@datagrok/peptides 1.0.1 → 1.0.2

package/src/package-test.ts

@@ -3,7 +3,6 @@ import {runTests, tests} from '@datagrok-libraries/utils/src/test';
 
 import './tests/core';
 import './tests/peptide-space-test';
-import './tests/msa-tests';
 
 export const _package = new DG.Package();
 export {tests};

package/src/package.ts

@@ -5,21 +5,13 @@ import * as DG from 'datagrok-api/dg';
 
 import * as C from './utils/constants';
 
-import {
-  AlignedSequenceCellRenderer,
-  AlignedSequenceDifferenceCellRenderer,
-  AminoAcidsCellRenderer,
-} from './utils/cell-renderer';
-import {StackedBarChart} from './viewers/stacked-barchart-viewer';
-
 import {analyzePeptidesWidget} from './widgets/analyze-peptides';
 import {PeptideSimilaritySpaceWidget} from './utils/peptide-similarity-space';
 import {manualAlignmentWidget} from './widgets/manual-alignment';
 import {SARViewer, SARViewerVertical} from './viewers/sar-viewer';
-import {peptideMoleculeWidget, getMolecule} from './widgets/peptide-molecule';
-import {runKalign, testMSAEnoughMemory} from './utils/multiple-sequence-alignment';
-import {msaWidget} from './widgets/multiple-sequence-alignment';
+
 import {PeptideSpaceViewer} from './viewers/peptide-space-viewer';
+import {getSeparator} from './utils/misc';
 
 export const _package = new DG.Package();
 let currentTable: DG.DataFrame;
@@ -74,19 +66,16 @@ export async function Peptides(): Promise<void> {
     ui.divH([
       ui.button('Simple demo', () => main('aligned.csv'), ''),
       ui.button('Complex demo', () => main('aligned_2.csv'), ''),
-
+      ui.button('HELM demo', () => main('aligned_3.csv'), ''),
     ]),
   ]);
 }
 
 //name: Peptides
 //tags: panel, widgets
-//input: column col {semType: alignedSequence}
+//input: column col {semType: Macromolecule}
 //output: widget result
 export async function peptidesPanel(col: DG.Column): Promise<DG.Widget> {
-  if (!(col.temp['isAnalysisApplicable'] ?? true))
-    return new DG.Widget(ui.divText('Analysis is not applicable'));
-
   [currentTable, alignedSequenceColumn] = getOrDefine(col.dataFrame, col);
   return analyzePeptidesWidget(currentTable, alignedSequenceColumn);
 }
@@ -115,61 +104,9 @@ export function peptideSpace(): PeptideSpaceViewer {
   return new PeptideSpaceViewer();
 }
 
-//name: StackedBarchart Widget
-//tags: panel, widgets
-//input: column col {semType: aminoAcids}
-//output: widget result
-export async function stackedBarchartWidget(col: DG.Column): Promise<DG.Widget> {
-  const viewer = await col.dataFrame.plot.fromType('StackedBarChartAA');
-  const panel = ui.divH([viewer.root]);
-  return new DG.Widget(panel);
-}
-
-//name: Peptide Molecule
-//tags: panel, widgets
-//input: string peptide {semType: alignedSequence}
-//output: widget result
-export async function peptideMolecule(peptide: string): Promise<DG.Widget> {
-  [currentTable, alignedSequenceColumn] = getOrDefine();
-  return peptideMoleculeWidget(peptide, currentTable);
-}
-
-//name: Peptide Molecule
-//tags: panel, widgets
-//input: string _aar {semType: aminoAcids}
-//output: widget result
-export async function peptideMolecule2(_aar: string): Promise<DG.Widget> {
-  [currentTable, alignedSequenceColumn] = getOrDefine();
-  const peptide = alignedSequenceColumn.get(currentTable.currentRowIdx);
-  return peptideMolecule(peptide);
-}
-
-//name: StackedBarChartAA
-//tags: viewer
-//output: viewer result
-export function stackedBarChart(): DG.JsViewer {
-  return new StackedBarChart();
-}
-
-//name: alignedSequenceCellRenderer
-//tags: cellRenderer
-//meta.cellType: alignedSequence
-//output: grid_cell_renderer result
-export function alignedSequenceCellRenderer(): AlignedSequenceCellRenderer {
-  return new AlignedSequenceCellRenderer();
-}
-
-//name: aminoAcidsCellRenderer
-//tags: cellRenderer
-//meta.cellType: aminoAcids
-//output: grid_cell_renderer result
-export function aminoAcidsCellRenderer(): AminoAcidsCellRenderer {
-  return new AminoAcidsCellRenderer();
-}
-
 //name: Manual Alignment
 //tags: panel, widgets
-//input: string _monomer {semType: aminoAcids}
+//input: string _monomer {semType: Monomer}
 //output: widget result
 export function manualAlignment(_monomer: string): DG.Widget {
   [currentTable, alignedSequenceColumn] = getOrDefine();
@@ -179,7 +116,7 @@ export function manualAlignment(_monomer: string): DG.Widget {
 
