@datagrok/peptides 1.3.7 → 1.3.9

package/src/widgets/peptides.ts

@@ -1,41 +1,53 @@
 import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
-import * as bio from '@datagrok-libraries/bio';
 
 import '../styles.css';
 import * as C from '../utils/constants';
 import {PeptidesModel} from '../model';
 import $ from 'cash-dom';
 import {scaleActivity} from '../utils/misc';
+import {WebLogoViewer} from '@datagrok-libraries/bio';
 
 /** Peptide analysis widget.
  *
  * @param {DG.DataFrame} df Working table
  * @param {DG.Column} col Aligned sequence column
  * @return {Promise<DG.Widget>} Widget containing peptide analysis */
-export async function analyzePeptidesWidget(df: DG.DataFrame, col: DG.Column): Promise<DG.Widget> {
-  if (!col.tags['aligned']?.includes('MSA') && col.tags[DG.TAGS.UNITS].toLowerCase() != 'helm')
-    return new DG.Widget(ui.divText('Peptides analysis only works with aligned sequences'));
+export async function analyzePeptidesUI(df: DG.DataFrame, col?: DG.Column<string>):
+Promise<{host: HTMLElement, callback: () => Promise<void>}> {
+  let seqColInput: DG.InputBase | null = null;
+  if (typeof col === 'undefined') {
+    const sequenceColumns = df.columns.toList().filter((dfCol) => dfCol.semType === DG.SEMTYPE.MACROMOLECULE);
+    let potentialCol = DG.Utils.firstOrNull(sequenceColumns);
+    if (potentialCol === null)
+      throw new Error('Peptides Error: table doesn\'t contain sequence columns');
+    seqColInput = ui.columnInput('Sequence', df, potentialCol, () => {
+      const seqCol = seqColInput!.value;
+      if (!seqCol.tags['aligned']?.includes('MSA') && seqCol.tags[DG.TAGS.UNITS].toLowerCase() !== 'helm')
+        grok.shell.warning('Peptides analysis only works with aligned sequences');
+    });
+  } else if (!col.tags['aligned']?.includes('MSA') && col.tags[DG.TAGS.UNITS].toLowerCase() !== 'helm')
+    return {host: ui.label('Peptides analysis only works with aligned sequences'), callback: async () => {}};
 
   let funcs = DG.Func.find({package: 'Bio', name: 'webLogoViewer'});
   if (funcs.length == 0)
-    return new DG.Widget(ui.label('Bio package is missing or out of date. Please install the latest version.'));
+    return {host: ui.label('Bio package is missing or out of date. Please install the latest version.'), callback: async () => {}};
 
-  funcs = DG.Func.find({package: 'Helm', name: 'getMonomerLib'});
+  funcs = DG.Func.find({package: 'Bio', name: 'getBioLib'});
   if (funcs.length == 0)
-    return new DG.Widget(ui.label('Helm package is missing or out of date. Please install the latest version.'));
+    return {host: ui.label('Bio package is missing or out of date. Please install the latest version.'), callback: async () => {}};
 
   let scaledCol: DG.Column<number>;
 
   const defaultActivityColumn: DG.Column<number> | null =
-    df.col('activity') || df.col('IC50') || DG.Utils.firstOrNull(df.columns.numerical);;
+    df.col('activity') || df.col('IC50') || DG.Utils.firstOrNull(df.columns.numerical); ;
   const histogramHost = ui.div([], {id: 'pep-hist-host'});
 
   const activityScalingMethod = ui.choiceInput(
     'Scaling', 'none', ['none', 'lg', '-lg'],
     async (currentMethod: string): Promise<void> => {
-      scaledCol = scaleActivity(currentMethod, activityColumnChoice.value!);
+      scaledCol = scaleActivity(activityColumnChoice.value!, currentMethod);
 
       const hist = DG.DataFrame.fromColumns([scaledCol]).plot.histogram({
         filteringEnabled: false,
@@ -62,37 +74,48 @@ export async function analyzePeptidesWidget(df: DG.DataFrame, col: DG.Column): P
   activityScalingMethod.fireChanged();
 
   const inputsList = [activityColumnChoice, activityScalingMethod, clustersColumnChoice];
+  if (seqColInput !== null)
+    inputsList.splice(0, 0, seqColInput);
 
   const bitsetChanged = df.filter.onChanged.subscribe(() => {
     activityScalingMethodState();
-  })
+  });
 
