refactor!: update to cheminfo-types (#6)

* refactor!: update to cheminfo-types * fix: add peer-deps for eslint
cheminfo · Nov 5, 2021 · 12bf39a · 12bf39a
1 parent caac9dc
commit 12bf39a
Show file tree

Hide file tree

Showing 8 changed files with 103 additions and 69 deletions.
diff --git a/README.md b/README.md
@@ -5,7 +5,7 @@
 [![Test coverage][codecov-image]][codecov-url]
 [![npm download][download-image]][download-url]
 
-File parser for n-dimesional values.
+File parser for n-dimensional values.
 
 ## Installation
 

diff --git a/package.json b/package.json
@@ -1,7 +1,7 @@
 {
   "name": "ndim-parser",
   "version": "0.4.0",
-  "description": "File parser for n-dimesional values",
+  "description": "File parser for n-dimensional values",
   "main": "./lib/index.js",
   "module": "./lib-esm/index.js",
   "types": "./lib/index.d.ts",
@@ -15,6 +15,7 @@
   ],
   "scripts": {
     "clean": "rimraf lib lib-esm",
+    "check-types": "tsc --noEmit",
     "eslint": "eslint src --ext ts --cache",
     "eslint-fix": "npm run eslint -- --fix",
     "prepublishOnly": "npm run tsc",
@@ -44,14 +45,22 @@
     "tabWidth": 2,
     "trailingComma": "all"
   },
+  "dependencies": {
+    "cheminfo-types": "^0.6.0"
+  },
   "devDependencies": {
-    "@types/jest": "~26.0.15",
-    "eslint": "~7.14.0",
-    "eslint-config-cheminfo-typescript": "~8.0.5",
-    "jest": "~26.6.3",
-    "prettier": "~2.2.0",
-    "rimraf": "~3.0.2",
-    "ts-jest": "~26.4.4",
-    "typescript": "~4.1.2"
+    "@types/jest": "^27.0.2",
+    "@typescript-eslint/eslint-plugin": "^5.0.0",
+    "@typescript-eslint/parser": "^5.0.0",
+    "eslint": "^8.1.0",
+    "eslint-config-cheminfo-typescript": "^10.2.2",
+    "eslint-plugin-import": "^2.25.2",
+    "eslint-plugin-jest": "^25.2.1",
+    "eslint-plugin-jsdoc": "^37.0.0",
+    "jest": "^27.3.1",
+    "prettier": "^2.4.1",
+    "rimraf": "^3.0.2",
+    "ts-jest": "^27.0.7",
+    "typescript": "^4.4.4"
   }
 }
diff --git a/src/__tests__/appended.test.ts b/src/__tests__/appended.test.ts
@@ -11,8 +11,8 @@ test('multiple breakdown', () => {
   const parsed = appendedParser(csv);
   expect(parsed).toHaveLength(164);
   for (const serie of parsed) {
-    expect(serie.data).toHaveProperty('x');
-    expect(serie.data).toHaveProperty('y');
+    expect(serie.variables).toHaveProperty('x');
+    expect(serie.variables).toHaveProperty('y');
   }
 });
 
@@ -23,8 +23,8 @@ test('breakdown', () => {
   );
   const parsed = appendedParser(csv);
   expect(parsed).toHaveLength(1);
-  expect(parsed[0].data).toHaveProperty('x');
-  expect(parsed[0].data).toHaveProperty('y');
+  expect(parsed[0].variables).toHaveProperty('x');
+  expect(parsed[0].variables).toHaveProperty('y');
 });
 
 test('capacitance', () => {
@@ -34,8 +34,8 @@ test('capacitance', () => {
   );
   const parsed = appendedParser(csv);
   expect(parsed).toHaveLength(1);
-  expect(parsed[0].data).toHaveProperty('x');
-  expect(parsed[0].data).toHaveProperty('y');
+  expect(parsed[0].variables).toHaveProperty('x');
+  expect(parsed[0].variables).toHaveProperty('y');
 });
 
