@datagrok/helm 0.0.5 → 1.0.2

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Files changed (7) hide show
  1. package/.eslintignore +2 -0
  2. package/.eslintrc.json +51 -0
  3. package/package.json +58 -47
  4. package/src/package-test.ts +3 -3
  5. package/src/package.ts +127 -67
  6. package/src/tests/helm-tests.ts +16 -7
  7. package/webpack.config.js +10 -1
package/.eslintignore ADDED
@@ -0,0 +1,2 @@
1
+ src/**/*.d.ts*
2
+ src/seq_align.ts
package/.eslintrc.json ADDED
@@ -0,0 +1,51 @@
1
+ {
2
+ "env": {
3
+ "browser": true,
4
+ "es2021": true
5
+ },
6
+ "extends": [
7
+ "google"
8
+ ],
9
+ "parser": "@typescript-eslint/parser",
10
+ "parserOptions": {
11
+ "ecmaVersion": 12,
12
+ "sourceType": "module"
13
+ },
14
+ "plugins": [
15
+ "@typescript-eslint"
16
+ ],
17
+ "rules": {
18
+ "indent": [
19
+ "error",
20
+ 2
21
+ ],
22
+ "max-len": [
23
+ "error",
24
+ 120
25
+ ],
26
+ "no-unused-vars": "warn",
27
+ "require-jsdoc": "off",
28
+ "spaced-comment": "off",
29
+ "linebreak-style": "off",
30
+ "curly": [
31
+ "error",
32
+ "multi-or-nest",
33
+ "consistent"
34
+ ],
35
+ "brace-style": [
36
+ "error",
37
+ "1tbs",
38
+ {
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+ "allowSingleLine": true
40
+ }
41
+ ],
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+ "block-spacing": [2, "always"],
43
+ "comma-dangle": ["error", {
44
+ "arrays": "only-multiline",
45
+ "functions": "never",
46
+ "objects": "only-multiline",
47
+ "imports": "only-multiline"
48
+ }],
49
+ "guard-for-in": "off"
50
+ }
51
+ }
package/package.json CHANGED
@@ -1,49 +1,60 @@
1
1
  {
2
- "name": "@datagrok/helm",
3
- "beta": false,
4
- "friendlyName": "Helm",
5
- "version": "0.0.5",
6
- "description": "",
7
- "dependencies": {
8
- "datagrok-api": "latest",
9
- "cash-dom": "latest",
10
- "dayjs": "latest",
11
- "@datagrok-libraries/utils": "latest"
12
- },
13
- "sources": [
14
- "css/helm.css",
15
- "https://ajax.googleapis.com/ajax/libs/dojo/1.10.4/dojo/dojo.js",
16
- "helm/JSDraw/Scilligence.JSDraw2.Lite.js",
17
- "helm/JSDraw/Scilligence.JSDraw2.Resources.js",
18
- "helm/JSDraw/Pistoia.HELM-uncompressed.js"
19
- ],
20
- "devDependencies": {
21
- "webpack": "latest",
22
- "webpack-cli": "latest",
23
- "ts-loader": "latest",
24
- "typescript": "latest"
25
- },
26
- "scripts": {
27
- "link-all": "npm link datagrok-api @datagrok-libraries/utils",
28
- "debug-helm": "webpack && grok publish ",
29
- "release-helm": "webpack && grok publish --release",
30
- "build-helm": "webpack",
31
- "build": "webpack",
32
- "debug-helm-dev": "grok publish dev --rebuild",
33
- "release-helm-dev": "grok publish dev --rebuild --release",
34
- "debug-helm-public": "grok publish public --rebuild",