-  const startBtn = ui.button('Launch SAR', async () => {
-    await startAnalysis(activityColumnChoice.value!, col, clustersColumnChoice.value, df, scaledCol,
-      activityScalingMethod.value ?? 'none');
+  const startAnalysisCallback = async () => {
+    const sequencesCol = col ?? seqColInput!.value;
+    if (sequencesCol)
+      await startAnalysis(activityColumnChoice.value!, sequencesCol, clustersColumnChoice.value, df, scaledCol,
+        activityScalingMethod.value ?? 'none');
     bitsetChanged.unsubscribe();
-  });
-  startBtn.style.alignSelf = 'center';
+  };
+
+  const inputElements: HTMLElement[] = [ui.inputs(inputsList)];
+  $(inputElements[0]).find('label').css('width', 'unset');
+  if (typeof col !== 'undefined') {
+    const startBtn = ui.button('Launch SAR', startAnalysisCallback);
+    startBtn.style.alignSelf = 'center';
+    inputElements.push(startBtn);
+  }
 
-  const viewer = await df.plot.fromType('WebLogo') as bio.WebLogoViewer;
+  const viewer = await df.plot.fromType('WebLogo') as WebLogoViewer;
   viewer.root.style.setProperty('height', '130px');
   const logoHost = ui.div();
   $(logoHost).empty().append(viewer.root);
 
-  return new DG.Widget(
-    ui.divV([
-      logoHost,
-      ui.splitH([
-        ui.splitV([ui.inputs(inputsList), startBtn]),
-        histogramHost,
-      ], {style: {height: '215px'}}),
-    ]),
-  );
+  const mainHost = ui.divV([
+    logoHost,
+    ui.splitH([
+      ui.splitV(inputElements),
+      histogramHost,
+    ], {style: {height: '215px'}}),
+  ]);
+  mainHost.style.maxWidth = '400px';
+  return {host: mainHost, callback: startAnalysisCallback};
 }
 
 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> {
+): Promise<PeptidesModel | null> {
   const progress = DG.TaskBarProgressIndicator.create('Loading SAR...');
   let model = null;
   if (activityColumn.type === DG.TYPE.FLOAT || activityColumn.type === DG.TYPE.INT) {
@@ -112,9 +135,9 @@ export async function startAnalysis(activityColumn: DG.Column<number>, peptidesC
     newDf.name = 'Peptides analysis';
     if (clustersColumn) {
       newDf.getCol(clustersColumn.name).name = C.COLUMNS_NAMES.CLUSTERS;
-      newDf.tags[C.TAGS.CLUSTERS] = C.COLUMNS_NAMES.CLUSTERS;
+      newDf.setTag(C.TAGS.CLUSTERS, C.COLUMNS_NAMES.CLUSTERS);
     }
-    newDf.tags['scaling'] = scaling;
+    newDf.setTag('settings', JSON.stringify({scaling: scaling}));
 
     let monomerType = 'HELM_AA';
     if (peptidesCol.getTag(DG.TAGS.UNITS).toLowerCase() == 'helm') {
@@ -126,6 +149,7 @@ export async function startAnalysis(activityColumn: DG.Column<number>, peptidesC
     }
 
     newDf.setTag('monomerType', monomerType);
+    newDf.setTag('newAnalysis', '1');
     model = await PeptidesModel.getInstance(newDf);
   } else
     grok.shell.error('The activity column must be of numeric type!');