 //name: Peptide Space
 //tags: panel, widgets
-//input: column col {semType: alignedSequence}
+//input: column col {semType: Macromolecule}
 //output: widget result
 export async function peptideSpacePanel(col: DG.Column): Promise<DG.Widget> {
   [currentTable, alignedSequenceColumn] = getOrDefine(col.dataFrame, col);
@@ -187,56 +124,31 @@ export async function peptideSpacePanel(col: DG.Column): Promise<DG.Widget> {
   return widget.draw();
 }
 
+/*
 //name: Molfile
 //tags: panel, widgets
-//input: string peptide { semType: alignedSequence }
+//input: string peptide {semType: Macromolecule}
 //output: widget result
 export async function peptideMolfile(peptide: string): Promise<DG.Widget> {
   [currentTable, alignedSequenceColumn] = getOrDefine();
-  const smiles = getMolecule(peptide, alignedSequenceColumn.tags[C.TAGS.SEPARATOR]);
+  const smiles = getMolecule(peptide, getSeparator(alignedSequenceColumn));
   return grok.functions.call('Chem:molfile', {'smiles': smiles}) as Promise<DG.Widget>;
 }
 
 //name: Molfile
 //tags: panel, widgets
-//input: string _aar { semType: aminoAcids }
+//input: string _aar {semType: Monomer}
 //output: widget result
 export async function peptideMolfile2(_aar: string): Promise<DG.Widget> {
   [currentTable, alignedSequenceColumn] = getOrDefine();
   const peptide = alignedSequenceColumn.get(currentTable.currentRowIdx);
   return peptideMolfile(peptide);
 }
-
-//name: Multiple sequence alignment
-//tags: panel
-//input: column col {semType: alignedSequence}
-//output: dataframe result
-export async function multipleSequenceAlignment(col: DG.Column): Promise<DG.DataFrame> {
-  return msaWidget(col);
-}
-
-//name: Multiple sequence alignment for any column
-//input: dataframe table
-//input: column col
-//output: dataframe result
-export async function multipleSequenceAlignmentAny(table: DG.DataFrame, col: DG.Column): Promise<DG.DataFrame> {
-  const msaCol = await runKalign(col, false);
-  table.columns.add(msaCol);
-  return table;
-}
-
-//name: Test multiple sequence alignment for any column
-//input: dataframe _table
-//input: column col
-//output: column result
-export async function runTestMSAEnoughMemory(_table: DG.DataFrame, col: DG.Column<string>): Promise<DG.Column<string>> {
-  await testMSAEnoughMemory(col);
-  return col;
-}
+*/
 
