@datagrok/sequence-translator 0.0.9 → 0.0.12

package/package.json

@@ -1,12 +1,17 @@
 {
   "name": "@datagrok/sequence-translator",
   "friendlyName": "Sequence Translator",
-  "version": "0.0.9",
+  "version": "0.0.12",
   "description": "",
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/datagrok-ai/public.git",
+    "directory": "packages/SequenceTranslator"
+  },
   "dependencies": {
     "@datagrok-libraries/utils": "^0.1.0",
     "@types/react": "latest",
-    "datagrok-api": ">0.94.10",
+    "datagrok-api": "^0.151.0",
     "datagrok-tools": "^4.1.2",
     "npm": "^7.11.2",
     "save-svg-as-png": "^1.4.17",
@@ -28,6 +33,9 @@
     "test-dev": "set HOST=dev && jest",
     "test-local": "set HOST=localhost && jest"
   },
+  "sources": [
+    "css/style.css"
+  ],
   "devDependencies": {
     "@typescript-eslint/eslint-plugin": "^4.29.1",
     "@typescript-eslint/parser": "^4.29.1",
@@ -36,10 +44,10 @@
     "eslint-config-google": "^0.14.0",
     "webpack": "^5.31.0",
     "webpack-cli": "^4.6.0",
-    "@types/jest": "latest",
-    "jest": "latest",
-    "jest-html-reporter": "latest",
-    "puppeteer": "^13.1.2",
-    "ts-jest": "^27.1.2"
+    "jest-html-reporter": "^3.5.0",
+    "jest": "^27.0.0",
+    "@types/jest": "^27.0.0",
+    "ts-jest": "^27.0.0",
+    "puppeteer": "latest"
   }
 }

package/src/package.ts

@@ -7,7 +7,7 @@ import $ from 'cash-dom';
 import {defineAxolabsPattern} from './defineAxolabsPattern';
 import {saveSenseAntiSense} from './structures-works/save-sense-antisense';
 import {sequenceToSmiles, sequenceToMolV3000} from './structures-works/from-monomers';
-import {convertSequence, undefinedInputSequence} from './structures-works/sequence-codes-tools';
+import {convertSequence, undefinedInputSequence, isValidSequence} from './structures-works/sequence-codes-tools';
 import {map, COL_NAMES, MODIFICATIONS} from './structures-works/map';
 import {SALTS_CSV} from './salts';
 import {USERS_CSV} from './users';
@@ -17,7 +17,7 @@ import {IDPS} from './IDPs';
 
 export const _package = new DG.Package();
 
-const defaultInput = 'AGGTCCTCTTGACTTAGGCC';
+const defaultInput = 'fAmCmGmAmCpsmU';
 const sequenceWasCopied = 'Copied';
 const tooltipSequence = 'Copy sequence';
 
@@ -35,29 +35,31 @@ export function sequenceTranslator(): void {
     const pi = DG.TaskBarProgressIndicator.create('Rendering table and molecule...');
     let errorsExist = false;
     try {
-      const outputSequenceObj = convertSequence(sequence);
+      sequence = sequence.replace(/\s/g, '');
+      const output = isValidSequence(sequence);
+      const outputSequenceObj = convertSequence(sequence, output);
       const tableRows = [];
 
       for (const key of Object.keys(outputSequenceObj).slice(1)) {
-        const indexOfFirstNotValidCharacter = ('indexOfFirstNotValidCharacter' in outputSequenceObj) ?
-          JSON.parse(outputSequenceObj.indexOfFirstNotValidCharacter!).indexOfFirstNotValidCharacter :
+        const indexOfFirstNotValidChar = ('indexOfFirstNotValidChar' in outputSequenceObj) ?
+          JSON.parse(outputSequenceObj.indexOfFirstNotValidChar!).indexOfFirstNotValidChar :
           -1;
-        if ('indexOfFirstNotValidCharacter' in outputSequenceObj) {
-          const indexOfFirstNotValidCharacter = ('indexOfFirstNotValidCharacter' in outputSequenceObj) ?
-            JSON.parse(outputSequenceObj.indexOfFirstNotValidCharacter!).indexOfFirstNotValidCharacter :
+        if ('indexOfFirstNotValidChar' in outputSequenceObj) {
+          const indexOfFirstNotValidChar = ('indexOfFirstNotValidChar' in outputSequenceObj) ?
+            JSON.parse(outputSequenceObj.indexOfFirstNotValidChar!).indexOfFirstNotValidChar :
             -1;
-          if (indexOfFirstNotValidCharacter != -1)
+          if (indexOfFirstNotValidChar != -1)
             errorsExist = true;
         }
 
