diff --git a/src/perf-tests/cif-encoder.ts b/src/perf-tests/cif-encoder.ts
index 59f0eb3f62ebb8bd08bd23b26d9c09d7fae96f57..5749ba5a4f1cdf503dfe40e66baeea35a428bbef 100644
--- a/src/perf-tests/cif-encoder.ts
+++ b/src/perf-tests/cif-encoder.ts
@@ -60,7 +60,7 @@ function testBinary() {
enc.writeCategory(getCat('cat2'), [{ rowCount: 1, fields: category2fields }]);
enc.encode();
const data = enc.getData() as Uint8Array;
- fs.writeFileSync('e:/test/mol-star/test.bcif', new Buffer(data));
+ fs.writeFileSync('e:/test/mol-star/test.bcif', Buffer.from(data));
console.log('written binary');
}
diff --git a/src/servers/model/preprocess/preprocess.ts b/src/servers/model/preprocess/preprocess.ts
index 187a017b762e0c4bab1993e07ef2d54dc3404604..f36ee59ee64122cdf2f856a7c58960dbec67e06d 100644
--- a/src/servers/model/preprocess/preprocess.ts
+++ b/src/servers/model/preprocess/preprocess.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { readStructureWrapper, resolveStructures } from '../server/structure-wrapper';
+import { readStructureWrapper, resolveStructures, readDataAndFrame } from '../server/structure-wrapper';
import { classifyCif } from './converter';
import { Structure } from 'mol-model/structure';
import { CifWriter } from 'mol-io/writer/cif';
@@ -15,7 +15,14 @@ import { ModelPropertiesProvider } from '../property-provider';
// TODO: error handling
-export async function preprocessFile(filename: string, propertyProvider?: ModelPropertiesProvider, outputCif?: string, outputBcif?: string) {
+export function preprocessFile(filename: string, propertyProvider?: ModelPropertiesProvider, outputCif?: string, outputBcif?: string) {
+ return propertyProvider
+ ? preprocess(filename, propertyProvider, outputCif, outputBcif)
+ : convert(filename, outputCif, outputBcif);
+}
+
+
+async function preprocess(filename: string, propertyProvider?: ModelPropertiesProvider, outputCif?: string, outputBcif?: string) {
const input = await readStructureWrapper('entry', '_local_', filename, propertyProvider);
const categories = await classifyCif(input.cifFrame);
const inputStructures = (await resolveStructures(input))!;
@@ -36,6 +43,34 @@ export async function preprocessFile(filename: string, propertyProvider?: ModelP
}
}
+async function convert(filename: string, outputCif?: string, outputBcif?: string) {
+ const { frame } = await readDataAndFrame(filename);
+ const categories = await classifyCif(frame);
+
+ if (outputCif) {
+ const writer = wrapFileToWriter(outputCif);
+ const encoder = CifWriter.createEncoder({ binary: false });
+ encodeConvert(frame.header, categories, encoder, writer);
+ writer.end();
+ }
+
+ if (outputBcif) {
+ const writer = wrapFileToWriter(outputBcif);
+ const encoder = CifWriter.createEncoder({ binary: true, binaryAutoClassifyEncoding: true });
+ encodeConvert(frame.header, categories, encoder, writer);
+ writer.end();
+ }
+}
+
+function encodeConvert(header: string, categories: CifWriter.Category[], encoder: CifWriter.Encoder, writer: Writer) {
+ encoder.startDataBlock(header);
+ for (const cat of categories) {
+ encoder.writeCategory(cat);
+ }
+ encoder.encode();
+ encoder.writeTo(writer);
+}
+
function encode(structure: Structure, header: string, categories: CifWriter.Category[], encoder: CifWriter.Encoder, exportCtx: CifExportContext, writer: Writer) {
const skipCategoryNames = new Set<string>(categories.map(c => c.name));
encoder.startDataBlock(header);