35
- "release-helm-public": "grok publish public --rebuild --release"
36
- },
37
- "canEdit": [
38
- "Developers"
39
- ],
40
- "canView": [
41
- "All users"
42
- ],
43
- "repository": {
44
- "type": "git",
45
- "url": "https://github.com/datagrok-ai/public.git",
46
- "directory": "packages/Helm"
47
- },
48
- "category": "Bioinformatics"
2
+ "name": "@datagrok/helm",
3
+ "beta": false,
4
+ "friendlyName": "Helm",
5
+ "version": "1.0.2",
6
+ "description": "",
7
+ "dependencies": {
8
+ "datagrok-api": "^1.4.12",
9
+ "cash-dom": "latest",
10
+ "dayjs": "latest",
11
+ "@datagrok-libraries/utils": "latest",
12
+ "@datagrok-libraries/bio": "^2.8.3",
13
+ "ts-loader": "^9.2.5",
14
+ "typescript": "^4.4.2"
15
+ },
16
+ "sources": [
17
+ "css/helm.css",
18
+ "https://ajax.googleapis.com/ajax/libs/dojo/1.10.4/dojo/dojo.js",
19
+ "helm/JSDraw/Scilligence.JSDraw2.Lite.js",
20
+ "helm/JSDraw/Scilligence.JSDraw2.Resources.js",
21
+ "helm/JSDraw/Pistoia.HELM-uncompressed.js"
22
+ ],
23
+ "devDependencies": {
24
+ "@typescript-eslint/eslint-plugin": "latest",
25
+ "@typescript-eslint/parser": "latest",
26
+ "eslint": "latest",
27
+ "eslint-config-google": "latest",
28
+ "ts-loader": "latest",
29
+ "typescript": "latest",
30
+ "webpack": "latest",
31
+ "webpack-cli": "latest"
32
+ },
33
+ "scripts": {
34
+ "link-all": "npm link datagrok-api @datagrok-libraries/utils @datagrok-libraries/bio",
35
+ "debug-helm": "webpack && grok publish ",
36
+ "release-helm": "webpack && grok publish --release",
37
+ "build-helm": "webpack",
38
+ "build": "webpack",
39
+ "debug-local": "grok publish local",
40
+ "release-local": "grok publish local --release",
41
+ "debug-helm-dev": "grok publish dev --rebuild",
42
+ "release-helm-dev": "grok publish dev --rebuild --release",
43
+ "debug-helm-public": "grok publish public --rebuild",
44
+ "release-helm-public": "grok publish public --rebuild --release",
45
+ "lint": "eslint \"./src/**/*.ts\"",
46
+ "lint-fix": "eslint \"./src/**/*.ts\" --fix"
47
+ },
48
+ "canEdit": [
49
+ "Developers"
50
+ ],
51
+ "canView": [
52
+ "All users"
53
+ ],
54
+ "repository": {
55
+ "type": "git",
56
+ "url": "https://github.com/datagrok-ai/public.git",
57
+ "directory": "packages/Helm"
58
+ },
59
+ "category": "Bioinformatics"
49
60
  }
package/src/package-test.ts CHANGED
@@ -1,7 +1,7 @@
1
- import * as DG from "datagrok-api/dg";
2
- import * as grok from "datagrok-api/grok";
1
+ import * as DG from 'datagrok-api/dg';
2
+ import * as grok from 'datagrok-api/grok';
3
3
  import {runTests, tests} from '@datagrok-libraries/utils/src/test';
4
- import './tests/helm-tests.ts'
4
+ import './tests/helm-tests.ts';
5
5
 