         tableRows.push({
           'key': key,
-          'value': ('indexOfFirstNotValidCharacter' in outputSequenceObj) ?
+          'value': ('indexOfFirstNotValidChar' in outputSequenceObj) ?
             ui.divH([
-              ui.divText(sequence.slice(0, indexOfFirstNotValidCharacter), {style: {color: 'grey'}}),
+              ui.divText(sequence.slice(0, indexOfFirstNotValidChar), {style: {color: 'grey'}}),
               ui.tooltip.bind(
-                ui.divText(sequence.slice(indexOfFirstNotValidCharacter), {style: {color: 'red'}}),
-                'Expected format: ' + JSON.parse(outputSequenceObj.indexOfFirstNotValidCharacter!).expectedSynthesizer +
+                ui.divText(sequence.slice(indexOfFirstNotValidChar), {style: {color: 'red'}}),
+                'Expected format: ' + JSON.parse(outputSequenceObj.indexOfFirstNotValidChar!).synthesizer +
                 '. See tables with valid codes on the right',
               ),
             ]) : //@ts-ignore
@@ -67,13 +69,12 @@ export function sequenceTranslator(): void {
       }
 
       if (errorsExist) {
-        const expectedSynthesizer = JSON.parse(outputSequenceObj.indexOfFirstNotValidCharacter!)
-          .expectedSynthesizer.slice(0, -6);
+        const synthesizer = JSON.parse(outputSequenceObj.indexOfFirstNotValidChar!).synthesizer.slice(0, -6);
         asoGapmersGrid.onCellPrepare(function(gc) {
-          gc.style.backColor = (gc.gridColumn.name == expectedSynthesizer) ? 0xFFF00000 : 0xFFFFFFFF;
+          gc.style.backColor = (gc.gridColumn.name == synthesizer) ? 0xFFF00000 : 0xFFFFFFFF;
         });
         omeAndFluoroGrid.onCellPrepare(function(gc) {
-          gc.style.backColor = (gc.gridColumn.name == expectedSynthesizer) ? 0xFFF00000 : 0xFFFFFFFF;
+          gc.style.backColor = (gc.gridColumn.name == synthesizer) ? 0xFFF00000 : 0xFFFFFFFF;
         });
         switchInput.enabled = true;
       } else {
@@ -85,7 +86,7 @@ export function sequenceTranslator(): void {
         ui.div([
           DG.HtmlTable.create(tableRows, (item: { key: string; value: string; }) =>
             [item.key, item.value], ['Code', 'Sequence']).root,
-        ], 'table'),
+        ]),
       );
       semTypeOfInputSequence.textContent = 'Detected input type: ' + outputSequenceObj.type;
 
@@ -115,7 +116,7 @@ export function sequenceTranslator(): void {
 
   const semTypeOfInputSequence = ui.divText('');
   const moleculeSvgDiv = ui.block([]);
-  const outputTableDiv = ui.div([], 'table');
+  const outputTableDiv = ui.div([]);
   const inputSequenceField = ui.textInput('', defaultInput, (sequence: string) => updateTableAndMolecule(sequence));
 
   const asoDf = DG.DataFrame.fromObjects([
@@ -191,7 +192,7 @@ export function sequenceTranslator(): void {
               ui.div([
                 inputSequenceField.root,
               ], 'input-base'),
-            ], 'sequenceInput'),
+            ], 'inputSequence'),
             semTypeOfInputSequence,
             ui.block([
               ui.h1('Output'),
@@ -233,18 +234,6 @@ export function sequenceTranslator(): void {
   tabControl.onTabChanged.subscribe((_) =>
     v.setRibbonPanels([(tabControl.currentPane.name == 'MAIN') ? topPanel : []]));
   v.setRibbonPanels([topPanel]);
-
-  $('.sequence')
-    .children().css('padding', '5px 0');
-  $('.sequenceInput .input-base')
-    .css('margin', '0');
-  $('.sequenceInput textarea')
-    .css('resize', 'none')
-    .css('min-height', '50px')
-    .css('width', '100%')
-    .attr('spellcheck', 'false');
-  $('.sequenceInput select')
-    .css('width', '100%');
 }
 
