@datagrok/sequence-translator 1.0.7 → 1.0.9

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@datagrok/sequence-translator",
   "friendlyName": "Sequence Translator",
-  "version": "1.0.7",
+  "version": "1.0.9",
   "author": {
     "name": "Vadym Kovadlo",
     "email": "vkovadlo@datagrok.ai"
@@ -13,7 +13,7 @@
     "directory": "packages/SequenceTranslator"
   },
   "dependencies": {
-    "@datagrok-libraries/utils": "^0.1.0",
+    "@datagrok-libraries/utils": "^1.9.2",
     "@types/react": "^18.0.15",
     "datagrok-api": "^1.6.0",
     "datagrok-tools": "^4.1.2",

package/src/autostart/registration.ts

@@ -22,6 +22,26 @@ function stringify(items: string[]): string {
   return '["' + items.join('", "') + '"]';
 }
 
+function saltMass(saltNames: string[], molWeightCol: DG.Column, equivalentsCol: DG.Column, i: number,
+  saltCol: DG.Column) {
+  const saltRowIndex = saltNames.indexOf(saltCol.get(i));
+  return (
+    saltRowIndex == -1 || molWeightCol.get(saltRowIndex) == DG.FLOAT_NULL || equivalentsCol.get(i) == DG.INT_NULL) ?
+    DG.FLOAT_NULL :
+    molWeightCol.get(saltRowIndex) * equivalentsCol.get(i);
+}
+
+function saltMolWeigth(saltNamesList: string[], saltCol: DG.Column, molWeightCol: DG.Column, i: number) {
+  const saltRowIndex = saltNamesList.indexOf(saltCol.get(i));
+  return (saltRowIndex == -1) ? DG.FLOAT_NULL : molWeightCol.get(saltRowIndex);
+}
+
+function batchMolWeight(compoundMolWeightCol: DG.Column, saltMassCol: DG.Column, i: number) {
+  return (compoundMolWeightCol.getString(i) == '' || saltMassCol.getString(i) == '') ?
+    DG.FLOAT_NULL :
+    compoundMolWeightCol.get(i) + saltMassCol.get(i);
+}
+
 function molecularWeight(sequence: string, weightsObj: {[index: string]: number}): number {
   const codes = sortByStringLengthInDescendingOrder(Object.keys(weightsObj)).concat(Object.keys(MODIFICATIONS));
   let weight = 0;
@@ -117,14 +137,18 @@ export function oligoSdFile(table: DG.DataFrame) {
   const icdsDf = DG.DataFrame.fromCsv(ICDS);
   const idpsDf = DG.DataFrame.fromCsv(IDPS);
 
-  async function addColumns(t: DG.DataFrame, saltsDf: DG.DataFrame) {
+  const sequenceCol = table.getCol(COL_NAMES.SEQUENCE);
+  const saltCol = table.getCol(COL_NAMES.SALT);
+  const equivalentsCol = table.getCol(COL_NAMES.EQUIVALENTS);
+  const typeColumn = table.getCol(COL_NAMES.TYPE);
+
+  const molWeightCol = saltsDf.getCol('MOLWEIGHT');
+  const saltNamesList = saltsDf.getCol('DISPLAY').toList();
+
+  function addColumns(t: DG.DataFrame) {
     if (t.columns.contains(COL_NAMES.COMPOUND_NAME))
       return grok.shell.error('Columns already exist');
 
-    const sequenceCol = t.getCol(COL_NAMES.SEQUENCE);
-    const saltCol = t.getCol(COL_NAMES.SALT);
-    const equivalentsCol = t.getCol(COL_NAMES.EQUIVALENTS);
-
     for (let i = t.rowCount - 1; i > -1; i--) {
       if (sequenceCol.get(i) == '')
         t.rows.removeAt(i, 1, false);
@@ -132,12 +156,11 @@ export function oligoSdFile(table: DG.DataFrame) {
 
     t.columns.addNewString(COL_NAMES.COMPOUND_NAME).init((i: number) => sequenceCol.get(i));
 
