@datagrok/helm 2.1.5 → 2.1.7

package/package.json

@@ -1,14 +1,14 @@
 {
   "name": "@datagrok/helm",
   "friendlyName": "Helm",
-  "version": "2.1.5",
+  "version": "2.1.7",
   "author": {
     "name": "Oleksandra Serhiienko",
     "email": "oserhiienko@datagrok.ai"
   },
-  "description": "",
+  "description": "Provides support for HELM notation (importing, detecting, rendering, conversion). [Learn more](https://github.com/datagrok-ai/public/blob/master/packages/Helm/README.md)",
   "dependencies": {
-    "@datagrok-libraries/bio": "^5.22.0",
+    "@datagrok-libraries/bio": "^5.22.1",
     "@datagrok-libraries/utils": "^1.19.1",
     "cash-dom": "^8.1.1",
     "datagrok-api": "^1.10.2",

package/src/package.ts

@@ -10,6 +10,7 @@ import {IMonomerLib, Monomer} from '@datagrok-libraries/bio/src/types';
 import {NotationConverter} from '@datagrok-libraries/bio/src/utils/notation-converter';
 import {findMonomers} from './utils';
 import {errorToConsole} from '@datagrok-libraries/utils/src/to-console';
+import { NOTATION } from '@datagrok-libraries/bio/src/utils/macromolecule';
 
 export const _package = new DG.Package();
 let monomerLib: IMonomerLib | null = null;
@@ -93,16 +94,23 @@ export function helmCellRenderer(): HelmCellRenderer {
   return new HelmCellRenderer();
 }
 
+function checkMonomersAndOpenWebEditor(cell?: DG.Cell, value?: string, units?: string) {
+  const cellValue = typeof units === 'undefined' ? cell.value : value;
+  const monomers = findMonomers(cellValue);
+  if (monomers.size == 0) 
+    webEditor(cell, value, units);
+  else
+    grok.shell.warning(`Monomers ${Array.from(monomers).join(', ')} are absent! <br/>` +
+    `Please, upload the monomer library! <br/>` +
+    `<a href="https://datagrok.ai/help/domains/bio/macromolecules" target="_blank">Learn more</a>`);
+}
+
 //tags: cellEditor
 //description: Macromolecule  
 //input: grid_cell cell
+//meta.columnTags: quality=Macromolecule, units=helm
 export function editMoleculeCell(cell: DG.GridCell): void {
-  const monomers = findMonomers(cell.cell.value);
-  if (cell.gridColumn.column.tags[DG.TAGS.UNITS] === 'helm')
-    if (monomers.size == 0) 
-      webEditor(cell);
-    else
-      grok.shell.warning(`Monomers ${Array.from(monomers).join(', ')} are absent!`);
+  checkMonomersAndOpenWebEditor(cell.cell, undefined, undefined);
 }
 
 //name: Open Helm Web Editor
@@ -111,13 +119,13 @@ export function editMoleculeCell(cell: DG.GridCell): void {
 //input: string mol { semType: Macromolecule }
 export function openEditor(mol: string): void {
   let df = grok.shell.tv.grid.dataFrame;
-  let converter = new NotationConverter(df.columns.bySemType('Macromolecule'));
-  const resStr = converter.convertStringToHelm(mol, '/');
-  const monomers = findMonomers(resStr);
-  if (monomers.size == 0) 
-    webEditor(undefined, resStr);
-  else
-    grok.shell.warning(`Monomers ${Array.from(monomers).join(', ')} are absent!`);
+  let col = df.columns.bySemType('Macromolecule');
+  const colUnits = col.getTag(DG.TAGS.UNITS);
+  if (colUnits === NOTATION.HELM) 
+    checkMonomersAndOpenWebEditor(df.currentCell, undefined, undefined);
+  let converter = new NotationConverter(col);
+  const resStr = converter.convertStringToHelm(mol, '/');   
+  checkMonomersAndOpenWebEditor(df.currentCell, resStr, col.getTag(DG.TAGS.UNITS));
 }
 
 //name: Properties
@@ -146,8 +154,10 @@ export async function propertiesPanel(helmString: string) {
   );
 }
 