 async function saveTableAsSdFile(table: DG.DataFrame) {
@@ -324,6 +313,7 @@ export function oligoSdFile(table: DG.DataFrame) {
       return grok.shell.error('Columns already exist!');
 
     const sequence = t.col(COL_NAMES.SEQUENCE)!;
+    const salt = t.col(COL_NAMES.SALT)!;
     const equivalents = t.col(COL_NAMES.EQUIVALENTS)!;
 
     t.columns.addNewString(COL_NAMES.COMPOUND_NAME).init((i: number) => sequence.get(i));
@@ -331,11 +321,13 @@ export function oligoSdFile(table: DG.DataFrame) {
       sequence.getString(i) + '; duplex of SS: ' + sequence.getString(i - 2) + ' and AS: ' + sequence.getString(i - 1) :
       sequence.getString(i),
     );
+    const molWeightCol = saltsDf.col('MOLWEIGHT')!;
+    const saltNamesList = saltsDf.col('DISPLAY')!.toList();
     t.columns.addNewFloat(COL_NAMES.CPD_MW)
       .init((i: number) => molecularWeight(sequence.get(i), weightsObj));
-    const mwCol = t.col(COL_NAMES.CPD_MW)!;
     t.columns.addNewFloat(COL_NAMES.SALT_MASS).init((i: number) => {
-      const mw = mwCol.get(i);
+      const saltRowIndex = saltNamesList.indexOf(salt.get(i));
+      const mw = molWeightCol.get(saltRowIndex);
       return mw * equivalents.get(i);
     });
     t.columns.addNewCalculated(COL_NAMES.BATCH_MW,
@@ -367,7 +359,7 @@ export function oligoSdFile(table: DG.DataFrame) {
 
       view.table!.col(COL_NAMES.TYPE)!.setTag(DG.TAGS.CHOICES, '["AS", "SS", "Duplex"]');
       view.table!.col(COL_NAMES.OWNER)!.setTag(DG.TAGS.CHOICES, stringifyItems(usersDf.columns.byIndex(0).toList()));
-      view.table!.col(COL_NAMES.SALT)!.setTag(DG.TAGS.CHOICES, stringifyItems(saltsDf.columns.byIndex(1).toList()));
+      view.table!.col(COL_NAMES.SALT)!.setTag(DG.TAGS.CHOICES, stringifyItems(saltsDf.columns.byIndex(0).toList()));
       view.table!.col(COL_NAMES.SOURCE)!.setTag(DG.TAGS.CHOICES, stringifyItems(sourcesDf.columns.byIndex(0).toList()));
       view.table!.col(COL_NAMES.ICD)!.setTag(DG.TAGS.CHOICES, stringifyItems(icdsDf.columns.byIndex(0).toList()));
       view.table!.col(COL_NAMES.IDP)!.setTag(DG.TAGS.CHOICES, stringifyItems(idpsDf.columns.byIndex(0).toList()));

package/src/salts.ts

@@ -1,2 +1,2 @@
-export const SALTS_CSV = `CHARGE,DISPLAY,MOLWEIGHT
-  ,no Data Added,100`;
+export const SALTS_CSV = `DISPLAY,MOLWEIGHT
+no Data Added,100`;

package/src/structures-works/from-monomers.ts

@@ -92,9 +92,9 @@ function getObjectWithCodesAndSmiles(sequence: string) {
   }
   // TODO: create object based from synthesizer type to avoid key(codes) duplicates
   const output = isValidSequence(sequence);
-  if (output.expectedSynthesizer == SYNTHESIZERS.MERMADE_12)
+  if (output.synthesizer == SYNTHESIZERS.MERMADE_12)
     obj['g'] = map[SYNTHESIZERS.MERMADE_12][TECHNOLOGIES.SI_RNA]['g'].SMILES;
-  else if (output.expectedSynthesizer == SYNTHESIZERS.AXOLABS)
+  else if (output.synthesizer == SYNTHESIZERS.AXOLABS)
     obj['g'] = map[SYNTHESIZERS.AXOLABS][TECHNOLOGIES.SI_RNA]['g'].SMILES;
   return obj;
 }