diff --git a/src/servers/model/property-provider.ts b/src/servers/model/property-provider.ts
index d64e5b4cfbdfd3fd20b10d6d16f844f88715cdc3..77ab34c50f691af4eec5b94f8aef27d5adce1f13 100644
--- a/src/servers/model/property-provider.ts
+++ b/src/servers/model/property-provider.ts
@@ -18,11 +18,11 @@ export type AttachModelProperty = (args: { model: Model, params: any, cache: any
export type AttachModelProperties = (args: { model: Model, params: any, cache: any }) => Promise<any>[]
export type ModelPropertiesProvider = (model: Model, cache: any) => Promise<any>[]
-export function createModelPropertiesProviderFromConfig(): ModelPropertiesProvider {
+export function createModelPropertiesProviderFromConfig() {
return createModelPropertiesProvider(Config.customProperties);
}
-export function createModelPropertiesProvider(configOrPath: ModelPropertyProviderConfig | string | undefined): ModelPropertiesProvider {
+export function createModelPropertiesProvider(configOrPath: ModelPropertyProviderConfig | string | undefined): ModelPropertiesProvider | undefined {
let config: ModelPropertyProviderConfig;
if (typeof configOrPath === 'string') {
try {
@@ -35,7 +35,7 @@ export function createModelPropertiesProvider(configOrPath: ModelPropertyProvide
config = configOrPath!;
}
- if (!config || !config.sources || config.sources.length === 0) return () => [];
+ if (!config || !config.sources || config.sources.length === 0) return void 0;
const ps: AttachModelProperties[] = [];
for (const p of config.sources) {
diff --git a/src/servers/model/server/api-local.ts b/src/servers/model/server/api-local.ts
index 83fe022eb141e6fbf4ddeeaa30d15781978b19a4..74178f2c8204b35b48591d995b43eb9fd87e9c05 100644
--- a/src/servers/model/server/api-local.ts
+++ b/src/servers/model/server/api-local.ts
@@ -84,7 +84,7 @@ export function wrapFileToWriter(fn: string) {
},
writeBinary(this: any, data: Uint8Array) {
this.open();
- fs.writeSync(this.file, new Buffer(data.buffer));
+ fs.writeSync(this.file, Buffer.from(data.buffer));
return true;
},
writeString(this: any, data: string) {
diff --git a/src/servers/model/server/api-web.ts b/src/servers/model/server/api-web.ts
index a141dbfef311fc663fe1c8c6fde3cdbb9007aa20..a472a9f3da3d1f54e2c0658808d16dadc4bd71cc 100644
--- a/src/servers/model/server/api-web.ts
+++ b/src/servers/model/server/api-web.ts
@@ -39,7 +39,7 @@ function wrapResponse(fn: string, res: express.Response) {
},
writeBinary(this: any, data: Uint8Array) {
if (!this.headerWritten) this.writeHeader(true);
- return res.write(new Buffer(data.buffer));
+ return res.write(Buffer.from(data.buffer));
},
writeString(this: any, data: string) {
if (!this.headerWritten) this.writeHeader(false);
diff --git a/src/servers/model/server/structure-wrapper.ts b/src/servers/model/server/structure-wrapper.ts
index 615e57e758653a9aa27fd43ef896be644b3ed91b..6eef79c02a7d393f4a4a2f1dc3fde726e3e799d0 100644
--- a/src/servers/model/server/structure-wrapper.ts
+++ b/src/servers/model/server/structure-wrapper.ts
@@ -90,24 +90,30 @@ async function parseCif(data: string|Uint8Array) {
return parsed.result;
}
-export async function readStructureWrapper(key: string, sourceId: string | '_local_', entryId: string, propertyProvider: ModelPropertiesProvider | undefined) {
- const filename = sourceId === '_local_' ? entryId : Config.mapFile(sourceId, entryId);
- if (!filename) throw new Error(`Cound not map '${key}' to a valid filename.`);
