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Commit f8d085a0 authored by Sebastian Bittrich's avatar Sebastian Bittrich
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white-/blacklist filtering

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src/mol-io/writer/_spec/cif.spec.ts
+ 116
− 53
View file @ f8d085a0
......@@ -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());
});
})
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}
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