }
-  }
-
-  private convertSeparatorToFasta(
-    separator: string | null = null,
-    gapSymbol: string = '-'
-  ): DG.Column {
-    // TODO: implementation
-    // * similarly to fasta2separator, divide string into monomers
-    // * adjacent separators is a gap (symbol to be specified)
-    // * the monomers MUST be single-character onles, otherwise forbid
-    // * NO, they can be multi-characters
-    // conversion
-    // * consider automatic determining the separator
-
-    if (separator === null)
-      separator = this.separator;
-
-    // a function splitting FASTA sequence into an array of monomers
-    //const splitterAsSeparator = WebLogo.getSplitterWithSeparator(separator);
-    const splitter = WebLogo.getSplitterForColumn(this.sourceColumn);
-
-    const newColumn = this.getNewColumn(NOTATION.FASTA);
-    // assign the values to the empty column
-    newColumn.init((idx: number) => {
-      const separatorPolymer = this.sourceColumn.get(idx);
-      // items can be monomers or separators
-      const separatorItemsArray = splitter(separatorPolymer);
-      const fastaMonomersArray: string[] = [];
-      for (let i = 0; i < separatorItemsArray.length; i++) {
-        const item = separatorItemsArray[i];
-        if (item.length === 0) {
-          fastaMonomersArray.push(gapSymbol);
-        } else if (item.length > 1) {
-          // the case of a multi-character monomer
-          const monomer = '[' + item + ']';
-          fastaMonomersArray.push(monomer);
-        } else {
-          fastaMonomersArray.push(item);
-        }
-      }
-      return fastaMonomersArray.join('');
-    });
-    return newColumn;
-  }
-
-  private convertHelmToFasta(): DG.Column {
-    // TODO: implementation
-    return this.getNewColumn(NOTATION.FASTA);
-  }
-
-  private convertHelmToSeparator(): DG.Column {
-    // TODO: implementatioreturn this.getNewColumn();
-    return this.getNewColumn(NOTATION.SEPARATOR);
-  }
-
-  /** Dispatcher method for notation conversion
-   *
-   * @param {NOTATION} targetNotation   Notation we want to convert to
-   * @param {string | null} tgtSeparator   Possible separator
-   * @return {DG.Column}                Converted column
-   */
-  public convert(targetNotation: NOTATION, tgtSeparator: string | null = null): DG.Column {
-    // possible exceptions
-    if (this.sourceNotation === targetNotation)
-      throw new Error('Target notation is invalid');
-    if (this.toSeparator(targetNotation) && tgtSeparator === null)
-      throw new Error('Target separator is not specified');
-
-    if (this.isFasta() && this.toSeparator(targetNotation) && tgtSeparator !== null)
-      return this.convertFastaToSeparator(tgtSeparator);
-    else if ((this.isFasta() || this.isSeparator()) && this.toHelm(targetNotation))
-      return this.convertToHelm();
-    else if (this.isSeparator() && this.toFasta(targetNotation))
-      return this.convertSeparatorToFasta(tgtSeparator!);
-    else if (this.isHelm() && this.toFasta(targetNotation))
-      return this.convertHelmToFasta();
-    else
-      return this.convertHelmToSeparator();
-  }
-
-  public constructor(col: DG.Column) {
-    this._sourceColumn = col;
-    const units = this._sourceColumn.tags[DG.TAGS.UNITS];
-    if (units !== null)
-      this._sourceUnits = units;
-    else
-      throw new Error('Units are not specified in column');
-    this._sourceNotation = this.getSourceNotation();
-    this._defaultGapSymbol = (this.isFasta()) ? this._defaultGapSymbolsDict.fasta :
-      (this.isHelm()) ? this._defaultGapSymbolsDict.helm :
-        this._defaultGapSymbolsDict.separator;
-  }
-}