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

@@ -95,7 +95,7 @@ export function getNucleotidesMol(smilesCodes: string[], oclRender: boolean = fa
 
 export function linkV3000(molBlocks: string[], twoMolecules: boolean = false, oclRender: boolean = false) {
   let macroMolBlock = '\nDatagrok macromolecule handler\n\n';
-  macroMolBlock += '  0  0  0  0  0  0              0 V3000\n';
+  macroMolBlock += '  0  0  0  0  0  0            999 V3000\n';
   macroMolBlock += 'M  V30 BEGIN CTAB\n';
   let atomBlock = '';
   let bondBlock = '';
@@ -110,6 +110,8 @@ export function linkV3000(molBlocks: string[], twoMolecules: boolean = false, oc
     molBlocks[1] = invertNucleotidesV3000(molBlocks[1]);
 
   for (let i = 0; i < molBlocks.length; i++) {
+    molBlocks[i] = molBlocks[i].replaceAll('(-\nM  V30 ', '(')
+      .replaceAll('-\nM  V30 ', '').replaceAll(' )', ')');
     const numbers = extractAtomsBondsNumbersV3000(molBlocks[i]);
     const coordinates = extractAtomDataV3000(molBlocks[i]);
     let indexAtoms = molBlocks[i].indexOf('M  V30 BEGIN ATOM'); // V3000 index for atoms coordinates
@@ -184,7 +186,7 @@ export function linkV3000(molBlocks: string[], twoMolecules: boolean = false, oc
     while (indexCollection != -1) {
       indexCollection += 28;
       const collectionEnd = molBlocks[i].indexOf(')', indexCollection);
-      const collectionEntries = molBlocks[i].substring(indexCollection, collectionEnd).split(' ');
+      const collectionEntries = molBlocks[i].substring(indexCollection, collectionEnd).split(' ').slice(1);
       collectionEntries.forEach((e) => {
         collection.push(parseInt(e) + natom);
       });
@@ -209,13 +211,15 @@ export function linkV3000(molBlocks: string[], twoMolecules: boolean = false, oc
 
     collectionBlock += ')\n';
   } else {
+    collectionBlock += 'M  V30 MDLV30/STEABS ATOMS=(' + collection.length + ' -\n';
     for (let i = 0; i < collNumber; i++) {
-      collectionBlock += 'M  V30 MDLV30/STEABS ATOMS=(';
+      collectionBlock += 'M  V30 ';
       const entriesCurrent = i + 1 == collNumber ? collection.length - (collNumber - 1)*entries : entries;
-      for (let j = 0; j < entriesCurrent; j++)
-        collectionBlock += (j + 1 == entriesCurrent) ? collection[entries*i + j] : collection[entries*i + j] + ' ';
-
-      collectionBlock += ')\n';
+      for (let j = 0; j < entriesCurrent; j++) {
+        collectionBlock += (j + 1 == entriesCurrent) ?
+          (i == collNumber - 1 ? collection[entries*i + j] + ')\n' : collection[entries*i + j] + ' -\n') :
+          collection[entries*i + j] + ' ';
+      }
     }
   }
 

package/src/structures-works/sequence-codes-tools.ts

@@ -1,3 +1,6 @@
+import * as grok from 'datagrok-api/grok';
+import * as ui from 'datagrok-api/ui';
+// import * as DG from 'datagrok-api/dg';
 import {map, SYNTHESIZERS, TECHNOLOGIES, MODIFICATIONS} from './map';
 import {asoGapmersNucleotidesToBioSpring, asoGapmersNucleotidesToGcrs,
   asoGapmersBioSpringToNucleotides, asoGapmersBioSpringToGcrs, asoGapmersGcrsToNucleotides,
@@ -11,97 +14,112 @@ const noTranslationTableAvailable = 'No translation table available';
 export const undefinedInputSequence = 'Type of input sequence is undefined';
 