 test('IV', () => {
@@ -45,6 +45,6 @@ test('IV', () => {
   );
   const parsed = appendedParser(csv);
   expect(parsed).toHaveLength(1);
-  expect(parsed[0].data).toHaveProperty('x');
-  expect(parsed[0].data).toHaveProperty('y');
+  expect(parsed[0].variables).toHaveProperty('x');
+  expect(parsed[0].variables).toHaveProperty('y');
 });
diff --git a/src/__tests__/general.test.ts b/src/__tests__/general.test.ts
@@ -14,7 +14,7 @@ temp, volt, curr, temp_sup
 
 test('simpleExample', () => {
   expect(ndParse(simpleExample)).toStrictEqual({
-    data: {
+    variables: {
       x: { data: [1, 2, 3], label: 'temp' },
       y: { data: [1, 2, 3], label: 'volt' },
       c: { data: [1, 2, 3], label: 'curr' },
@@ -39,7 +39,7 @@ test('with options', () => {
       ],
     }),
   ).toStrictEqual({
-    data: {
+    variables: {
       x: { data: [1, 2, 3], label: 'ground volts' },
       y: { data: [1, 2, 3], label: 'temperature' },
       c: { data: [1, 2, 3], label: 'ground current' },
@@ -59,8 +59,8 @@ test('real file', () => {
   );
   const parsed = ndParse(csv);
   const keys = ['x', 'y', 'G', 'Q', 'C', 'A', 'I', 'F', 'B'];
-  expect(parsed.meta['Channel.Mode']).toBe('V');
-  expect(Object.keys(parsed.data)).toStrictEqual(keys);
+  expect(parsed.meta?.['Channel.Mode']).toBe('V');
+  expect(Object.keys(parsed.variables)).toStrictEqual(keys);
 });
 
 test('breakdown', () => {
@@ -70,5 +70,5 @@ test('breakdown', () => {
   );
   const parsed = ndParse(csv, { isTagged: true });
   const keys = ['x', 'y', 'I', 'A', 'B', 'C'];
-  expect(Object.keys(parsed.data)).toStrictEqual(keys);
+  expect(Object.keys(parsed.variables)).toStrictEqual(keys);
 });
diff --git a/src/appended.ts b/src/appended.ts
@@ -1,10 +1,17 @@
-import type { DataType, AppendedOptionsType, OutputType } from './types';
+import type {
+  MeasurementXY,
+  MeasurementXYVariables,
+  OneLowerCase,
+  MeasurementVariable,
+} from 'cheminfo-types';
+
+import type { AppendedOptionsType } from './types';
 import { isNumber, isNumericRow, orderedKeyMap } from './utils';
 
 export function appendedParser(
   text: string,
   options: AppendedOptionsType = {},
-): OutputType[] {
+): MeasurementXY[] {
   const { separator = ',', minNumericRows = 5 } = options;
 
   const lines = text
@@ -49,7 +56,7 @@ export function appendedParser(
   let headers: number[] = [];
   let start: number[] = [0];
   for (let i = 0; i < startNumeric.length; i++) {
-    // Last item in endNumec array
+    // Last item in array
     if (i === startNumeric.length - 1) {
       headers.push(startNumeric[i]);
     }
@@ -65,18 +72,22 @@ export function appendedParser(
     throw new Error('Unable to retrieve structure');
   }
   if (headers.length !== start.length) {
-    throw new Error('Unconsistent amount of headers an series');
+    throw new Error('Inconsistent amount of headers an series');
   }
 
   // If has tags ignore first row
   const isTagged = !isNumber(lines[headers[0] + 1][0]);
 
