From f8d085a0348cc139ed39ca120663cb6080e78bc2 Mon Sep 17 00:00:00 2001
From: Sebastian Bittrich <bittrich@hs-mittweida.de>
Date: Fri, 7 Jun 2019 15:38:06 -0700
Subject: [PATCH] white-/blacklist filtering
---
src/mol-io/writer/_spec/cif.spec.ts | 169 +++++++++++++++++++---------
1 file changed, 116 insertions(+), 53 deletions(-)
diff --git a/src/mol-io/writer/_spec/cif.spec.ts b/src/mol-io/writer/_spec/cif.spec.ts
index 7231c5d82..b0c3bfc61 100644
--- a/src/mol-io/writer/_spec/cif.spec.ts
+++ b/src/mol-io/writer/_spec/cif.spec.ts
@@ -2,17 +2,20 @@ import * as Data from '../../reader/cif/data-model'
import { CifWriter } from '../cif';
import decodeMsgPack from '../../common/msgpack/decode'
import { EncodedFile, EncodedCategory } from '../../common/binary-cif';
-import Field from '../../reader/cif/binary/field'
+import Field from '../../reader/cif/binary/field';
+import * as C from '../cif/encoder';
const cartn_x = Data.CifField.ofNumbers([1.001, 1.002, 1.003, 1.004, 1.005, 1.006, 1.007, 1.008, 1.009]);
const cartn_y = Data.CifField.ofNumbers([-3.0, -2.666, -2.3333, -2.0, -1.666, -1.333, -1.0, -0.666, -0.333]);
const cartn_z = Data.CifField.ofNumbers([1, 2, 3, 4, 5, 6, 7, 8, 9].map(i => Math.sqrt(i)));
const label_seq_id = Data.CifField.ofNumbers([1, 2, 3, 6, 11, 23, 47, 106, 235]);
const atom_site = Data.CifCategory.ofFields('atom_site', { 'Cartn_x': cartn_x, 'Cartn_y': cartn_y, 'Cartn_z': cartn_z, 'label_seq_id': label_seq_id });
+const field1 = Data.CifField.ofNumbers([1, 2, 3, 6, 11, 23, 47, 106, 235]);
+const field2 = Data.CifField.ofNumbers([-1, -2, -3, -6, -11, -23, -47, -106, -235]);
+const other_fields = Data.CifCategory.ofFields('other_fields', { 'field1': field1, 'field2': field2 });
-const encoder = CifWriter.createEncoder({
+const encoding_aware_encoder = CifWriter.createEncoder({
binary: true,
- encoderName: 'mol*',
binaryAutoClassifyEncoding: true,
binaryEncodingPovider: CifWriter.createEncodingProviderFromJsonConfig([
{
@@ -35,6 +38,115 @@ const encoder = CifWriter.createEncoder({
])
});
+describe('encoding-config', () => {
+ const decoded = process(encoding_aware_encoder);
+
+ const decoded_atom_site = decoded.blocks[0].categories['atom_site'];
+ const decoded_cartn_x = decoded_atom_site.getField('Cartn_x')!;
+ const decoded_cartn_y = decoded_atom_site.getField('Cartn_y')!;
+ const decoded_cartn_z = decoded_atom_site.getField('Cartn_z')!;
+ const decoded_label_seq_id = decoded_atom_site.getField('label_seq_id')!;
+
+ const delta = 0.001;
+ function assert(e: ArrayLike<number>, a: ArrayLike<number>) {
+ expect(e.length).toBe(a.length);
+ for (let i = 0; i < e.length; i++) {
+ expect(Math.abs(e[i] - a[i])).toBeLessThan(delta);
+ }
+ }
+
+ function join(field: Data.CifField) {
+ return field.binaryEncoding!.map(e => e.kind).join();
+ }
+
+ it('strategy', () => {
+ expect(join(decoded_cartn_x)).toBe('FixedPoint,Delta,IntegerPacking,ByteArray');
+ expect(join(decoded_cartn_y)).toBe('FixedPoint,RunLength,IntegerPacking,ByteArray');
+ expect(join(decoded_cartn_z)).toBe('FixedPoint,Delta,IntegerPacking,ByteArray');
+ expect(join(decoded_label_seq_id)).toBe('Delta,RunLength,IntegerPacking,ByteArray');
+ });
+
+ it('precision', () => {
+ assert(decoded_cartn_x.toFloatArray(), cartn_x.toFloatArray());
+ assert(decoded_cartn_y.toFloatArray(), cartn_y.toFloatArray().map(d => Math.round(d)));
+ assert(decoded_cartn_z.toFloatArray(), cartn_z.toFloatArray().map(d => Math.round(d * 10) / 10));
+ assert(decoded_label_seq_id.toIntArray(), label_seq_id.toIntArray());
+ });
+});
+
+const filter_aware_encoder1 = CifWriter.createEncoder({
+ binary: true,
+ binaryAutoClassifyEncoding: true
+});
+filter_aware_encoder1.setFilter(C.Category.whitelistBlacklistFilter(['atom_site'], // allow only category atom_site
+ [], // blacklist no categories
+ ['atom_site.Cartn_x', 'atom_site.Cartn_y'], // for atom_site: allow only Cartn_x and Cartn_y
+ [])); // blacklist no fields
+
+const filter_aware_encoder2 = CifWriter.createEncoder({
+ binary: true
+});
+filter_aware_encoder2.setFilter(C.Category.whitelistBlacklistFilter([],
+ ['atom_site'], // ignore atom_site category
+ [],
+ ['other_fields.field2'])); // exclude field2
+
+describe('filtering-config', () => {