 export function isValidSequence(sequence: string): {
-  indexOfFirstNotValidCharacter: number,
-  expectedSynthesizer: string | null,
-  expectedTechnology: string | null
+  indexOfFirstNotValidChar: number,
+  synthesizer: string | null,
+  technology: string | null
 } {
-  const possibleSynthesizers = getListOfPossibleSynthesizersByFirstMatchedCode(sequence);
-  if (possibleSynthesizers.length == 0)
-    return {indexOfFirstNotValidCharacter: 0, expectedSynthesizer: null, expectedTechnology: null};
-
-  let outputIndices = Array(possibleSynthesizers.length).fill(0);
+  let possibleSynthesizers = getListOfPossibleSynthesizersByFirstMatchedCode(sequence);
+
+  if (possibleSynthesizers.length > 1) {
+    const synthesizer = ui.choiceInput('Choose synthesizer from list: ', possibleSynthesizers[0], possibleSynthesizers);
+    ui.dialog('Choose Synthesizer')
+      .add(ui.panel([synthesizer.root], {style: {fontWeight: 'bold'}}))
+      .onOK(() => possibleSynthesizers = [synthesizer.value])
+      .onCancel(() => {
+        possibleSynthesizers = [possibleSynthesizers[0]];
+        grok.shell.warning('Input sequence is expected to be in format ' + possibleSynthesizers[0]);
+      })
+      .show();
+  } else if (possibleSynthesizers.length == 0)
+    return {indexOfFirstNotValidChar: 0, synthesizer: null, technology: null};
+
+  let outputIndex = 0;
 
   const firstUniqueCharacters = ['r', 'd'];
   const nucleotides = ['A', 'U', 'T', 'C', 'G'];
 
-  possibleSynthesizers.forEach((synthesizer, synthesizerIndex) => {
+  possibleSynthesizers.forEach((synthesizer) => {
     const codes = getAllCodesOfSynthesizer(synthesizer);
-    while (outputIndices[synthesizerIndex] < sequence.length) {
-      const matchedCode = codes
-        .find((c) => c == sequence.slice(outputIndices[synthesizerIndex], outputIndices[synthesizerIndex] + c.length));
+    while (outputIndex < sequence.length) {
+      const matchedCode = codes.find((c) => c == sequence.slice(outputIndex, outputIndex + c.length));
 
       if (matchedCode == null)
         break;
 
       if ( // for mistake pattern 'rAA'
-        outputIndices[synthesizerIndex] > 1 &&
-        nucleotides.includes(sequence[outputIndices[synthesizerIndex]]) &&
-        firstUniqueCharacters.includes(sequence[outputIndices[synthesizerIndex] - 2])
+        outputIndex > 1 &&
+        nucleotides.includes(sequence[outputIndex]) &&
+        firstUniqueCharacters.includes(sequence[outputIndex - 2])
       ) break;
 
       if ( // for mistake pattern 'ArA'
-        firstUniqueCharacters.includes(sequence[outputIndices[synthesizerIndex] + 1]) &&
-        nucleotides.includes(sequence[outputIndices[synthesizerIndex]])
+        firstUniqueCharacters.includes(sequence[outputIndex + 1]) &&
+        nucleotides.includes(sequence[outputIndex])
       ) {
-        outputIndices[synthesizerIndex]++;
+        outputIndex++;
         break;
       }
 
-      outputIndices[synthesizerIndex] += matchedCode.length;
+      outputIndex += matchedCode.length;
     }
   });
 
-  const indexOfExpectedSythesizer = Math.max(...outputIndices);
-  const indexOfFirstNotValidCharacter = (indexOfExpectedSythesizer == sequence.length) ? -1 : indexOfExpectedSythesizer;
-  const expectedSynthesizer = possibleSynthesizers[outputIndices.indexOf(indexOfExpectedSythesizer)];
-  if (indexOfFirstNotValidCharacter != -1) {
+  const indexOfFirstNotValidChar = (outputIndex == sequence.length) ? -1 : outputIndex;
+  if (indexOfFirstNotValidChar != -1) {
     return {
-      indexOfFirstNotValidCharacter: indexOfFirstNotValidCharacter,
-      expectedSynthesizer: expectedSynthesizer,
-      expectedTechnology: null,
+      indexOfFirstNotValidChar: indexOfFirstNotValidChar,
+      synthesizer: possibleSynthesizers[0],
+      technology: null,
     };
   }
 
