@datagrok/peptides 1.3.3 → 1.3.5

package/src/widgets/peptides.ts

@@ -26,32 +26,18 @@ export async function analyzePeptidesWidget(df: DG.DataFrame, col: DG.Column): P
   if (funcs.length == 0)
     return new DG.Widget(ui.label('Helm package is missing or out of date. Please install the latest version.'));
 
-  let tempCol = null;
-  let scaledDf: DG.DataFrame;
-  let newScaledColName: string;
-  let scalingFormula: (x: number) => number;
+  let scaledCol: DG.Column<number>;
 
-  for (const column of df.columns.numerical)
-    tempCol = column.type === DG.TYPE.FLOAT ? column : null;
-
-  const defaultActivityColumn: DG.Column<number> | null = df.col('activity') || df.col('IC50') || tempCol;
+  const defaultActivityColumn: DG.Column<number> | null =
+    df.col('activity') || df.col('IC50') || DG.Utils.firstOrNull(df.columns.numerical);;
   const histogramHost = ui.div([], {id: 'pep-hist-host'});
 
-  const indexes: number[] = [];
-  const f = df.filter;
-  df.onFilterChanged.subscribe(() => {
-    for (let i = 0; i < f.length; ++i) {
-      if (f.get(i))
-        indexes.push(i);
-    }
-  });
   const activityScalingMethod = ui.choiceInput(
     'Scaling', 'none', ['none', 'lg', '-lg'],
     async (currentMethod: string): Promise<void> => {
-      [scaledDf, scalingFormula, newScaledColName] =
-        scaleActivity(currentMethod, activityColumnChoice.value!, indexes.length !== 0 ? indexes : undefined);
+      scaledCol = scaleActivity(currentMethod, activityColumnChoice.value!);
 
-      const hist = scaledDf.plot.histogram({
+      const hist = DG.DataFrame.fromColumns([scaledCol]).plot.histogram({
         filteringEnabled: false,
         valueColumnName: C.COLUMNS_NAMES.ACTIVITY_SCALED,
         legendVisibility: 'Never',
@@ -65,9 +51,9 @@ export async function analyzePeptidesWidget(df: DG.DataFrame, col: DG.Column): P
     });
   activityScalingMethod.setTooltip('Function to apply for each value in activity column');
 
-  const activityScalingMethodState = (_: any): void => {
+  const activityScalingMethodState = (): void => {
     activityScalingMethod.enabled = (activityColumnChoice.value ?? false) &&
-      DG.Stats.fromColumn(activityColumnChoice.value!, df.filter).min > 0;
+      DG.Stats.fromColumn(activityColumnChoice.value!).min > 0;
     activityScalingMethod.fireChanged();
   };
   const activityColumnChoice = ui.columnInput('Activity', df, defaultActivityColumn, activityScalingMethodState);
@@ -77,13 +63,18 @@ export async function analyzePeptidesWidget(df: DG.DataFrame, col: DG.Column): P
 
   const inputsList = [activityColumnChoice, activityScalingMethod, clustersColumnChoice];
 
+  const bitsetChanged = df.filter.onChanged.subscribe(() => {
+    activityScalingMethodState();
+  })
+
   const startBtn = ui.button('Launch SAR', async () => {
-    await startAnalysis(activityColumnChoice.value, col, clustersColumnChoice.value, df, scalingFormula,
-      newScaledColName, activityScalingMethod.value ?? 'none', indexes);
+    await startAnalysis(activityColumnChoice.value!, col, clustersColumnChoice.value, df, scaledCol,
+      activityScalingMethod.value ?? 'none');
+    bitsetChanged.unsubscribe();
   });
   startBtn.style.alignSelf = 'center';
 
-  const viewer = await df.plot.fromType('WebLogo') as bio.WebLogo;
+  const viewer = await df.plot.fromType('WebLogo') as bio.WebLogoViewer;
   viewer.root.style.setProperty('height', '130px');
   const logoHost = ui.div();
   $(logoHost).empty().append(viewer.root);
@@ -99,43 +90,30 @@ export async function analyzePeptidesWidget(df: DG.DataFrame, col: DG.Column): P
   );
 }
 