-function webEditor(cell?: DG.GridCell, value?: string) {
+function webEditor(cell?: DG.Cell, value?: string, units?: string) {
   let view = ui.div();
+  let df = grok.shell.tv.grid.dataFrame;
+  let converter = new NotationConverter(df.columns.bySemType('Macromolecule'));
   org.helm.webeditor.MolViewer.molscale = 0.8;
   let app = new scil.helm.App(view, {
     showabout: false,
@@ -172,8 +182,8 @@ function webEditor(cell?: DG.GridCell, value?: string) {
   app.structureview.resize(sizes.rightwidth, sizes.bottomheight + app.toolbarheight);
   app.mex.resize(sizes.topheight - 80);
   setTimeout(function() {
-    if (typeof cell !== 'undefined') {
-      app.canvas.helm.setSequence(cell.cell.value, 'HELM');
+    if (typeof units === 'undefined') {
+      app.canvas.helm.setSequence(cell.value, 'HELM');
     } else {
       app.canvas.helm.setSequence(value, 'HELM');
     }
@@ -182,59 +192,16 @@ function webEditor(cell?: DG.GridCell, value?: string) {
   ui.dialog({showHeader: false, showFooter: true})
     .add(view)
     .onOK(() => {
-      if (typeof cell !== 'undefined') {
-        cell.cell.value = app.canvas.getHelm(true).replace(/<\/span>/g, '').replace(/<span style='background:#bbf;'>/g, '');
+      let helmValue = app.canvas.getHelm(true).replace(/<\/span>/g, '').replace(/<span style='background:#bbf;'>/g, '');
+      if (typeof units === 'undefined') {
+        cell.value = helmValue;
+      } else {
+        let convertedRes = converter.convertHelmToFastaSeparator(helmValue, units);
+        cell.value = convertedRes;
       }
     }).show({modal: true, fullScreen: true});
 }
 
-async function accessServer(url: string, key: string) {
-  const params: RequestInit = {
-    method: 'GET',
-    headers: {
-      'Accept': 'application/json',
-    }
-  };
-  const response = await fetch(url, params);
-  const json = await response.json();
-  return json[key];
-}
-
-//name: helmToFasta
-//input: string helmString {semType: Macromolecule}
-//output: string res
-export async function helmToFasta(helmString: string) {
-  const url = `http://localhost:8081/WebService/service/Fasta/Produce/${helmString}`;
-  return await accessServer(url, 'FastaFile');
-}
-
-//name: helmToRNA
-//description: converts to rna analogue sequence
-//input: string helmString {semType: Macromolecule}
-//output: string res
-export async function helmToRNA(helmString: string) {
-  const url = `http://localhost:8081/WebService/service/Fasta/Convert/RNA/${helmString}`;
-  return await accessServer(url, 'Sequence');
-}
-
-//name: helmToPeptide
-//description: converts to peptide analogue sequence
-//input: string helmString {semType: Macromolecule}
-//output: string res
-export async function helmToPeptide(helmString: string) {
-  const url = `http://localhost:8081/WebService/service/Fasta/Convert/PEPTIDE/${helmString}`;
-  return await accessServer(url, 'Sequence');
-}
-
-//name: helmToSmiles
-//description: converts to smiles
-//input: string helmString {semType: Macromolecule}
-//output: string smiles {semType: Molecule}
-export async function helmToSmiles(helmString: string) {
-  const url = `http://localhost:8081/WebService/service/SMILES/${helmString}`;
-  return await accessServer(url, 'SMILES');
-}
-
 function getRS(smiles: string) {
   const newS = smiles.match(/(?<=\[)[^\][]*(?=])/gm);
   const res = {};

package/tsconfig.json

@@ -12,7 +12,7 @@
     // "jsx": "preserve",                           /* Specify JSX code generation: 'preserve', 'react-native', 'react', 'react-jsx' or 'react-jsxdev'. */
     // "declaration": true,                         /* Generates corresponding '.d.ts' file. */
     // "declarationMap": true,                      /* Generates a sourcemap for each corresponding '.d.ts' file. */
-    // "sourceMap": true,                           /* Generates corresponding '.map' file. */
+    "sourceMap": true,                              /* Generates corresponding '.map' file. */
     // "outFile": "./",                             /* Concatenate and emit output to single file. */
     // "outDir": "./",                              /* Redirect output structure to the directory. */
     // "rootDir": "./",                             /* Specify the root directory of input files. Use to control the output directory structure with --outDir. */

package/webpack.config.js

@@ -28,7 +28,7 @@ module.exports = {
       },
     ],
   },
-  devtool: 'inline-source-map',
+  devtool: 'source-map',
   externals: {
     'datagrok-api/dg': 'DG',
     'datagrok-api/grok': 'grok',