-  const possibleTechnologies = getListOfPossibleTechnologiesByFirstMatchedCode(sequence, expectedSynthesizer);
-  if (possibleTechnologies.length == 0)
-    return {indexOfFirstNotValidCharacter: 0, expectedSynthesizer: null, expectedTechnology: null};
+  let possibleTechnologies = getListOfPossibleTechnologiesByFirstMatchedCode(sequence, possibleSynthesizers[0]);
+
+  if (possibleTechnologies.length > 1) {
+    const technology = ui.choiceInput('Choose technology from list: ', possibleTechnologies[0], possibleTechnologies);
+    ui.dialog('Choose Technology')
+      .add(ui.panel([technology.root], {style: {fontWeight: 'bold'}}))
+      .onOK(() => possibleTechnologies = [technology.value])
+      .onCancel(() => {
+        possibleTechnologies = [possibleTechnologies[0]];
+        grok.shell.warning('Input sequence is expected to be in format ' + possibleTechnologies[0]);
+      })
+      .show();
+  } else if (possibleTechnologies.length == 0)
+    return {indexOfFirstNotValidChar: 0, synthesizer: null, technology: null};
 
-  outputIndices = Array(possibleTechnologies.length).fill(0);
+  outputIndex = 0;
 
-  possibleTechnologies.forEach((technology: string, technologyIndex: number) => {
-    const codes = Object.keys(map[expectedSynthesizer][technology]);
-    while (outputIndices[technologyIndex] < sequence.length) {
-      const matchedCode = codes
-        .find((c) => c == sequence.slice(outputIndices[technologyIndex], outputIndices[technologyIndex] + c.length));
+  possibleTechnologies.forEach((technology: string) => {
+    const codes = Object.keys(map[possibleSynthesizers[0]][technology]);
+    while (outputIndex < sequence.length) {
+      const matchedCode = codes.find((c) => c == sequence.slice(outputIndex, outputIndex + c.length));
 
       if (matchedCode == null)
         break;
 
       if ( // for mistake pattern 'rAA'
-        outputIndices[technologyIndex] > 1 &&
-        nucleotides.includes(sequence[outputIndices[technologyIndex]]) &&
-        firstUniqueCharacters.includes(sequence[outputIndices[technologyIndex] - 2])
+        outputIndex > 1 &&
+        nucleotides.includes(sequence[outputIndex]) &&
+        firstUniqueCharacters.includes(sequence[outputIndex - 2])
       ) break;
 
       if ( // for mistake pattern 'ArA'
-        firstUniqueCharacters.includes(sequence[outputIndices[technologyIndex] + 1]) &&
-        nucleotides.includes(sequence[outputIndices[technologyIndex]])
+        firstUniqueCharacters.includes(sequence[outputIndex + 1]) &&
+        nucleotides.includes(sequence[outputIndex])
       ) {
-        outputIndices[technologyIndex]++;
+        outputIndex++;
         break;
       }
 
-      outputIndices[technologyIndex] += matchedCode.length;
+      outputIndex += matchedCode.length;
     }
   });
 
-  const indexOfExpectedTechnology = Math.max(...outputIndices);
-  const expectedTechnology = possibleTechnologies[outputIndices.indexOf(indexOfExpectedTechnology)];
-
   return {
-    indexOfFirstNotValidCharacter: indexOfFirstNotValidCharacter,
-    expectedSynthesizer: expectedSynthesizer,
-    expectedTechnology: expectedTechnology,
+    indexOfFirstNotValidChar: indexOfFirstNotValidChar,
+    synthesizer: possibleSynthesizers[0],
+    technology: possibleTechnologies[outputIndex],
   };
 }
 
@@ -140,93 +158,91 @@ function getListOfPossibleTechnologiesByFirstMatchedCode(sequence: string, synth
   return technologies;
 }
 