- if (!fs.existsSync(filename)) throw new Error(`Could not find source file for '${key}'.`);
-
+export async function readDataAndFrame(filename: string, key?: string) {
perf.start('read');
let data;
try {
data = await readFile(filename);
} catch (e) {
- ConsoleLogger.error(key, '' + e);
- throw new Error(`Could not read the file for '${key}' from disk.`);
+ ConsoleLogger.error(key || filename, '' + e);
+ throw new Error(`Could not read the file for '${key || filename}' from disk.`);
}
perf.end('read');
perf.start('parse');
const frame = (await parseCif(data)).blocks[0];
perf.end('parse');
+
+ return { data, frame };
+}
+
+export async function readStructureWrapper(key: string, sourceId: string | '_local_', entryId: string, propertyProvider: ModelPropertiesProvider | undefined) {
+ const filename = sourceId === '_local_' ? entryId : Config.mapFile(sourceId, entryId);
+ if (!filename) throw new Error(`Cound not map '${key}' to a valid filename.`);
+ if (!fs.existsSync(filename)) throw new Error(`Could not find source file for '${key}'.`);
+
+ const { data, frame } = await readDataAndFrame(filename, key);
perf.start('createModel');
const models = await trajectoryFromMmCIF(frame).run();
perf.end('createModel');
diff --git a/src/servers/model/test.ts b/src/servers/model/test.ts
index 8d7f85b1e4dcbd354389f57bb6227c346e728608..b250de2ef48f836723eeb758a0c62c1bc08ac847 100644
--- a/src/servers/model/test.ts
+++ b/src/servers/model/test.ts
@@ -13,7 +13,7 @@ function wrapFile(fn: string) {
},
writeBinary(this: any, data: Uint8Array) {
this.open();
- fs.writeSync(this.file, new Buffer(data));
+ fs.writeSync(this.file, Buffer.from(data));
return true;
},
writeString(this: any, data: string) {
diff --git a/src/servers/volume/common/binary-schema.ts b/src/servers/volume/common/binary-schema.ts
index 3bd0b10cc276d19f6fee996b42e398d0bb473913..cdc72fb51d33c5190dfb511225c11c63538be095 100644
--- a/src/servers/volume/common/binary-schema.ts
+++ b/src/servers/volume/common/binary-schema.ts
@@ -97,7 +97,7 @@ function writeElement(e: Element, buffer: Buffer, src: any, offset: number) {
function write(element: Element, src: any) {
const size = byteCount(element, src);
- const buffer = new Buffer(size);
+ const buffer = Buffer.alloc(size);
writeElement(element, buffer, src, 0);
return buffer;
}
diff --git a/src/servers/volume/common/file.ts b/src/servers/volume/common/file.ts
index c01670aa19473a7ff5f4ffe5981ad2e61e006907..f641faf7e1c47d393f80f1c12389c652ec3f1d35 100644
--- a/src/servers/volume/common/file.ts
+++ b/src/servers/volume/common/file.ts
@@ -57,7 +57,7 @@ export function createFile(filename: string) {
});
}
-const smallBuffer = SimpleBuffer.fromBuffer(new Buffer(8));
+const smallBuffer = SimpleBuffer.fromBuffer(Buffer.alloc(8));
export async function writeInt(file: FileHandle, value: number, position: number) {
smallBuffer.writeInt32LE(value, 0);
await file.writeBuffer(position, smallBuffer, 4);
diff --git a/src/servers/volume/pack/main.ts b/src/servers/volume/pack/main.ts
index a43bddae2d571cfb11f13b0953e01175d681591f..270682fbeb6f061f1752420102d9f1faa579238a 100644
--- a/src/servers/volume/pack/main.ts
+++ b/src/servers/volume/pack/main.ts
@@ -40,7 +40,7 @@ function updateAllocationProgress(progress: Data.Progress, progressDone: number)
*/
async function allocateFile(ctx: Data.Context) {
const { totalByteSize, file } = ctx;
- const buffer = new Buffer(Math.min(totalByteSize, 8 * 1024 * 1024));