6
6
  export const _package = new DG.Package();
7
7
  export {tests};
package/src/package.ts CHANGED
@@ -2,67 +2,80 @@
2
2
  import * as grok from 'datagrok-api/grok';
3
3
  import * as ui from 'datagrok-api/ui';
4
4
  import * as DG from 'datagrok-api/dg';
5
+ //import {lru} from '../../Bio/src/utils/cell-renderer';
6
+ import {NotationConverter, NOTATION} from '@datagrok-libraries/bio/src/utils/notation-converter';
7
+ import {WebLogo} from '@datagrok-libraries/bio/src/viewers/web-logo';
8
+ //import {ConverterFunc, DfReaderFunc} from '../../Bio/src/tests/types';
5
9
 
6
10
  export const _package = new DG.Package();
7
11
 
8
- const lru = new DG.LruCache<any, any>();
12
+ const lru = new DG.LruCache<any, any>();
13
+
9
14
 
10
15
  //tags: init
11
16
  export async function initChem(): Promise<void> {
12
17
  // apparently HELMWebEditor requires dojo to be initialized first
13
18
  return new Promise((resolve, reject) => {
14
19
  // @ts-ignore
15
- dojo.ready(function () { resolve(null); });
20
+ dojo.ready(function() { resolve(null); });
16
21
  });
17
22
  }
18
23
 
19
-
20
- //name: helmCellRenderer
21
- //tags: cellRenderer,cellRenderer-Macromolecule
22
- //meta.cellType: Macromolecule
23
- //meta-cell-renderer-sem-type: Macromolecule
24
- //output: grid_cell_renderer result
25
- export function helmCellRenderer(): DG.GridCellRenderer {
26
- return new HelmCellRenderer();
27
- }
28
-
29
24
  //tags: cellEditor
30
25
  //description: Macromolecule
31
26
  //input: grid_cell cell
32
27
  export function editMoleculeCell(cell: DG.GridCell): void {
33
- let view = ui.div();
28
+ const view = ui.div();
34
29
  org.helm.webeditor.MolViewer.molscale = 0.8;
35
- let app = new scil.helm.App(view, { showabout: false, mexfontsize: "90%", mexrnapinontab: true, topmargin: 20, mexmonomerstab: true, sequenceviewonly: false, mexfavoritefirst: true, mexfilter: true });
36
- var sizes = app.calculateSizes();
30
+ const app = new scil.helm.App(view, {
31
+ showabout: false,
32
+ mexfontsize: '90%',
33
+ mexrnapinontab: true,
34
+ topmargin: 20,
35
+ mexmonomerstab: true,
36
+ sequenceviewonly: false,
37
+ mexfavoritefirst: true,
38
+ mexfilter: true
39
+ });
40
+ const sizes = app.calculateSizes();
37
41
  app.canvas.resize(sizes.rightwidth, sizes.topheight - 210);
38
- var s = { width: sizes.rightwidth + "px", height: sizes.bottomheight + "px" };
42
+ let s = {width: sizes.rightwidth + 'px', height: sizes.bottomheight + 'px'};
39
43
  //@ts-ignore
40
44
  scil.apply(app.sequence.style, s);
41
45
  //@ts-ignore
42
46
  scil.apply(app.notation.style, s);
43
- s = { width: sizes.rightwidth + "px", height: (sizes.bottomheight + app.toolbarheight) + "px" };
47
+ s = {width: sizes.rightwidth + 'px', height: (sizes.bottomheight + app.toolbarheight) + 'px'};
44
48
  //@ts-ignore
45
49
  scil.apply(app.properties.parent.style, s);
46
50
  app.structureview.resize(sizes.rightwidth, sizes.bottomheight + app.toolbarheight);
47
51
  app.mex.resize(sizes.topheight - 80);
52
+
53
+ let dialogValue: string;
54
+ if (cell.gridColumn.column.tags[DG.TAGS.UNITS] === 'HELM') {
55
+ dialogValue = cell.cell.value;
56
+ } else {
57
+ const converter: NotationConverter = new NotationConverter(cell.cell.column);
58
+ dialogValue = converter.convertStringToHelm(cell.cell.value);
59
+ }
60
+
48
61
  setTimeout(function() {
49
- app.canvas.helm.setSequence(cell.cell.value , 'HELM');
62
+ app.canvas.helm.setSequence(dialogValue, 'HELM');
50
63
  }, 200);
51
64
  //@ts-ignore
52
- ui.dialog({ showHeader: false, showFooter: true })
53
- .add(view)
54
- .onOK(() => {
55
- cell.cell.value = app.canvas.getHelm(true);
56
- }).show({ modal: true, fullScreen: true});
65
+ ui.dialog({showHeader: false, showFooter: true})
66
+ .add(view)
67
+ .onOK(() => {
68
+ cell.cell.value;
69
+ }).show({modal: true, fullScreen: true});
57
70
  }
58
71
 