-export function convertSequence(text: string) {
-  text = text.replace(/\s/g, '');
-  const seq = text;
-  const output = isValidSequence(seq);
-  if (output.indexOfFirstNotValidCharacter != -1) {
+export function convertSequence(sequence: string, output: {
+  indexOfFirstNotValidChar: number, synthesizer: string | null, technology: string | null}) {
+  if (output.indexOfFirstNotValidChar != -1) {
     return {
       // type: '',
-      indexOfFirstNotValidCharacter: JSON.stringify(output),
+      indexOfFirstNotValidChar: JSON.stringify(output),
       Error: undefinedInputSequence,
     };
   }
-  if (output.expectedSynthesizer == SYNTHESIZERS.RAW_NUCLEOTIDES && output.expectedTechnology == TECHNOLOGIES.DNA) {
+  if (output.synthesizer == SYNTHESIZERS.RAW_NUCLEOTIDES && output.technology == TECHNOLOGIES.DNA) {
     return {
       type: SYNTHESIZERS.RAW_NUCLEOTIDES + ' ' + TECHNOLOGIES.DNA,
-      Nucleotides: seq,
-      BioSpring: asoGapmersNucleotidesToBioSpring(seq),
-      GCRS: asoGapmersNucleotidesToGcrs(seq),
+      Nucleotides: sequence,
+      BioSpring: asoGapmersNucleotidesToBioSpring(sequence),
+      GCRS: asoGapmersNucleotidesToGcrs(sequence),
     };
   }
-  if (output.expectedSynthesizer == SYNTHESIZERS.BIOSPRING && output.expectedTechnology == TECHNOLOGIES.ASO_GAPMERS) {
+  if (output.synthesizer == SYNTHESIZERS.BIOSPRING && output.technology == TECHNOLOGIES.ASO_GAPMERS) {
     return {
       type: SYNTHESIZERS.BIOSPRING + ' ' + TECHNOLOGIES.ASO_GAPMERS,
-      Nucleotides: asoGapmersBioSpringToNucleotides(seq),
-      BioSpring: seq,
-      GCRS: asoGapmersBioSpringToGcrs(seq),
+      Nucleotides: asoGapmersBioSpringToNucleotides(sequence),
+      BioSpring: sequence,
+      GCRS: asoGapmersBioSpringToGcrs(sequence),
     };
   }
-  if (output.expectedSynthesizer == SYNTHESIZERS.GCRS && output.expectedTechnology == TECHNOLOGIES.ASO_GAPMERS) {
+  if (output.synthesizer == SYNTHESIZERS.GCRS && output.technology == TECHNOLOGIES.ASO_GAPMERS) {
     return {
       type: SYNTHESIZERS.GCRS + ' ' + TECHNOLOGIES.ASO_GAPMERS,
-      Nucleotides: asoGapmersGcrsToNucleotides(seq),
-      BioSpring: asoGapmersGcrsToBioSpring(seq),
-      Mermade12: gcrsToMermade12(seq),
-      GCRS: seq,
+      Nucleotides: asoGapmersGcrsToNucleotides(sequence),
+      BioSpring: asoGapmersGcrsToBioSpring(sequence),
+      Mermade12: gcrsToMermade12(sequence),
+      GCRS: sequence,
     };
   }
-  if (output.expectedSynthesizer == SYNTHESIZERS.RAW_NUCLEOTIDES && output.expectedTechnology == TECHNOLOGIES.RNA) {
+  if (output.synthesizer == SYNTHESIZERS.RAW_NUCLEOTIDES && output.technology == TECHNOLOGIES.RNA) {
     return {
       type: SYNTHESIZERS.RAW_NUCLEOTIDES + ' ' + TECHNOLOGIES.RNA,
-      Nucleotides: seq,
-      BioSpring: siRnaNucleotideToBioSpringSenseStrand(seq),
-      Axolabs: siRnaNucleotideToAxolabsSenseStrand(seq),
-      GCRS: siRnaNucleotidesToGcrs(seq),
+      Nucleotides: sequence,
+      BioSpring: siRnaNucleotideToBioSpringSenseStrand(sequence),
+      Axolabs: siRnaNucleotideToAxolabsSenseStrand(sequence),
+      GCRS: siRnaNucleotidesToGcrs(sequence),
     };
   }
-  if (output.expectedSynthesizer == SYNTHESIZERS.BIOSPRING && output.expectedTechnology == TECHNOLOGIES.SI_RNA) {
+  if (output.synthesizer == SYNTHESIZERS.BIOSPRING && output.technology == TECHNOLOGIES.SI_RNA) {
     return {
       type: SYNTHESIZERS.BIOSPRING + ' ' + TECHNOLOGIES.SI_RNA,
-      Nucleotides: siRnaBioSpringToNucleotides(seq),
-      BioSpring: seq,
-      Axolabs: siRnaBioSpringToAxolabs(seq),
-      GCRS: siRnaBioSpringToGcrs(seq),
+      Nucleotides: siRnaBioSpringToNucleotides(sequence),
