sdf-parser 6.0.0 → 6.0.1

package/lib/index.js

@@ -194,7 +194,7 @@ function parse(sdf, options = {}) {
 
 /**
  *  Parse a SDF file
- * @param {string|ArrayBuffer|Uint8Array} sdf SDF file to parse
+ * @param {NodeJS.ReadableStream} readStream SDF file to parse
  * @param {object} [options={}]
  * @param {Function} [options.filter] Callback allowing to filter the molecules
  * @param {boolean} [options.dynamicTyping] Dynamically type the data

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "sdf-parser",
-  "version": "6.0.0",
+  "version": "6.0.1",
   "description": "SDF parser",
   "main": "lib/index.js",
   "module": "src/index.js",
@@ -8,9 +8,12 @@
     "lib",
     "src"
   ],
+  "browser": {
+    "./src/iterator.js": "./src/iterator.browser.js"
+  },
   "sideEffects": false,
   "scripts": {
-    "build": "npm run compile && cheminfo-build --root SDFParser",
+    "build": "cheminfo-build  --entry src/index.js  --root SDFParser",
     "compile": "rollup -c",
     "eslint": "eslint src",
     "eslint-fix": "npm run eslint -- --fix",
@@ -21,9 +24,6 @@
     "test-coverage": "jest --coverage",
     "test-only": "jest"
   },
-  "browser": {
-    "./src/stream.js": "./src/stream.browser.js"
-  },
   "repository": {
     "type": "git",
     "url": "https://github.com/cheminfo/sdf-parser.git"
@@ -44,13 +44,14 @@
   "homepage": "https://github.com/cheminfo/sdf-parser",
   "devDependencies": {
     "@babel/plugin-transform-modules-commonjs": "^7.18.6",
+    "@types/jest": "^29.1.2",
     "babel-eslint": "^10.1.0",
     "callback-stream": "^1.1.0",
     "cheminfo-build": "^1.1.11",
-    "eslint": "^8.22.0",
+    "eslint": "^8.25.0",
     "eslint-config-cheminfo": "^8.0.2",
-    "filelist-utils": "^0.6.0",
-    "jest": "^28.1.3",
+    "filelist-utils": "^1.0.1",
+    "jest": "^29.2.0",
     "openchemlib": "^8.0.1",
     "prettier": "^2.7.1"
   },

package/src/__tests__/__snapshots__/getEntriesBoundaries.test.js.snap

@@ -1,8 +1,8 @@
 // Jest Snapshot v1, https://goo.gl/fbAQLP
 
 exports[`should parse sdf files without EOL in the EOF 1`] = `
-Array [
-  Array [
+[
+  [
     0,
     1473,
   ],

package/src/__tests__/iterator.test.js

@@ -1,22 +1,24 @@
-import { createReadStream } from 'fs';
+import { createReadStream, ReadStream } from 'fs';
 import { join } from 'path';
 import { createGunzip } from 'zlib';
 
-import { fileListFromPath } from 'filelist-utils';
+import { fileCollectionFromPath } from 'filelist-utils';
 
 import { iterator } from '../iterator';
 
 test('iterator', async () => {
-  const fileList = (await fileListFromPath(join(__dirname, '.'))).filter(
-    (file) => file.name === 'test.sdf',
-  );
+  const files = (
+    await fileCollectionFromPath(join(__dirname, '.'))
+  ).files.filter((file) => file.name === 'test.sdf');
   const results = [];
-  for await (const entry of iterator(fileList[0].stream())) {
-    results.push(entry);
-  }
-  expect(results).toHaveLength(128);
-  expect(results[0]).toMatchInlineSnapshot(`
-    Object {
+
+  if (parseInt(process.versions.node) >= 18) {
+    for await (const entry of iterator(ReadStream.fromWeb(files[0].stream()))) {
+      results.push(entry);
+    }
+    expect(results).toHaveLength(128);
+    expect(results[0]).toMatchInlineSnapshot(`
+    {
       "CLogP": 2.7,
       "Code": 100380824,
       "Number of H-Acceptors": 3,
@@ -61,6 +63,7 @@ test('iterator', async () => {
     ",
     }
   `);
+  }
 });
 
 test('iterator on stream', async () => {
@@ -72,7 +75,7 @@ test('iterator on stream', async () => {
   }
   expect(results).toHaveLength(128);
   expect(results[0]).toMatchInlineSnapshot(`
-    Object {
+    {
       "CLogP": 2.7,
       "Code": 100380824,
       "Number of H-Acceptors": 3,
@@ -118,3 +121,63 @@ test('iterator on stream', async () => {
     }
   `);
 });
+
+test('iterator on fileCollection stream', async () => {
+  const file = (await fileCollectionFromPath(join(__dirname, '.'))).filter(
+    (file) => file.size === 32233,
+  ).files[0];
+  const results = [];
+
+  if (parseInt(process.versions.node) >= 18) {
+    for await (const entry of iterator(ReadStream.fromWeb(file.stream()))) {
+      results.push(entry);
+    }
+    expect(results).toHaveLength(128);
+    expect(results[0]).toMatchInlineSnapshot(`
+    {
+      "CLogP": 2.7,
+      "Code": 100380824,
+      "Number of H-Acceptors": 3,
+      "Number of H-Donors": 1,
+      "Number of Rotatable bonds": 1,
+      "molfile": "
+      -ISIS-  04231216572D
+
+     15 16  0  0  0  0  0  0  0  0999 V2000
+        2.4792    1.7000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+        2.4292    0.3500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+        0.4042    1.1208    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+        1.2167    2.1833    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+        1.1542   -0.0000    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
+       -0.9208    1.1208    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+        3.4792   -0.4500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+        0.8792    3.4458    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+       -1.6000   -0.0292    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+       -0.9625   -1.1792    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+       -1.6208   -2.3292    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+       -0.9125   -3.4375    0.0000 Br  0  0  0  0  0  0  0  0  0  0  0  0
+       -3.5958   -1.1792    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+       -2.9208   -0.0292    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+       -3.0333   -2.3292    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+      2  1  1  0  0  0  0
+      3  4  1  0  0  0  0
+      4  1  1  0  0  0  0
+      5  2  1  0  0  0  0
+      6  3  2  0  0  0  0
+      7  2  2  0  0  0  0
+      8  4  2  0  0  0  0
+      9  6  1  0  0  0  0
+     10  9  2  0  0  0  0
+     11 10  1  0  0  0  0
+     12 11  1  0  0  0  0
+     13 14  2  0  0  0  0
+     14  9  1  0  0  0  0
+     15 13  1  0  0  0  0
+      3  5  1  0  0  0  0
+     15 11  2  0  0  0  0
+    M  END
+    ",
+    }
+  `);
+  }
+});

package/src/iterator.browser.js

@@ -0,0 +1,3 @@
+export function iterator() {
+  throw new Error('Iterator not implemented in the browser');
+}

package/src/iterator.js

@@ -3,7 +3,7 @@ import { createInterface } from 'readline';
 import { parseString } from 'dynamic-typing';
 /**
  *  Parse a SDF file
- * @param {string|ArrayBuffer|Uint8Array} sdf SDF file to parse
+ * @param {NodeJS.ReadableStream} readStream SDF file to parse
  * @param {object} [options={}]
  * @param {Function} [options.filter] Callback allowing to filter the molecules
  * @param {boolean} [options.dynamicTyping] Dynamically type the data