-    t.columns.addNewString(COL_NAMES.COMPOUND_COMMENTS).init((i: number) => (i > 0 && i % 2 == 0) ?
+    t.columns.addNewString(COL_NAMES.COMPOUND_COMMENTS).init((i: number) => (i > 2 && typeColumn.get(i) == 'Duplex') ?
       sequenceCol.get(i) + '; duplex of SS: ' + sequenceCol.get(i - 2) + ' and AS: ' + sequenceCol.get(i - 1) :
       sequenceCol.get(i),
     );
-    const molWeightCol = saltsDf.getCol('MOLWEIGHT');
-    const saltNamesList = saltsDf.getCol('DISPLAY').toList();
+
     const weightsObj: {[code: string]: number} = {};
     for (const synthesizer of Object.keys(map)) {
       for (const technology of Object.keys(map[synthesizer])) {
@@ -154,19 +177,14 @@ export function oligoSdFile(table: DG.DataFrame) {
         DG.FLOAT_NULL;
     });
 
-    t.columns.addNewFloat(COL_NAMES.SALT_MASS).init((i: number) => {
-      const saltRowIndex = saltNamesList.indexOf(saltCol.get(i));
-      return (saltRowIndex == -1) ? DG.FLOAT_NULL : molWeightCol.get(saltRowIndex) * equivalentsCol.get(i);
-    });
+    t.columns.addNewFloat(COL_NAMES.SALT_MASS).init((i: number) =>
+      saltMass(saltNamesList, molWeightCol, equivalentsCol, i, saltCol));
 
-    t.columns.addNewFloat(COL_NAMES.SALT_MOL_WEIGHT).init((i: number) => {
-      const saltRowIndex = saltNamesList.indexOf(saltCol.get(i));
-      return (saltRowIndex == -1) ? DG.FLOAT_NULL : molWeightCol.get(saltRowIndex);
-    });
+    t.columns.addNewFloat(COL_NAMES.SALT_MOL_WEIGHT).init((i: number) =>
+      saltMolWeigth(saltNamesList, saltCol, molWeightCol, i));
 
-    await t.columns.addNewCalculated(COL_NAMES.BATCH_MW,
-      '${' + COL_NAMES.CPD_MW + '} + ${' + COL_NAMES.SALT_MASS + '}', DG.COLUMN_TYPE.FLOAT, false,
-    );
+    t.columns.addNewFloat(COL_NAMES.BATCH_MW).init((i: number) =>
+      batchMolWeight(t.getCol(COL_NAMES.CPD_MW), t.getCol(COL_NAMES.SALT_MASS), i));
 
     addColumnsPressed = true;
     return newDf = t;
@@ -181,8 +199,8 @@ export function oligoSdFile(table: DG.DataFrame) {
       if (table.getCol(COL_NAMES.IDP).type != DG.COLUMN_TYPE.STRING)
         table.changeColumnType(COL_NAMES.IDP, DG.COLUMN_TYPE.STRING);
       d.append(
-        ui.link('Add Columns', async () => {
-          await addColumns(table, saltsDf);
+        ui.link('Add Columns', () => {
+          addColumns(table);
           view.grid.columns.setOrder(Object.values(COL_NAMES));
         }, 'Add columns: \'' + [COL_NAMES.COMPOUND_NAME, COL_NAMES.COMPOUND_COMMENTS, COL_NAMES.CPD_MW,
           COL_NAMES.SALT_MASS, COL_NAMES.BATCH_MW].join('\', \''), '',
@@ -205,9 +223,26 @@ export function oligoSdFile(table: DG.DataFrame) {
           args.args.menu.item('Fill Column With Value', () => {
             const v = args.args.context.table.currentCell.value;
             args.args.context.table.currentCell.column.init(v);
+            for (let i = 0; i < view.dataFrame.rowCount; i++)
+              updateCalculatedColumns(view.dataFrame, i);
           });
         }
       });
+
+      view.dataFrame.onDataChanged.subscribe(() => {
+        const colName = view.dataFrame.currentCol.name;
+        if ([COL_NAMES.SALT, COL_NAMES.EQUIVALENTS, COL_NAMES.SALT_MOL_WEIGHT].includes(colName))
+          updateCalculatedColumns(view.dataFrame, view.dataFrame.currentRowIdx);
+      });
+
+      function updateCalculatedColumns(t: DG.DataFrame, i: number): void {
+        const smValue = saltMass(saltNamesList, molWeightCol, equivalentsCol, i, saltCol);
+        t.getCol(COL_NAMES.SALT_MASS).set(i, smValue, false);
+        const smwValue = saltMolWeigth(saltNamesList, saltCol, molWeightCol, i);
+        t.getCol(COL_NAMES.SALT_MOL_WEIGHT).set(i, smwValue, false);
+        const bmw = batchMolWeight(t.getCol(COL_NAMES.CPD_MW), t.getCol(COL_NAMES.SALT_MASS), i);
+        t.getCol(COL_NAMES.BATCH_MW).set(i, bmw, false);
+      }
     }),
   ]);
   grok.shell.v.setRibbonPanels([[d]]);