   // Split in metadata, header and data
-  let series = new Array(headers.length);
-  for (let serieIndex = 0; serieIndex < headers.length; serieIndex++) {
+  let series: MeasurementXY[] = new Array(headers.length);
+  for (let seriesIndex = 0; seriesIndex < headers.length; seriesIndex++) {
     // Add metadata
     let meta: Record<string, string> = {};
-    for (let index = start[serieIndex]; index < headers[serieIndex]; index++) {
+    for (
+      let index = start[seriesIndex];
+      index < headers[seriesIndex];
+      index++
+    ) {
       if (lines[index].length === 2) {
         meta[lines[index][0]] = lines[index][1];
       }
@@ -91,23 +102,35 @@ export function appendedParser(
     }
 
     // Add variables structure to add units
-    const labels = lines[headers[serieIndex]];
+    const labels = lines[headers[seriesIndex]];
     const keys = orderedKeyMap(labels, isTagged);
 
     // Add data
     const endDataIndex =
-      serieIndex + 1 === headers.length
+      seriesIndex + 1 === headers.length
         ? lines.length - 1
-        : start[serieIndex + 1];
-    let data: Record<string, DataType> = {};
+        : start[seriesIndex + 1];
+    let variables: Partial<Record<OneLowerCase, MeasurementVariable>> = {};
     for (let keyIndex = isTagged ? 1 : 0; keyIndex < keys.length; keyIndex++) {
-      data[keys[keyIndex]] = { data: [], label: labels[keyIndex] };
-      for (let index = headers[serieIndex] + 1; index < endDataIndex; index++) {
-        data[keys[keyIndex]].data.push(parseFloat(lines[index][keyIndex]));
+      let data: number[] = [];
+      for (
+        let index = headers[seriesIndex] + 1;
+        index < endDataIndex;
+        index++
+      ) {
+        data.push(parseFloat(lines[index][keyIndex]));
       }
+      variables[keys[keyIndex]] = { data, label: labels[keyIndex] };
+    }
+
+    if (!variables.x || !variables.y) {
+      throw new Error('x and y variables are necessary');
     }
 
-    series[serieIndex] = { data, meta };
+    series[seriesIndex] = {
+      variables: variables as MeasurementXYVariables,
+      meta,
+    };
   }
 
   return series;

diff --git a/src/general.ts b/src/general.ts
@@ -1,21 +1,23 @@
-import type { GeneralOptionsType, OutputType } from './types';
+import type { MeasurementXY, OneLowerCase } from 'cheminfo-types';
+
+import type { GeneralOptionsType } from './types';
 import { defaultKeyMapper, defaultLabelMap, intToChar } from './utils';
 
 export function ndParse(
   text: string,
   options?: GeneralOptionsType,
-): OutputType {
+): MeasurementXY<number[]> {
   const {
     separator = ',',
     isTagged = false,
     keyMap = defaultKeyMapper,
     labelMap = defaultLabelMap,
   } = options || {};
-  let meta: OutputType['meta'] = {};
-  let data: OutputType['data'] = {};
+  let meta: MeasurementXY['meta'] = {};
+  let variables: Partial<MeasurementXY<number[]>['variables']> = {};
 
   let tempHeader: string[] = [];
-  let header: string[] | undefined;
+  let header: OneLowerCase[] | undefined;
   let labels: string[] = [];
   let prevTag: string | undefined;
   let tag: string | undefined;
@@ -30,7 +32,7 @@ export function ndParse(
     const isNumeric =
       line && (isTagged ? tag === 'DataValue' : !isNaN(Number(fields[0])));
 
-    // Checks if the header is setted
+    // Checks if the header is set
     if (!header) {
       // Classifies if it's a header
       if (isNumeric) {
@@ -41,10 +43,10 @@ export function ndParse(
           const label = labels[index] || intToChar(index);
           const value = Number(fields[index]);
           const key = header[index];
-          if (!isNaN(value)) data[key] = { data: [value], label };
+          if (!isNaN(value)) variables[key] = { data: [value], label };
         }
       } else {
-        // Add metavalues
+        // Add meta-values
         if (tempHeader) {
           const [key, ...values] = tempHeader.filter((t) => t);
           if (
@@ -70,11 +72,13 @@ export function ndParse(
       for (let index = 0; index < fields.length; index++) {
         const key = header ? header[index] : intToChar(index);
         const value = Number(fields[index]);
-        if (!isNaN(value)) data[key]?.data.push(value);
+        if (!isNaN(value)) variables[key]?.data.push(value);
       }
     }
   }
 