59
72
  //name: Details
60
73
  //tags: panel, widgets
61
74
  //input: string helmString {semType: Macromolecule}
62
75
  //output: widget result
63
- export function detailsPanel(helmString: string){
76
+ export function detailsPanel(helmString: string) {
64
77
  //return new DG.Widget(ui.divText(lru.get(helmString)));
65
- var result = lru.get(helmString).split(',');
78
+ const result = lru.get(helmString).split(',');
66
79
  return new DG.Widget(
67
80
  ui.tableFromMap({
68
81
  'formula': result[0].replace(/<sub>/g, '').replace(/<\/sub>/g, ''),
@@ -72,14 +85,42 @@ export function detailsPanel(helmString: string){
72
85
  'fasta': ui.wait(async () => ui.divText(await helmToFasta(helmString))),
73
86
  'rna analogue sequence': ui.wait(async () => ui.divText(await helmToRNA(helmString))),
74
87
  'smiles': ui.wait(async () => ui.divText(await helmToSmiles(helmString))),
75
- 'peptide analogue sequence': ui.wait(async () => ui.divText(await helmToPeptide(helmString))),
88
+ //'peptide analogue sequence': ui.wait(async () => ui.divText(await helmToPeptide(helmString))),
76
89
  })
77
- )
90
+ );
91
+ }
92
+
93
+
94
+ async function loadDialog() {
95
+ //@ts-ignore
96
+ let res = await grok.dapi.files.list('System:AppData/Helm', false, '');
97
+ //@ts-ignore
98
+ res = res.map((e) => e.path);
99
+ //@ts-ignore
100
+ const FilesList = await ui.choiceInput('Monomer Libraries', ' ', res);
101
+ const grid = grok.shell.tv.grid;
102
+ ui.dialog('Load library from file')
103
+ .add(FilesList)
104
+ .onOK(async () => {
105
+ await monomerManager(FilesList.value);
106
+ grid.invalidate();
107
+ }).show();
108
+ };
109
+
110
+ //name: Library
111
+ //tags: panel, widgets
112
+ //input: string helmString {semType: Macromolecule}
113
+ //output: widget result
114
+ export function libraryPanel(helmString: string) {
115
+ //@ts-ignore
116
+ const loadButton = ui.button('Load Library');
117
+ loadButton.addEventListener('click', loadDialog);
118
+ return new DG.Widget(ui.divH([loadButton]));
78
119
  }
79
120
 
80
121
  async function accessServer(url: string, key: string) {
81
122
  const params: RequestInit = {
82
- method: 'GET',
123
+ method: 'GET',
83
124
  headers: {
84
125
  'Accept': 'application/json',
85
126
  }
@@ -94,7 +135,7 @@ async function accessServer(url: string, key: string) {
94
135
  //input: string helmString {semType: Macromolecule}
95
136
  //output: string res
96
137
  export async function helmToFasta(helmString: string) {
97
- const url = `http://localhost:8081/WebService/service/Fasta/Produce/${helmString}`
138
+ const url = `http://localhost:8081/WebService/service/Fasta/Produce/${helmString}`;
98
139
  return await accessServer(url, 'FastaFile');
99
140
  }
100
141
 
@@ -103,7 +144,7 @@ export async function helmToFasta(helmString: string) {
103
144
  //input: string helmString {semType: Macromolecule}
104
145
  //output: string res
105
146
  export async function helmToRNA(helmString: string) {
106
- const url = `http://localhost:8081/WebService/service/Fasta/Convert/RNA/${helmString}`
147
+ const url = `http://localhost:8081/WebService/service/Fasta/Convert/RNA/${helmString}`;
107
148
  return await accessServer(url, 'Sequence');
108
149
  }
109
150
 