-export async function startAnalysis(activityColumn: DG.Column<number> | null, peptidesCol: DG.Column<string>,
-  clustersColumn: DG.Column | null, currentDf: DG.DataFrame, scaleNum: (x: number) => number, newScaledColName: string,
-  scaling: string, indexes: number[]): Promise<PeptidesModel | null> {
+export async function startAnalysis(activityColumn: DG.Column<number>, peptidesCol: DG.Column<string>,
+  clustersColumn: DG.Column | null, currentDf: DG.DataFrame, scaledCol: DG.Column<number>, scaling: string,
+  ): Promise<PeptidesModel | null> {
   const progress = DG.TaskBarProgressIndicator.create('Loading SAR...');
   let model = null;
-  if (activityColumn?.type === DG.TYPE.FLOAT) {
-    const f = currentDf.filter;
+  if (activityColumn.type === DG.TYPE.FLOAT || activityColumn.type === DG.TYPE.INT) {
     //prepare new DF
-    const newDf = DG.DataFrame.create(f.trueCount);
-    const getIndex = indexes.length !== 0 ? (i: number): number => indexes[i] : (i: number): number => i;
-    let activityCol: DG.Column<number> | null = null;
+    const newDf = DG.DataFrame.create(currentDf.rowCount);
+    const newDfCols = newDf.columns;
     for (const col of currentDf.columns.toList()) {
-      let virtualCol: DG.Column<any>;
-      if (col === activityColumn) {
-        virtualCol = newDf.columns.addNewVirtual(
-          C.COLUMNS_NAMES.ACTIVITY, (i) => activityColumn.get(getIndex(i)!), DG.TYPE.FLOAT);
-        activityCol = virtualCol;
-      } else if (col === peptidesCol) {
-        virtualCol = newDf.columns.addNewVirtual(
-          C.COLUMNS_NAMES.MACROMOLECULE, (i) => peptidesCol.get(getIndex(i)!), DG.TYPE.STRING);
-      } else
-        virtualCol = newDf.columns.addNewVirtual(col.name, (i) => col.get(getIndex(i)!), col.type as DG.TYPE);
-      virtualCol.setTag(C.TAGS.VISIBLE, '0');
+      const currentCol = newDfCols.add(col);
+      if (col === activityColumn)
+        currentCol.name = C.COLUMNS_NAMES.ACTIVITY;
+      else if (col === peptidesCol)
+        currentCol.name = C.COLUMNS_NAMES.MACROMOLECULE;
+      col.setTag(C.TAGS.VISIBLE, '0');
     }
-    activityCol!.semType = C.SEM_TYPES.ACTIVITY;
-    const activityScaledCol = newDf.columns.addNewVirtual(C.COLUMNS_NAMES.ACTIVITY_SCALED, (i) => {
-      const val = activityCol!.get(getIndex(i)!);
-      return val ? scaleNum(val) : val;
-    }, DG.TYPE.FLOAT);
-    activityScaledCol.semType = C.SEM_TYPES.ACTIVITY_SCALED;
+    activityColumn.semType = C.SEM_TYPES.ACTIVITY;
+    newDfCols.add(scaledCol);
     newDf.name = 'Peptides analysis';
-    newDf.tags[C.COLUMNS_NAMES.ACTIVITY_SCALED] = newScaledColName;
     if (clustersColumn) {
       newDf.getCol(clustersColumn.name).name = C.COLUMNS_NAMES.CLUSTERS;
       newDf.tags[C.TAGS.CLUSTERS] = C.COLUMNS_NAMES.CLUSTERS;
     }
-    // newDf.tags[C.PEPTIDES_ANALYSIS] = 'true';
     newDf.tags['scaling'] = scaling;
 
     let monomerType = 'HELM_AA';
@@ -148,10 +126,9 @@ export async function startAnalysis(activityColumn: DG.Column<number> | null, pe
     }
 
     newDf.setTag('monomerType', monomerType);
-
     model = await PeptidesModel.getInstance(newDf);
   } else
-    grok.shell.error('The activity column must be of floating point number type!');
+    grok.shell.error('The activity column must be of numeric type!');
   progress.close();
   return model;
 }