package/src/widgets/settings.ts

@@ -0,0 +1,67 @@
+import * as ui from 'datagrok-api/ui';
+import * as grok from 'datagrok-api/grok';
+import * as DG from 'datagrok-api/dg';
+
+import * as type from '../utils/types';
+import {PeptidesModel} from '../model';
+
+import $ from 'cash-dom';
+import wu from 'wu';
+
+//TODO: show sliderInput values
+export function getSettingsDialog(model: PeptidesModel): DG.Dialog {
+  const accordion = ui.accordion();
+  const settings = model.settings;
+  const result: type.PeptidesSettings = {columns: {}};
+  const activityScaling = ui.choiceInput('Activity scaling', settings.scaling ?? 'none', ['none', 'lg', '-lg'],
+    () => result.scaling = activityScaling.value! as type.ScalingMethods);
+  const bidirectionalAnalysis = ui.boolInput('Bidirectional analysis', settings.isBidirectional ?? false,
+    () => result.isBidirectional = bidirectionalAnalysis.value!);
+  accordion.addPane('General', () => ui.inputs([activityScaling, bidirectionalAnalysis]), true);
+
+  const maxMutations = ui.sliderInput('Max mutations', settings.maxMutations ?? 1, 0, 50, () => {
+    const val = Math.round(maxMutations.value!);
+    $(maxMutations.root).find('label.ui-input-description').remove();
+    result.maxMutations = val;
+    maxMutations.addPostfix(val.toString());
+  });
+  maxMutations.addPostfix((settings.maxMutations ?? 1).toString());
+  const minActivityDelta = ui.sliderInput('Min activity delta', settings.minActivityDelta ?? 0, 0, 100, () => {
+    const val = Math.round(minActivityDelta.value!);
+    result.minActivityDelta = val;
+    $(minActivityDelta.root).find('label.ui-input-description').remove();
+    minActivityDelta.addPostfix(val.toString());
+  });
+  minActivityDelta.addPostfix((settings.minActivityDelta ?? 0).toString());
+  accordion.addPane('Mutation Cliffs', () => ui.inputs([maxMutations, minActivityDelta]), true);
+
+  const inputsRows: HTMLElement[] = [];
+  for (const col of model.df.columns.numerical) {
+    const isIncluded = ui.boolInput('', typeof (settings.columns ?? {})[col.name] !== 'undefined',
+      () => {
+        if (isIncluded)
+          result.columns![col.name] = aggregation.stringValue;
+        else
+          delete result.columns![col.name];
+      }) as DG.InputBase<boolean>;
+    const aggregation = ui.choiceInput('Aggregation', (settings.columns ?? {})[col.name] ?? 'avg', Object.values(DG.STATS),
+      () => {
+        if (isIncluded)
+          result.columns![col.name] = aggregation.stringValue;
+        else
+          delete result.columns![col.name];
+      }) as DG.InputBase<string>;
+    $(aggregation.root).find('label').css('width', 'auto');
+    const inputsRow = ui.inputsRow(col.name, [isIncluded, aggregation]);
+    $(inputsRow).find('div.ui-div').css('display', 'inline-flex');
+    inputsRows.push(inputsRow);
+  }
+  accordion.addPane('Columns to include', () => ui.divV(inputsRows), false);
+
+  const dialog = ui.dialog('Peptides settings').add(accordion);
+  dialog.root.style.width = '400px';
+  dialog.onOK(() => model.settings = result);
+  dialog.show();
+
+  return dialog.show();
+}