 //name: Get Peptides Structure
 //tags: panel, widgets
-//input: column col {semType: alignedSequence}
+//input: column col {semType: Macromolecule}
 //output: widget result
 export function getPeptidesStructure(col: DG.Column): DG.Widget {
   const getButtonTooltip = 'Retrieves peptides structure from customer database by special id column';
@@ -256,17 +168,9 @@ export function getPeptidesStructure(col: DG.Column): DG.Widget {
   return new DG.Widget(getButton);
 }
 
-//name: alignedSequenceDifferenceCellRenderer
-//tags: cellRenderer
-//meta.cellType: alignedSequenceDifference
-//output: grid_cell_renderer result
-export function alignedSequenceDifferenceCellRenderer(): AlignedSequenceDifferenceCellRenderer {
-  return new AlignedSequenceDifferenceCellRenderer();
-}
-
 function getOrDefine(dataframe?: DG.DataFrame, column?: DG.Column | null): [DG.DataFrame, DG.Column] {
   dataframe ??= grok.shell.t;
-  column ??= dataframe.columns.bySemType(C.SEM_TYPES.ALIGNED_SEQUENCE);
+  column ??= dataframe.columns.bySemType(C.SEM_TYPES.MACROMOLECULE);
   if (column === null)
     throw new Error('Table does not contain aligned sequence columns');
 

package/src/tests/core.ts

@@ -1,12 +1,13 @@
 import * as grok from 'datagrok-api/grok';
 import * as DG from 'datagrok-api/dg';
 
-import {category, test, expect} from '@datagrok-libraries/utils/src/test';
+import {category, test, expect, delay} from '@datagrok-libraries/utils/src/test';
 
 import {_package} from '../package-test';
 import {startAnalysis} from '../widgets/analyze-peptides';
 import {PeptidesModel} from '../model';
 import * as C from '../utils/constants';
+import {scaleActivity} from '../utils/misc';
 
 category('Core', () => {
   let simpleTable: DG.DataFrame;
@@ -20,7 +21,7 @@ category('Core', () => {
   let complexAlignedSeqCol: DG.Column<string>;
   let complexScaledDf: DG.DataFrame;
   let complexScaledColName: string;
-  const alignedSeuqnceCol = 'AlignedSequence';
+  const alignedSequenceCol = 'AlignedSequence';
 
   let model: PeptidesModel | null = null;
 
@@ -28,10 +29,9 @@ category('Core', () => {
     const simpleActivityColName = 'IC50';
     simpleTable = DG.DataFrame.fromCsv(await _package.files.readAsText('aligned.csv'));
     simpleActivityCol = simpleTable.getCol(simpleActivityColName);
-    simpleAlignedSeqCol = simpleTable.getCol(alignedSeuqnceCol);
-    simpleAlignedSeqCol.semType = C.SEM_TYPES.ALIGNED_SEQUENCE;
-    [simpleScaledDf, simpleScaledColName] =
-      await PeptidesModel.scaleActivity('-lg', simpleTable, simpleActivityColName, true);
+    simpleAlignedSeqCol = simpleTable.getCol(alignedSequenceCol);
+    simpleAlignedSeqCol.semType = C.SEM_TYPES.MACROMOLECULE;
+    [simpleScaledDf, simpleScaledColName] = scaleActivity('-lg', simpleTable, simpleActivityColName, true);
 
     model = await startAnalysis(
       simpleActivityCol, simpleAlignedSeqCol, simpleTable, simpleScaledDf, simpleScaledColName, _package);
@@ -39,21 +39,17 @@ category('Core', () => {
 
     if (model != null) {
       model.currentSelection = {'11': ['D']};
-      grok.shell.closeTable(model._dataFrame);
+      grok.shell.closeTable(model.df);
     }
   });
 