package/test-Peptides-916a90d7d48b-44350c85.html

@@ -1,276 +0,0 @@
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-</style></head><body><div id="jesthtml-content"><header><h1 id="title">Peptides Test Report. Datagrok version datagrok/datagrok:latest SHA=916a90d7d48b. Commit 44350c85.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-10-14 10:11:35</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/Peptides/src/__jest__/remote.test.ts</div><div class="suite-time warn">96.64s</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">76.108s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: Test result : Failed : 610 : Peptides.Core.Start analysis: simple : Unable to get project asset "getMonomerLib"
-Test result : Failed : 372 : Peptides.Core.Start analysis: сomplex : Unable to get project asset "getMonomerLib"
-Test result : Failed : 382 : Peptides.Core.Save and load project : Unable to get project asset "getMonomerLib"
-
-    at /home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts:68:20
-    at Generator.next (&lt;anonymous&gt;)
-    at fulfilled (/home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts:31:58)
-    at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre></div></div></div><div class="suite-consolelog"><div class="suite-consolelog-header">Console Log</div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/Peptides/src/__jest__/test-node.ts:62:11)
-    at Generator.next (&lt;anonymous&gt;)
-    at fulfilled (/home/runner/work/public/public/packages/Peptides/src/__jest__/test-node.ts:28:58)
-    at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Using web root: http://localhost:8080</pre></div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at /home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts:40:11
-    at Generator.next (&lt;anonymous&gt;)
-    at /home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts:34:71
-    at new Promise (&lt;anonymous&gt;)
-    at Object.&lt;anonymous&gt;.__awaiter (/home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts:30:12)
-    at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts:38:23)
-    at Promise.then.completed (/home/runner/work/public/public/packages/Peptides/node_modules/jest-circus/build/utils.js:391:28)
-    at new Promise (&lt;anonymous&gt;)</pre><pre class="suite-consolelog-item-message">Testing Peptides package</pre></div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at /home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts:66:11
-    at Generator.next (&lt;anonymous&gt;)
-    at fulfilled (/home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts:31:58)
-    at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Test result : Success : 0 : Peptides.Peptide space.test_table.is_not_empty : OK
-Test result : Success : 6368 : Peptides.Peptide space.PeptideSimilaritySpaceWidget.is_drawing : OK
-Test result : Success : 2 : Peptides.Peptide space.test_deminsionality_reducer : OK
-Test result : Success : 1 : Peptides.Peptide space.test_peptide_similarity_space_viewer : OK
-Test result : Success : 2945 : Peptides.Peptide space.peptide_space.DimensinalityReducer.UMAP.Levenshtein.is_numeric : OK
-Test result : Success : 3009 : Peptides.Peptide space.peptide_space.DimensinalityReducer.UMAP.Jaro-Winkler.is_numeric : OK
-Test result : Success : 3394 : Peptides.Peptide space.peptide_space.DimensinalityReducer.t-SNE.Levenshtein.is_numeric : OK
-Test result : Success : 3685 : Peptides.Peptide space.peptide_space.DimensinalityReducer.t-SNE.Jaro-Winkler.is_numeric : OK
-Test result : Success : 205 : Peptides.Peptide space.peptide_space.DimensinalityReducer.SPE.Levenshtein.is_numeric : OK
-Test result : Success : 629 : Peptides.Peptide space.peptide_space.DimensinalityReducer.SPE.Jaro-Winkler.is_numeric : OK
-Test result : Success : 174 : Peptides.Peptide space.peptide_space.DimensinalityReducer.pSPE.Levenshtein.is_numeric : OK
-Test result : Success : 731 : Peptides.Peptide space.peptide_space.DimensinalityReducer.pSPE.Jaro-Winkler.is_numeric : OK
-Test result : Success : 7686 : Peptides.Peptide space.peptide_space.DimensinalityReducer.OriginalSPE.Levenshtein.is_numeric : OK
-Test result : Success : 9316 : Peptides.Peptide space.peptide_space.DimensinalityReducer.OriginalSPE.Jaro-Winkler.is_numeric : OK
-Test result : Success : 1837 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.UMAP.Levenshtein.is_proper : OK
-Test result : Success : 2670 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.UMAP.Jaro-Winkler.is_proper : OK
-Test result : Success : 3278 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.t-SNE.Levenshtein.is_proper : OK
-Test result : Success : 4073 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.t-SNE.Jaro-Winkler.is_proper : OK
-Test result : Success : 244 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.SPE.Levenshtein.is_proper : OK
-Test result : Success : 666 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.SPE.Jaro-Winkler.is_proper : OK
-Test result : Success : 578 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.pSPE.Levenshtein.is_proper : OK
-Test result : Success : 612 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.pSPE.Jaro-Winkler.is_proper : OK
-Test result : Success : 9654 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.OriginalSPE.Levenshtein.is_proper : OK
-Test result : Success : 9749 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.OriginalSPE.Jaro-Winkler.is_proper : OK
-</pre></div></div></div></div></body></html>