package/test-Peptides-62cc009524f3-0949dc07.html

@@ -0,0 +1,276 @@
+<html><head><meta charset="utf-8"/><title>Peptides Test Report. Datagrok version datagrok/datagrok:latest SHA=62cc009524f3. Commit 0949dc07.</title><style type="text/css">html,
+body {
+  font-family: Arial, Helvetica, sans-serif;
+  font-size: 1rem;
+  margin: 0;
+  padding: 0;
+  color: #333;
+}
+body {
+  padding: 2rem 1rem;
+  font-size: 0.85rem;
+}
+#jesthtml-content {
+  margin: 0 auto;
+  max-width: 70rem;
+}
+header {
+  display: flex;
+  align-items: center;
+}
+#title {
+  margin: 0;
+  flex-grow: 1;
+}
+#logo {
+  height: 4rem;
+}
+#timestamp {
+  color: #777;
+  margin-top: 0.5rem;
+}
+
+/** SUMMARY */
+#summary {
+  color: #333;
+  margin: 2rem 0;
+  display: flex;
+  font-family: monospace;
+  font-size: 1rem;
+}
+#summary > div {
+  margin-right: 2rem;
+  background: #eee;
+  padding: 1rem;
+  min-width: 15rem;
+}
+#summary > div:last-child {
+  margin-right: 0;
+}
+@media only screen and (max-width: 720px) {
+  #summary {
+    flex-direction: column;
+  }
+  #summary > div {
+    margin-right: 0;
+    margin-top: 2rem;
+  }
+  #summary > div:first-child {
+    margin-top: 0;
+  }
+}
+
+.summary-total {
+  font-weight: bold;
+  margin-bottom: 0.5rem;
+}
+.summary-passed {
+  color: #4f8a10;
+  border-left: 0.4rem solid #4f8a10;
+  padding-left: 0.5rem;
+}
+.summary-failed,
+.summary-obsolete-snapshots {
+  color: #d8000c;
+  border-left: 0.4rem solid #d8000c;
+  padding-left: 0.5rem;
+}
+.summary-pending {
+  color: #9f6000;
+  border-left: 0.4rem solid #9f6000;
+  padding-left: 0.5rem;
+}
+.summary-empty {
+  color: #999;
+  border-left: 0.4rem solid #999;
+}
+
+.test-result {
+  padding: 1rem;
+  margin-bottom: 0.25rem;
+}
+.test-result:last-child {
+  border: 0;
+}
+.test-result.passed {
+  background-color: #dff2bf;
+  color: #4f8a10;
+}
+.test-result.failed {
+  background-color: #ffbaba;
+  color: #d8000c;
+}
+.test-result.pending {
+  background-color: #ffdf61;
+  color: #9f6000;
+}
+
+.test-info {
+  display: flex;
+  justify-content: space-between;
+}
+.test-suitename {
+  width: 20%;
+  text-align: left;
+  font-weight: bold;
+  word-break: break-word;
+}
+.test-title {
+  width: 40%;
+  text-align: left;
+  font-style: italic;
+}
+.test-status {
+  width: 20%;
+  text-align: right;
+}
+.test-duration {
+  width: 10%;
+  text-align: right;
+  font-size: 0.75rem;
+}
+
+.failureMessages {
+  padding: 0 1rem;
+  margin-top: 1rem;
+  border-top: 1px dashed #d8000c;
+}
+.failureMessages.suiteFailure {
+  border-top: none;
+}
+.failureMsg {
+  white-space: pre-wrap;
+  white-space: -moz-pre-wrap;
+  white-space: -pre-wrap;
+  white-space: -o-pre-wrap;
+  word-wrap: break-word;
+}
+
+.suite-container {
+  margin-bottom: 2rem;
+}
+.suite-info {
+  padding: 1rem;
+  background-color: #eee;
+  color: #777;
+  display: flex;
+  align-items: center;
+  margin-bottom: 0.25rem;
+}
+.suite-info .suite-path {
+  word-break: break-all;
+  flex-grow: 1;
+  font-family: monospace;
+  font-size: 1rem;
+}
+.suite-info .suite-time {
+  margin-left: 0.5rem;
+  padding: 0.2rem 0.3rem;
+  font-size: 0.75rem;
+}
+.suite-info .suite-time.warn {
+  background-color: #d8000c;
+  color: #fff;
+}
+
+/* CONSOLE LOGS */
+.suite-consolelog {
+  margin-bottom: 0.25rem;
+  padding: 1rem;
+  background-color: #efefef;
+}
+.suite-consolelog-header {
+  font-weight: bold;
+}
+.suite-consolelog-item {
+  padding: 0.5rem;
+}
+.suite-consolelog-item pre {
+  margin: 0.5rem 0;
+  white-space: pre-wrap;
+  white-space: -moz-pre-wrap;
+  white-space: -pre-wrap;
+  white-space: -o-pre-wrap;
+  word-wrap: break-word;
+}
+.suite-consolelog-item-origin {
+  color: #777;
+  font-weight: bold;
+}
+.suite-consolelog-item-message {
+  color: #000;
+  font-size: 1rem;
+  padding: 0 0.5rem;
+}
+
+/* OBSOLETE SNAPSHOTS */
+.suite-obsolete-snapshots {
+  margin-bottom: 0.25rem;
+  padding: 1rem;
+  background-color: #ffbaba;
+  color: #d8000c;
+}
+.suite-obsolete-snapshots-header {