   test('Start analysis: сomplex', async () => {
-    const measureCategory = 'interleukin 23 receptor_h_wt_DC_HEK293_SPR_biotin_BIND Dose Response (Kd (uM):koff)';
-    const complexActivityColName = 'Value';
+    const complexActivityColName = 'Activity';
     complexTable = DG.DataFrame.fromCsv(await _package.files.readAsText('aligned_2.csv'));
-    const measuredCol: DG.Column<string> = complexTable.getCol('Measured');
-    complexTable.filter.init((idx) => measuredCol.get(idx) == measureCategory);
     complexActivityCol = complexTable.getCol(complexActivityColName);
-    complexAlignedSeqCol = complexTable.getCol(alignedSeuqnceCol);
-    complexAlignedSeqCol.semType = C.SEM_TYPES.ALIGNED_SEQUENCE;
-    [complexScaledDf, complexScaledColName] =
-      await PeptidesModel.scaleActivity('-lg', complexTable, complexActivityColName, true);
+    complexAlignedSeqCol = complexTable.getCol('MSA');
+    complexAlignedSeqCol.semType = C.SEM_TYPES.MACROMOLECULE;
+    [complexScaledDf, complexScaledColName] = scaleActivity('-lg', complexTable, complexActivityColName, true);
 
     model = await startAnalysis(
       complexActivityCol, complexAlignedSeqCol, complexTable, complexScaledDf, complexScaledColName, _package);
@@ -61,7 +57,43 @@ category('Core', () => {
 
     if (model != null) {
       model.currentSelection = {'13': ['-']};
-      grok.shell.closeTable(model._dataFrame);
+      grok.shell.closeTable(model.df);
     }
   });
+
+  test('Save and load project', async () => {
+    const simpleActivityColName = 'IC50';
+    simpleTable = DG.DataFrame.fromCsv(await _package.files.readAsText('aligned.csv'));
+    simpleActivityCol = simpleTable.getCol(simpleActivityColName);
+    simpleAlignedSeqCol = simpleTable.getCol(alignedSequenceCol);
+    simpleAlignedSeqCol.semType = C.SEM_TYPES.MACROMOLECULE;
+    [simpleScaledDf, simpleScaledColName] = scaleActivity('-lg', simpleTable, simpleActivityColName, true);
+
+    model = await startAnalysis(
+      simpleActivityCol, simpleAlignedSeqCol, simpleTable, simpleScaledDf, simpleScaledColName, _package);
+    let v = grok.shell.getTableView('Peptides analysis');
+    const d = v.dataFrame;
+    const layout = v.saveLayout();
+    const tableInfo = d.getTableInfo();
+
+    const project = DG.Project.create();
+    project.name = 'Peptides project unique test';
+    project.addChild(tableInfo);
+    project.addChild(layout);
+    const sl = await grok.dapi.layouts.save(layout);
+    await grok.dapi.tables.uploadDataFrame(d);
+    const sti = await grok.dapi.tables.save(tableInfo);
+    const sp = await grok.dapi.projects.save(project);
+
+    grok.shell.closeTable(d);
+    await delay(500);
+
+    await grok.dapi.projects.open('Peptides project unique test');
+    v = grok.shell.getTableView('Peptides analysis');
+    grok.shell.closeTable(v.dataFrame);
+
+    await grok.dapi.layouts.delete(sl);
+    await grok.dapi.tables.delete(sti);
+    await grok.dapi.projects.delete(sp);
+  });
 });

package/src/tests/utils.ts

@@ -78,14 +78,3 @@ export async function _testPeptideSimilaritySpaceViewer(table: DG.DataFrame, ali
   for (const ax of axes)
     expect(ax.every((v) => v !== null && v !== NaN), true);
 }
-
-/**
- * Tests if MSA works and returns consistent result.
- *
- * @export
- * @param {DG.Column} col Aligned sequences column.
- */
-export async function _testMSAIsCorrect(col: DG.Column): Promise<void> {
-  const msaCol = await runKalign(col, true);
-  expect(msaCol.toList().every((v, i) => v == col.get(i)), true);
-}