+ const decoded1 = process(filter_aware_encoder1);
+
+ const atom_site1 = decoded1.blocks[0].categories['atom_site'];
+ const cartn_x1 = atom_site1.getField('Cartn_x');
+ const cartn_y1 = atom_site1.getField('Cartn_y');
+ const cartn_z1 = atom_site1.getField('Cartn_z');
+ const label_seq_id1 = atom_site1.getField('label_seq_id');
+ const fields1 = decoded1.blocks[0].categories['other_fields'];
+
+ it('whitelist-filtering', () => {
+ expect(atom_site1).toBeDefined();
+ expect(cartn_x1).toBeDefined();
+ expect(cartn_y1).toBeDefined();
+ expect(cartn_z1).toBeUndefined();
+ expect(label_seq_id1).toBeUndefined();
+ expect(fields1).toBeUndefined();
+ });
+
+ const decoded2 = process(filter_aware_encoder2);
+
+ const atom_site2 = decoded2.blocks[0].categories['atom_site'];
+ const fields2 = decoded2.blocks[0].categories['other_fields'];
+ const field12 = fields2.getField('field1');
+ const field22 = fields2.getField('field2');
+
+ it('blacklist-filtering', () => {
+ expect(atom_site2).toBeUndefined();
+ expect(fields2).toBeDefined();
+ expect(field12).toBeDefined();
+ expect(field22).toBeUndefined();
+ });
+});
+
+function process(encoder: C.Encoder) {
+ encoder.startDataBlock('test');
+
+ for (const cat of [atom_site, other_fields]) {
+ const fields: CifWriter.Field[] = [];
+ for (const f of cat.fieldNames) {
+ fields.push(wrap(f, cat.getField(f)!))
+ }
+ encoder.writeCategory(getCategoryInstanceProvider(cat, fields));
+ }
+
+ const encoded = encoder.getData() as Uint8Array;
+
+ const unpacked = decodeMsgPack(encoded) as EncodedFile;
+ return Data.CifFile(unpacked.dataBlocks.map(block => {
+ const cats = Object.create(null);
+ for (const cat of block.categories) cats[cat.name.substr(1)] = Category(cat);
+ return Data.CifBlock(block.categories.map(c => c.name.substr(1)), cats, block.header);
+ }));
+}
+
+
function getCategoryInstanceProvider(cat: Data.CifCategory, fields: CifWriter.Field[]): CifWriter.Category {
return {
name: cat.name,
@@ -69,53 +181,4 @@ function Category(data: EncodedCategory): Data.CifCategory {
return cache[name];
}
}
-}
-describe('config', () => {
- encoder.startDataBlock('test');
- const fields: CifWriter.Field[] = [];
- for (const f of atom_site.fieldNames) {
- fields.push(wrap(f, atom_site.getField(f)!))
- }
-
- encoder.writeCategory(getCategoryInstanceProvider(atom_site, fields));
- const encoded = encoder.getData() as Uint8Array;
-
- const unpacked = decodeMsgPack(encoded) as EncodedFile;
- const decoded = Data.CifFile(unpacked.dataBlocks.map(block => {
- const cats = Object.create(null);
- for (const cat of block.categories) cats[cat.name.substr(1)] = Category(cat);
- return Data.CifBlock(block.categories.map(c => c.name.substr(1)), cats, block.header);
- }));
-
- const decoded_atom_site = decoded.blocks[0].categories['atom_site'];
- const decoded_cartn_x = decoded_atom_site.getField('Cartn_x')!;
- const decoded_cartn_y = decoded_atom_site.getField('Cartn_y')!;
- const decoded_cartn_z = decoded_atom_site.getField('Cartn_z')!;
- const decoded_label_seq_id = decoded_atom_site.getField('label_seq_id')!;
-
- const delta = 0.001;
- function assert(e: ArrayLike<number>, a: ArrayLike<number>) {
- expect(e.length).toBe(a.length);
- for (let i = 0; i < e.length; i++) {
- expect(Math.abs(e[i] - a[i])).toBeLessThan(delta);
- }
- }
-
- function join(field: Data.CifField) {
- return field.binaryEncoding!.map(e => e.kind).join();
- }
-
- it('strategy', () => {
- expect(join(decoded_cartn_x)).toBe('FixedPoint,Delta,IntegerPacking,ByteArray');
- expect(join(decoded_cartn_y)).toBe('FixedPoint,RunLength,IntegerPacking,ByteArray');
- expect(join(decoded_cartn_z)).toBe('FixedPoint,Delta,IntegerPacking,ByteArray');
- expect(join(decoded_label_seq_id)).toBe('Delta,RunLength,IntegerPacking,ByteArray');
- });
-
- it('precision', () => {
- assert(decoded_cartn_x.toFloatArray(), cartn_x.toFloatArray());
- assert(decoded_cartn_y.toFloatArray(), cartn_y.toFloatArray().map(d => Math.round(d)));
- assert(decoded_cartn_z.toFloatArray(), cartn_z.toFloatArray().map(d => Math.round(d * 10) / 10));
- assert(decoded_label_seq_id.toIntArray(), label_seq_id.toIntArray());
- });
-})
\ No newline at end of file
+}
\ No newline at end of file
--
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