+  font-weight: bold;
+}
+.suite-obsolete-snapshots-item {
+  padding: 0.5rem;
+}
+.suite-obsolete-snapshots-item pre {
+  margin: 0.5rem 0;
+  white-space: pre-wrap;
+  white-space: -moz-pre-wrap;
+  white-space: -pre-wrap;
+  white-space: -o-pre-wrap;
+  word-wrap: break-word;
+}
+.suite-obsolete-snapshots-item-message {
+  color: #000;
+  font-size: 1rem;
+  padding: 0 0.5rem;
+}
+</style></head><body><div id="jesthtml-content"><header><h1 id="title">Peptides Test Report. Datagrok version datagrok/datagrok:latest SHA=62cc009524f3. Commit 0949dc07.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-11-11 14:09:20</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">96.038s</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">82.695s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: Test result : Failed : 329 : Peptides.Core.Start analysis: сomplex : Error: For column 'macromolecule' of alphabet 'UN' tag '.alphabetSize' is mandatory.
+
+    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 : 4295 : Peptides.Core.Start analysis: simple : OK
+Test result : Success : 7421 : Peptides.Core.Save and load project : OK
+Test result : Success : 0 : Peptides.Peptide space.test_table.is_not_empty : OK
+Test result : Success : 2686 : Peptides.Peptide space.PeptideSimilaritySpaceWidget.is_drawing : OK
+Test result : Success : 2 : Peptides.Peptide space.test_deminsionality_reducer : OK
+Test result : Success : 0 : Peptides.Peptide space.test_peptide_similarity_space_viewer : OK
+Test result : Success : 2238 : Peptides.Peptide space.peptide_space.DimensinalityReducer.UMAP.Levenshtein.is_numeric : OK
+Test result : Success : 2625 : Peptides.Peptide space.peptide_space.DimensinalityReducer.UMAP.Jaro-Winkler.is_numeric : OK
+Test result : Success : 3350 : Peptides.Peptide space.peptide_space.DimensinalityReducer.t-SNE.Levenshtein.is_numeric : OK
+Test result : Success : 3819 : Peptides.Peptide space.peptide_space.DimensinalityReducer.t-SNE.Jaro-Winkler.is_numeric : OK
+Test result : Success : 208 : Peptides.Peptide space.peptide_space.DimensinalityReducer.SPE.Levenshtein.is_numeric : OK
+Test result : Success : 594 : Peptides.Peptide space.peptide_space.DimensinalityReducer.SPE.Jaro-Winkler.is_numeric : OK
+Test result : Success : 171 : Peptides.Peptide space.peptide_space.DimensinalityReducer.pSPE.Levenshtein.is_numeric : OK
+Test result : Success : 556 : Peptides.Peptide space.peptide_space.DimensinalityReducer.pSPE.Jaro-Winkler.is_numeric : OK
+Test result : Success : 8614 : Peptides.Peptide space.peptide_space.DimensinalityReducer.OriginalSPE.Levenshtein.is_numeric : OK
+Test result : Success : 9838 : Peptides.Peptide space.peptide_space.DimensinalityReducer.OriginalSPE.Jaro-Winkler.is_numeric : OK
+Test result : Success : 2113 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.UMAP.Levenshtein.is_proper : OK
+Test result : Success : 2618 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.UMAP.Jaro-Winkler.is_proper : OK
+Test result : Success : 3392 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.t-SNE.Levenshtein.is_proper : OK
+Test result : Success : 3850 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.t-SNE.Jaro-Winkler.is_proper : OK
+Test result : Success : 232 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.SPE.Levenshtein.is_proper : OK
+Test result : Success : 818 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.SPE.Jaro-Winkler.is_proper : OK
+Test result : Success : 193 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.pSPE.Levenshtein.is_proper : OK
+Test result : Success : 587 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.pSPE.Jaro-Winkler.is_proper : OK
+Test result : Success : 8223 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.OriginalSPE.Levenshtein.is_proper : OK
+Test result : Success : 9416 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.OriginalSPE.Jaro-Winkler.is_proper : OK
+</pre></div></div></div></div></body></html>