drops browser test, creates spec

src/mol-io/writer/_spec/cif.spec.ts

@@ -1,6 +1,15 @@
+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'
+
+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 cif = await downloadFromPdb('1brr')
 const encoder = CifWriter.createEncoder({
     binary: true,
     encoderName: 'mol*',
@@ -24,4 +33,89 @@ const encoder = CifWriter.createEncoder({
             'encoding': 'delta-rle'
         }
     ])
-});
+});
+
+function getCategoryInstanceProvider(cat: Data.CifCategory, fields: CifWriter.Field[]): CifWriter.Category {
+    return {
+        name: cat.name,
+        instance: () => CifWriter.categoryInstance(fields, { data: cat, rowCount: cat.rowCount })
+    };
+}
+
+function wrap(name: string, field: Data.CifField): CifWriter.Field {
+    const type = Data.getCifFieldType(field);
+    if (type['@type'] === 'str') {
+        return { name, type: CifWriter.Field.Type.Str, value: field.str, valueKind: field.valueKind };
+    } else if (type['@type'] === 'float') {
+        return { name, type: CifWriter.Field.Type.Float, value: field.float, valueKind: field.valueKind };
+    } else {
+        return { name, type: CifWriter.Field.Type.Int, value: field.int, valueKind: field.valueKind };
+    }
+}
+
+function Category(data: EncodedCategory): Data.CifCategory {
+    const map = Object.create(null);
+    const cache = Object.create(null);
+    for (const col of data.columns) map[col.name] = col;
+    return {
+        rowCount: data.rowCount,
+        name: data.name.substr(1),
+        fieldNames: data.columns.map(c => c.name),
+        getField(name) {
+            const col = map[name];
+            if (!col) return void 0;
+            if (!!cache[name]) return cache[name];
+            cache[name] = Field(col);
+            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());
+    });
+})