@@ -113,7 +154,7 @@ export async function helmToRNA(helmString: string) {
113
154
  //input: string helmString {semType: Macromolecule}
114
155
  //output: string res
115
156
  export async function helmToPeptide(helmString: string) {
116
- const url = `http://localhost:8081/WebService/service/Fasta/Convert/PEPTIDE/${helmString}`
157
+ const url = `http://localhost:8081/WebService/service/Fasta/Convert/PEPTIDE/${helmString}`;
117
158
  return await accessServer(url, 'Sequence');
118
159
  }
119
160
 
@@ -122,24 +163,23 @@ export async function helmToPeptide(helmString: string) {
122
163
  //input: string helmString {semType: Macromolecule}
123
164
  //output: string smiles {semType: Molecule}
124
165
  export async function helmToSmiles(helmString: string) {
125
- const url = `http://localhost:8081/WebService/service/SMILES/${helmString}`
166
+ const url = `http://localhost:8081/WebService/service/SMILES/${helmString}`;
126
167
  return await accessServer(url, 'SMILES');
127
168
  }
128
169
 
129
170
  function getRS(smiles: string) {
130
- var new_s = smiles.match(/(?<=\[)[^\][]*(?=])/gm);
131
- var res = {};
132
- var el = '';
133
- var digit;
134
- for (var i = 0; i < new_s.length; i++) {
135
- if (new_s[i] != null){
136
- if (/\d/.test(new_s[i])) {
137
- digit = new_s[i][new_s[i].length - 1];
138
- new_s[i] = new_s[i].replace(/[0-9]/g, '');
139
- for (var j = 0; j < new_s[i].length; j++) {
140
- if (new_s[i][j] != ':'){
141
- el += new_s[i][j];
142
- }
171
+ const newS = smiles.match(/(?<=\[)[^\][]*(?=])/gm);
172
+ const res = {};
173
+ let el = '';
174
+ let digit;
175
+ for (let i = 0; i < newS.length; i++) {
176
+ if (newS[i] != null) {
177
+ if (/\d/.test(newS[i])) {
178
+ digit = newS[i][newS[i].length - 1];
179
+ newS[i] = newS[i].replace(/[0-9]/g, '');
180
+ for (let j = 0; j < newS[i].length; j++) {
181
+ if (newS[i][j] != ':')
182
+ el += newS[i][j];
143
183
  }
144
184
  res['R' + digit] = el;
145
185
  el = '';
@@ -149,53 +189,73 @@ function getRS(smiles: string) {
149
189
  return res;
150
190
  }
151
191
 
152
- //name: Monomer Manager
153
- //input: column helmColumn {semType: Macromolecule}
154
- export async function monomerManager(helmColumn: DG.Column) {
155
- const file = await _package.files.readAsText('HELMCoreLibrary.json');
192
+ async function monomerManager(value: string) {
193
+ const file = await _package.files.readAsText(value.split('/')[1]);
156
194
  const df = DG.DataFrame.fromJson(file);
157
- var m;
158
- for (var i = 0; i < df.rowCount; i++){
195
+ let m;
196
+ for (let i = 0; i < df.rowCount; i++) {
159
197
  m = {
160
- 'id': df.get('symbol', i).toString(),
198
+ 'id': df.get('symbol', i).toString(),
161
199
  'n': df.get('name', i).toString(),
162
200
  'na': df.get('naturalAnalog', i).toString(),
163
201
  'type': df.get('polymerType', i).toString(),
164
- 'mt': df.get('monomerType', i).toString(),
165
- 'm': df.get('molfile', i).toString(),
166
- rs: Object.keys(getRS(df.get('smiles', i).toString())).length,
167
- at: getRS(df.get('smiles', i).toString()),
168
- }
202
+ 'mt': df.get('monomerType', i).toString(),
203
+ 'm': df.get('molfile', i).toString(),
204
+ 'rs': Object.keys(getRS(df.get('smiles', i).toString())).length,
205
+ 'at': getRS(df.get('smiles', i).toString()),
206
+ };
169
207
  org.helm.webeditor.Monomers.addOneMonomer(m);
170
208
  }
171
209
  }
172
210
 