+ const buffer = Buffer.alloc(Math.min(totalByteSize, 8 * 1024 * 1024));
const progress: Data.Progress = { current: 0, max: Math.ceil(totalByteSize / buffer.byteLength) };
let written = 0;
while (written < totalByteSize) {
diff --git a/src/servers/volume/pack/sampling.ts b/src/servers/volume/pack/sampling.ts
index 97d77961d06c77960d7b0450831e762e6e374284..299c1fb8cb802b6aeb76faf85bfffe861763802b 100644
--- a/src/servers/volume/pack/sampling.ts
+++ b/src/servers/volume/pack/sampling.ts
@@ -20,11 +20,11 @@ export async function createContext(filename: string, channels: Format.Context[]
const { extent, valueType, grid, origin } = channels[0].data.header;
const samplingCounts = getSamplingCounts(extent, blockSize);
- const cubeBuffer = new Buffer(new ArrayBuffer(channels.length * blockSize * blockSize * blockSize * getElementByteSize(valueType)));
+ const cubeBuffer = Buffer.from(new ArrayBuffer(channels.length * blockSize * blockSize * blockSize * getElementByteSize(valueType)));
const litteEndianCubeBuffer = SimpleBuffer.IsNativeEndianLittle
? cubeBuffer
- : new Buffer(new ArrayBuffer(channels.length * blockSize * blockSize * blockSize * getElementByteSize(valueType)));
+ : Buffer.from(new ArrayBuffer(channels.length * blockSize * blockSize * blockSize * getElementByteSize(valueType)));
// The data can be periodic iff the extent is the same as the grid and origin is 0.
if (grid.some((v, i) => v !== extent[i]) || origin.some(v => v !== 0)) {
@@ -100,7 +100,7 @@ function createBlockBuffer(sampleCount: number[], blockSize: number, valueType:
for (let i = 0; i < numChannels; i++) values[i] = createTypedArray(valueType, sampleCount[0] * sampleCount[1] * blockSize);
return {
values,
- buffers: values.map(xs => new Buffer(xs.buffer)),
+ buffers: values.map(xs => Buffer.from(xs.buffer)),
slicesWritten: 0
};
}
diff --git a/src/servers/volume/server/local-api.ts b/src/servers/volume/server/local-api.ts
index 8a4a514db1cb3cb4234c4b03e3766e5096d6779b..387d72a3139394630d09d3288a062509f3b9b7f9 100644
--- a/src/servers/volume/server/local-api.ts
+++ b/src/servers/volume/server/local-api.ts
@@ -121,7 +121,7 @@ function wrapFile(fn: string) {
},
writeBinary(this: any, data: Uint8Array) {
this.open();
- fs.writeSync(this.file, new Buffer(data));
+ fs.writeSync(this.file, Buffer.from(data));
return true;
},
writeString(this: any, data: string) {
diff --git a/src/servers/volume/server/web-api.ts b/src/servers/volume/server/web-api.ts
index 5040ba702e85fd1c6396f7c3a016fc8295d555eb..28a0b33845f65f6d833217651d0498d8f0624da7 100644
--- a/src/servers/volume/server/web-api.ts
+++ b/src/servers/volume/server/web-api.ts
@@ -60,7 +60,7 @@ function wrapResponse(fn: string, res: express.Response) {
},
writeBinary(this: any, data: Uint8Array) {
if (!this.headerWritten) this.writeHeader(true);
- return res.write(new Buffer(data.buffer));
+ return res.write(Buffer.from(data.buffer));
},
writeString(this: any, data: string) {
if (!this.headerWritten) this.writeHeader(false);
diff --git a/webpack.config.js b/webpack.config.js
index 8271634c5e16fae7baeffaece602852313099714..e3d711da35516237d7e9a559daa50ef8fa032e1f 100644
--- a/webpack.config.js
+++ b/webpack.config.js
@@ -88,6 +88,7 @@ module.exports = [
createApp('viewer'),
createApp('basic-wrapper'),
createNodeApp('state-docs'),
+ createNodeEntryPoint('preprocess', 'servers/model', 'model-server'),
createApp('model-server-query'),
createBrowserTest('font-atlas'),