-  const { x, y, ...unorderData } = data;
-  return { meta, data: { x, y, ...unorderData } };
+  const { x, y, ...unorderedData } = variables;
+  if (!x || !y) throw new Error('x and y variables are necessary');
+
+  return { meta, variables: { x, y, ...unorderedData } };
 }
diff --git a/src/types.ts b/src/types.ts
@@ -1,21 +1,13 @@
-export interface DataType {
-  data: number[];
-  label: string;
-}
+import type { OneLowerCase } from 'cheminfo-types';
 
 export interface AppendedOptionsType {
   separator?: string;
   minNumericRows?: number;
 }
 
-export interface OutputType {
-  meta: Record<string, string>;
-  data: Record<string, DataType>;
-}
-
 export interface GeneralOptionsType {
   separator?: string;
   isTagged?: boolean;
-  keyMap?: (keys: string[]) => string[];
+  keyMap?: (keys: string[]) => OneLowerCase[];
   labelMap?: (keys: string[]) => string[];
 }
diff --git a/src/utils.ts b/src/utils.ts
@@ -1,26 +1,29 @@
-export function intToChar(int: number): string {
-  return String.fromCharCode(65 + int);
+import type { OneLowerCase } from 'cheminfo-types';
+
+export function intToChar(int: number) {
+  return String.fromCharCode(65 + int) as OneLowerCase;
 }
 
-export function nextChar(keys: string[]): string {
+export function nextChar(keys: string[]): OneLowerCase {
   for (let int = 0; int < 52; int++) {
     const char = intToChar(int);
     if (!keys.includes(char)) return char;
   }
   throw new Error('To many variables for key mapper');
 }
 
-export function defaultKeyMapper(keys: string[]): string[] {
-  let currKeys: string[] = new Array(keys.length);
+export function defaultKeyMapper(keys: string[]): OneLowerCase[] {
+  let currKeys: OneLowerCase[] = new Array(keys.length);
   for (let index = 0; index < keys.length; index++) {
     const key = keys[index];
     if (index === 0) {
       currKeys[index] = 'x';
     } else if (index === 1) {
       currKeys[index] = 'y';
     } else {
-      currKeys[index] = !currKeys.includes(key[0])
-        ? key[0]
+      const firstChar = key[0] as OneLowerCase;
+      currKeys[index] = !currKeys.includes(firstChar)
+        ? firstChar
         : nextChar(currKeys);
     }
   }
@@ -33,7 +36,7 @@ export function defaultLabelMap(keys: string[]): string[] {
 
 export function isNumericRow(line: string[]): boolean {
   // eslint-disable-next-line @typescript-eslint/no-unused-vars
-  const [_first, ...list] = line;
+  const [first, ...list] = line;
   const filtered = list.filter((val) => !!val);
   if (filtered.length === 0) return false;
   return filtered.reduce((acc: boolean, curr) => acc && isNumber(curr), true);
@@ -43,8 +46,11 @@ export function isNumber(str: string): boolean {
   return !isNaN(parseFloat(str));
 }
 
-export function orderedKeyMap(keys: string[], ignoreFirst: boolean): string[] {
-  let currKeys: string[] = new Array(keys.length);
+export function orderedKeyMap(
+  keys: string[],
+  ignoreFirst: boolean,
+): OneLowerCase[] {
+  let currKeys: OneLowerCase[] = new Array(keys.length);
   const start = ignoreFirst ? 1 : 0;
   for (let index = 0; index < keys.length; index++) {
     if (index === start) {