173
211
  //name: helmColumnToSmiles
174
- //input: column helmColumn {semType: HELM}
212
+ //input: column helmColumn {semType: Macromolecule}
175
213
  export function helmColumnToSmiles(helmColumn: DG.Column) {
176
214
  //todo: add column with smiles to col.dataFrame.
177
215
  }
178
216
 
217
+ // Synonym to overcome eslint error
218
+ const GetMonomerSet = scil.helm.Monomers.getMonomerSet;
179
219
 
180
- class HelmCellRenderer extends DG.GridCellRenderer {
220
+ //name: findMonomers
221
+ //input: string helmString { semType: Macromolecule }
222
+ export async function findMonomers(helmString: string) {
223
+ const types = Object.keys(org.helm.webeditor.monomerTypeList());
224
+ const monomers = [];
225
+ const monomerNames = [];
226
+ for (let i = 0; i < types.length; i++) {
227
+ monomers.push(new GetMonomerSet(types[i]));
228
+ Object.keys(monomers[i]).forEach((k) => {
229
+ monomerNames.push(monomers[i][k].id);
230
+ });
231
+ }
232
+ const splitString = WebLogo.splitterAsHelm(helmString);
233
+ return new Set(splitString.filter((val) => !monomerNames.includes(val)));
234
+ }
181
235
 
236
+ class HelmCellRenderer extends DG.GridCellRenderer {
182
237
  get name() { return 'macromolecule'; }
238
+
183
239
  get cellType() { return 'macromolecule'; }
240
+
184
241
  get defaultWidth(): number | null { return 400; }
242
+
185
243
  get defaultHeight(): number | null { return 100; }
186
244
 
187
- render(g: CanvasRenderingContext2D, x: number, y: number, w: number, h: number, gridCell: DG.GridCell, cellStyle: DG.GridCellStyle) {
188
- let host = ui.div([], { style: { width: `${w}px`, height: `${h}px`}});
245
+ render(g: CanvasRenderingContext2D, x: number, y: number, w: number, h: number,
246
+ gridCell: DG.GridCell, cellStyle: DG.GridCellStyle
247
+ ) {
248
+ const host = ui.div([], {style: {width: `${w}px`, height: `${h}px`}});
189
249
  host.setAttribute('dataformat', 'helm');
190
250
  host.setAttribute('data', gridCell.cell.value);
191
251
 
192
252
  gridCell.element = host;
193
- var canvas = new JSDraw2.Editor(host, { width: w, height: h, skin: "w8", viewonly: true });
194
- var formula = canvas.getFormula(true);
195
- var molWeight = Math.round(canvas.getMolWeight() * 100) / 100;
196
- var coef = Math.round(canvas.getExtinctionCoefficient(true) * 100) / 100;
197
- var molfile = canvas.getMolfile();
198
- var result = formula + ', ' + molWeight + ', ' + coef + ', ' + molfile;
253
+ const canvas = new JSDraw2.Editor(host, {width: w, height: h, skin: 'w8', viewonly: true});
254
+ const formula = canvas.getFormula(true);
255
+ const molWeight = Math.round(canvas.getMolWeight() * 100) / 100;
256
+ const coef = Math.round(canvas.getExtinctionCoefficient(true) * 100) / 100;
257
+ const molfile = canvas.getMolfile();
258
+ const result = formula + ', ' + molWeight + ', ' + coef + ', ' + molfile;
199
259
  lru.set(gridCell.cell.value, result);
200
260
  }
201
261
  }
package/src/tests/helm-tests.ts CHANGED
@@ -1,35 +1,44 @@
1
1
  import {before, category, expect, test} from '@datagrok-libraries/utils/src/test';
2
- import { helmToFasta, helmToPeptide, helmToRNA } from '../package';
3
- import { _package } from '../package-test';
2
+ import {helmToFasta, helmToPeptide, helmToRNA} from '../package';
3
+ import {_package} from '../package-test';
4
4
  import * as DG from 'datagrok-api/dg';
5
5
  import * as grok from 'datagrok-api/grok';
6
6
 