+      BioSpring: sequence,
+      Axolabs: siRnaBioSpringToAxolabs(sequence),
+      GCRS: siRnaBioSpringToGcrs(sequence),
     };
   }
-  if (output.expectedSynthesizer == SYNTHESIZERS.AXOLABS && output.expectedTechnology == TECHNOLOGIES.SI_RNA) {
+  if (output.synthesizer == SYNTHESIZERS.AXOLABS && output.technology == TECHNOLOGIES.SI_RNA) {
     return {
       type: SYNTHESIZERS.AXOLABS + ' ' + TECHNOLOGIES.SI_RNA,
-      Nucleotides: siRnaAxolabsToNucleotides(seq),
-      BioSpring: siRnaAxolabsToBioSpring(seq),
-      Axolabs: seq,
-      GCRS: siRnaAxolabsToGcrs(seq),
+      Nucleotides: siRnaAxolabsToNucleotides(sequence),
+      BioSpring: siRnaAxolabsToBioSpring(sequence),
+      Axolabs: sequence,
+      GCRS: siRnaAxolabsToGcrs(sequence),
     };
   }
-  if (output.expectedSynthesizer == SYNTHESIZERS.GCRS && output.expectedTechnology == TECHNOLOGIES.SI_RNA) {
+  if (output.synthesizer == SYNTHESIZERS.GCRS && output.technology == TECHNOLOGIES.SI_RNA) {
     return {
       type: SYNTHESIZERS.GCRS + ' ' + TECHNOLOGIES.SI_RNA,
-      Nucleotides: siRnaGcrsToNucleotides(seq),
-      BioSpring: siRnaGcrsToBioSpring(seq),
-      Axolabs: siRnaGcrsToAxolabs(seq),
-      MM12: gcrsToMermade12(seq),
-      GCRS: seq,
+      Nucleotides: siRnaGcrsToNucleotides(sequence),
+      BioSpring: siRnaGcrsToBioSpring(sequence),
+      Axolabs: siRnaGcrsToAxolabs(sequence),
+      MM12: gcrsToMermade12(sequence),
+      GCRS: sequence,
     };
   }
-  if (output.expectedSynthesizer == SYNTHESIZERS.GCRS) {
+  if (output.synthesizer == SYNTHESIZERS.GCRS) {
     return {
       type: SYNTHESIZERS.GCRS,
-      Nucleotides: gcrsToNucleotides(seq),
-      GCRS: seq,
-      Mermade12: gcrsToMermade12(seq),
+      Nucleotides: gcrsToNucleotides(sequence),
+      GCRS: sequence,
+      Mermade12: gcrsToMermade12(sequence),
     };
   }
-  if (output.expectedSynthesizer == SYNTHESIZERS.MERMADE_12) {
+  if (output.synthesizer == SYNTHESIZERS.MERMADE_12) {
     return {
       type: SYNTHESIZERS.MERMADE_12,
       Nucleotides: noTranslationTableAvailable,
       GCRS: noTranslationTableAvailable,
-      Mermade12: seq,
+      Mermade12: sequence,
     };
   }
   return {

package/{test-SequenceTranslator-2e08c8e54bde-1367d435.html → test-SequenceTranslator-c2bbc2b235db-afc0e1c5.html}

@@ -1,4 +1,4 @@
-<html><head><meta charset="utf-8"/><title>SequenceTranslator Test Report. Datagrok version datagrok/datagrok:latest SHA=2e08c8e54bde. Commit 1367d435.</title><style type="text/css">html,
+<html><head><meta charset="utf-8"/><title>SequenceTranslator Test Report. Datagrok version datagrok/datagrok:latest SHA=c2bbc2b235db. Commit afc0e1c5.</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">SequenceTranslator Test Report. Datagrok version datagrok/datagrok:latest SHA=2e08c8e54bde. Commit 1367d435.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-04-20 13:02:23</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">18.061s</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">0.524s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: Evaluation failed: Unable to find JS function "test"
+</style></head><body><div id="jesthtml-content"><header><h1 id="title">SequenceTranslator Test Report. Datagrok version datagrok/datagrok:latest SHA=c2bbc2b235db. Commit afc0e1c5.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-05-13 15:45:08</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">26.07s</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">2.12s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: Evaluation failed: Unable to find JS function "test"
     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)