white-/blacklist filtering

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());
-    });
-})
+}