7
7
 
8
8
  category('Helm', () => {
9
-
10
9
  test('helmToFasta', async () => {
11
10
  expect(await helmToFasta('RNA1{R(U)P.R(T)P.R(G)P.R(C)P.R(A)}$$$$'), '>RNA1UTGCA');
12
11
  expect(await helmToFasta('RNA1{P.R(U).P.R(T)}$$$$'), '>RNA1UT');
13
- expect(await helmToFasta('PEPTIDE1{A.G}$$$$V2.0'), '>PEPTIDE1AG')
12
+ expect(await helmToFasta('PEPTIDE1{A.G}$$$$V2.0'), '>PEPTIDE1AG');
14
13
  });
15
14
 
16
15
  test('helmToRNA', async () => {
17
16
  expect(await helmToRNA('RNA1{R(U)P.R(T)P.R(G)P.R(C)P.R(A)}$$$$'), 'UTGCA');
18
17
  expect(await helmToRNA('RNA1{P.R(U).P.R(T)}$$$$'), 'UT');
18
+ // eslint-disable-next-line max-len
19
19
  expect(await helmToRNA('RNA1{R(U)P.R(T)P}|RNA2{P.R(A)P.R(A)}$RNA1,RNA2,2:pair-6:pair|RNA1,RNA2,5:pair-3:pair$$$'), 'UT AA');
20
20
  });
21
21
 
22
22
  test('helmToPeptide', async () => {
23
23
  expect(await helmToPeptide('PEPTIDE1{A.G}$$$$V2.0'), 'AG');
24
24
  expect(await helmToPeptide('PEPTIDE1{L.V.A}|PEPTIDE2{L.V.A}$$$$'), 'LVA LVA');
25
+ // eslint-disable-next-line max-len
25
26
  expect(await helmToPeptide('PEPTIDE1{A.R.C.A.A.K.T.C.D.A}$PEPTIDE1,PEPTIDE1,8:R3-3:R3$$$'), 'ARCAAKTCDA');
26
27
  });
27
28
 
29
+ test('detectMacromolecule', async () => {
30
+ const file = await _package.files.readAsText('test.csv');
31
+ const df = DG.DataFrame.fromCsv(file);
32
+ const col = df.columns.byName('HELM string');
33
+ await grok.data.detectSemanticTypes(df);
34
+ expect(col.semType, DG.SEMTYPE.MACROMOLECULE);
35
+ });
36
+
28
37
  test('detectHelm', async () => {
29
- const file = await _package.files.readAsText('test.csv')
38
+ const file = await _package.files.readAsText('test.csv');
30
39
  const df = DG.DataFrame.fromCsv(file);
31
- let col = df.columns.byName('HELM string');
40
+ const col = df.columns.byName('HELM string');
32
41
  await grok.data.detectSemanticTypes(df);
33
- expect(col.semType, DG.SEMTYPE.HELM);
42
+ expect(col.tags[DG.TAGS.UNITS], 'HELM');
34
43
  });
35
44
  });
package/webpack.config.js CHANGED
@@ -16,7 +16,16 @@ module.exports = {
16
16
  },
17
17
  module: {
18
18
  rules: [
19
- { test: /\.tsx?$/, loader: 'ts-loader' }
19
+ {
20
+ test: /\.ts(x?)$/,
21
+ use: 'ts-loader',
22
+ exclude: /node_modules/,
23
+ },
24
+ {
25
+ test: /\.css$/,
26
+ use: ['style-loader', 'css-loader'],
27
+ exclude: /node_modules/,
28
+ },
20
29
  ],
21
30
  },
22
31
  devtool: 'inline-source-map',