package/src/axolabs/constants.ts

@@ -13,17 +13,17 @@ export const axolabsMap:
     symbols: ['dA', 'dC', 'dG', 'dT'],
     color: 'rgb(197,224,180)',
   },
-  '2\'-Fluoro': {
+  "2\"-Fluoro": {
     fullName: '2\'-Fluoro nucleotides',
     symbols: ['Af', 'Cf', 'Gf', 'Uf'],
     color: 'rgb(68,114,196)',
   },
-  '2\'-O-Methyl': {
+  "2\"-O-Methyl": {
     fullName: '2\'-O-Methyl nucleotides',
     symbols: ['a', 'c', 'g', 'u'],
     color: 'rgb(166,166,166)',
   },
-  '2\'-O-MOE': {
+  "2\"-O-MOE": {
     fullName: '2\'-O-MOE nucleotides (including 5-Methyl C)',
     symbols: ['Am', 'Cm', 'Gm', 'Tm'],
     color: 'rgb(112,48,160)',
@@ -83,7 +83,7 @@ export const axolabsMap:
     symbols: ['(invabasic)', '(invabasic)', '(invabasic)', '(invabasic)'],
     color: invAbasicColor,
   },
-  '5\'-vinylps': {
+  "5\"-vinylps": {
     fullName: '5\'-vinylphosphonate-2\'-OMe-uridine',
     symbols: ['(vinu)', '(vinu)', '(vinu)', '(vinu)'],
     color: 'rgb(0,0,139)',
@@ -93,7 +93,7 @@ export const axolabsMap:
     symbols: ['(invabasic)', '(invabasic)', '(invabasic)', '(invabasic)'],
     color: invAbasicColor,
   },
-  '2\'-OMe-U(o)': {
+  "2\"-OMe-U(o)": {
     fullName: 'Nucleotide Uridine with 2\'O-Methyl protection (overhang)',
     symbols: ['mU', 'mU', 'mU', 'mU'],
     color: 'rgb(65,233,80)',

package/src/structures-works/mol-transformations.ts

@@ -56,7 +56,7 @@ M  V30 BEGIN ATOM
 M  V30 1 O 1.0934 -2.1636 0 0
 M  V30 2 C 1.8365 -1.4945 0 0 CFG=2
 M  V30 3 C 2.8147 -1.7024 0 0
-M  V30 4 C 3.3147 -0.8364 0 0 VAL=3
+M  V30 4 C 3.3147 -0.8364 0 0
 M  V30 5 O 2.6455 -0.0932 0 0
 M  V30 6 C 1.732 -0.5 0 0 CFG=1
 M  V30 7 C 0.866 0 0 0

package/src/structures-works/save-sense-antisense.ts

@@ -29,8 +29,8 @@ export function saveSenseAntiSense() {
   const moleculeSvgDiv = ui.block([]);
   const ssInput = ui.textInput('Sense Strand', '');
   const asInput = ui.textInput('Anti Sense', '');
-  const straight = '5\' ->3\'';
-  const inverse = '3\' ->5\'';
+  const straight = "5 prime -> 3 prime";
+  const inverse = "3 prime -> 5 prime";
   let ssInverse = false;
   let asInverse = false;
 

package/{test-SequenceTranslator-4ba776b36f56-5798c6fc.html → test-SequenceTranslator-7770371320b2-1d307ddc.html}

@@ -1,4 +1,4 @@
-<html><head><meta charset="utf-8"/><title>SequenceTranslator Test Report. Datagrok version datagrok/datagrok:latest SHA=4ba776b36f56. Commit 5798c6fc.</title><style type="text/css">html,
+<html><head><meta charset="utf-8"/><title>SequenceTranslator Test Report. Datagrok version datagrok/datagrok:latest SHA=7770371320b2. Commit 1d307ddc.</title><style type="text/css">html,
 body {
   font-family: Arial, Helvetica, sans-serif;
   font-size: 1rem;
@@ -229,11 +229,7 @@ header {
   font-size: 1rem;
   padding: 0 0.5rem;
 }
-</style></head><body><div id="jesthtml-content"><header><h1 id="title">SequenceTranslator Test Report. Datagrok version datagrok/datagrok:latest SHA=4ba776b36f56. Commit 5798c6fc.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-09-15 14:52:27</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/SequenceTranslator/src/__jest__/remote.test.ts</div><div class="suite-time warn">40.999s</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">24.16s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: Evaluation failed: TypeError: Cannot read properties of null (reading 'get')
-    at __puppeteer_evaluation_script__:14:72
-    at ExecutionContext._evaluateInternal (/home/runner/work/public/public/packages/SequenceTranslator/node_modules/puppeteer/src/common/ExecutionContext.ts:273:13)
-    at processTicksAndRejections (internal/process/task_queues.js:97:5)
-    at ExecutionContext.evaluate (/home/runner/work/public/public/packages/SequenceTranslator/node_modules/puppeteer/src/common/ExecutionContext.ts:140:12)</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/SequenceTranslator/src/__jest__/test-node.ts:62:11)
+</style></head><body><div id="jesthtml-content"><header><h1 id="title">SequenceTranslator Test Report. Datagrok version datagrok/datagrok:latest SHA=7770371320b2. Commit 1d307ddc.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-09-29 08:43:13</div><div id="summary"><div id="suite-summary"><div class="summary-total">Suites (1)</div><div class="summary-passed">1 passed</div><div class="summary-failed summary-empty">0 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">1 passed</div><div class="summary-failed summary-empty">0 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/SequenceTranslator/src/__jest__/remote.test.ts</div><div class="suite-time warn">17.787s</div></div><div class="suite-tests"><div class="test-result passed"><div class="test-info"><div class="test-suitename"> </div><div class="test-title">TEST</div><div class="test-status">passed</div><div class="test-duration">2.717s</div></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/SequenceTranslator/src/__jest__/test-node.ts:62:11)
     at Generator.next (&lt;anonymous&gt;)
     at fulfilled (/home/runner/work/public/public/packages/SequenceTranslator/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/SequenceTranslator/src/__jest__/remote.test.ts:40:11
@@ -243,4 +239,18 @@ header {
     at Object.&lt;anonymous&gt;.__awaiter (/home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/remote.test.ts:27:12)
     at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/remote.test.ts:38:23)
     at Promise.then.completed (/home/runner/work/public/public/packages/SequenceTranslator/node_modules/jest-circus/build/utils.js:391:28)
-    at new Promise (&lt;anonymous&gt;)</pre><pre class="suite-consolelog-item-message">Testing SequenceTranslator package</pre></div></div></div></div></body></html>
+    at new Promise (&lt;anonymous&gt;)</pre><pre class="suite-consolelog-item-message">Testing SequenceTranslator package</pre></div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at /home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/remote.test.ts:66:11
+    at Generator.next (&lt;anonymous&gt;)
+    at fulfilled (/home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/remote.test.ts:28:58)
+    at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Test result : Success : 2 : SequenceTranslator.sequence-translator.usCfCfUfGfAf : OK
+Test result : Success : 1 : SequenceTranslator.sequence-translator.usAfsusgsgsg : OK
+Test result : Success : 0 : SequenceTranslator.sequence-translator.UfUfUfsCfsuacg : OK
+Test result : Success : 0 : SequenceTranslator.sequence-translator.susususauasu : OK
+Test result : Success : 0 : SequenceTranslator.sequence-translator.CfGfCfsGfsCf : OK
+Test result : Success : 1 : SequenceTranslator.sequence-translator.acacacsacsac : OK
+Test result : Success : 0 : SequenceTranslator.sequence-translator.cccgggusug : OK
+Test result : Success : 0 : SequenceTranslator.sequence-translator.UfAfCfGfGfCfAfUf : OK
+Test result : Success : 0 : SequenceTranslator.sequence-translator.(invabasic)cuCfuUfsc : OK
+Test result : Success : 0 : SequenceTranslator.sequence-translator.(invabasic)usAfsucuCfuUfAfgcugUfgCfacususu : OK
+Test result : Success : 0 : SequenceTranslator.sequence-translator.(invabasic)asacgGfuGfCfAfacucuauuca : OK
+</pre></div></div></div></div></body></html>