molstar
Version:
A comprehensive macromolecular library.
158 lines (157 loc) • 6.57 kB
JavaScript
;
/**
* Copyright (c) 2018-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
* @author David Sehnal <david.sehnal@gmail.com>
* @author Adam Midlik <midlik@gmail.com>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.fileHandleFromPathOrUrl = fileHandleFromPathOrUrl;
exports.fileHandleFromDescriptor = fileHandleFromDescriptor;
exports.fileHandleFromGS = fileHandleFromGS;
exports.fileHandleFromHTTP = fileHandleFromHTTP;
const tslib_1 = require("tslib");
const fs = tslib_1.__importStar(require("fs"));
const node_fetch_1 = tslib_1.__importDefault(require("node-fetch"));
const file_handle_1 = require("../../mol-io/common/file-handle");
const simple_buffer_1 = require("../../mol-io/common/simple-buffer");
const mol_util_1 = require("../../mol-util");
const file_1 = require("../volume/common/file");
const google_cloud_storage_1 = require("./google-cloud-storage");
/** Create a file handle from either a file path or a URL (supports file://, http(s)://, gs:// protocols). */
async function fileHandleFromPathOrUrl(pathOrUrl, name) {
if (pathOrUrl.startsWith('gs://')) {
return fileHandleFromGS(pathOrUrl, name);
}
else if (pathOrUrl.startsWith('http://') || pathOrUrl.startsWith('https://')) {
return fileHandleFromHTTP(pathOrUrl, name);
}
else if (pathOrUrl.startsWith('file://')) {
return fileHandleFromDescriptor(await (0, file_1.openRead)(pathOrUrl.slice('file://'.length)), name);
}
else {
return fileHandleFromDescriptor(await (0, file_1.openRead)(pathOrUrl), name);
}
}
function fileHandleFromDescriptor(file, name) {
if (fs === undefined)
throw new Error('fs module not available');
return {
name,
readBuffer: (position, sizeOrBuffer, length, byteOffset) => {
return new Promise((res, rej) => {
let outBuffer;
if (typeof sizeOrBuffer === 'number') {
byteOffset = (0, mol_util_1.defaults)(byteOffset, 0);
length = (0, mol_util_1.defaults)(length, sizeOrBuffer);
outBuffer = simple_buffer_1.SimpleBuffer.fromArrayBuffer(new ArrayBuffer(sizeOrBuffer));
}
else {
byteOffset = (0, mol_util_1.defaults)(byteOffset, 0);
length = (0, mol_util_1.defaults)(length, sizeOrBuffer.length);
outBuffer = sizeOrBuffer;
}
fs.read(file, outBuffer, byteOffset, length, position, (err, bytesRead, buffer) => {
if (err) {
rej(err);
return;
}
if (length !== bytesRead) {
console.warn(`byteCount ${length} and bytesRead ${bytesRead} differ`);
}
res({ bytesRead, buffer });
});
});
},
writeBuffer: (position, buffer, length) => {
length = (0, mol_util_1.defaults)(length, buffer.length);
return new Promise((res, rej) => {
fs.write(file, buffer, 0, length, position, (err, written) => {
if (err)
rej(err);
else
res(written);
});
});
},
writeBufferSync: (position, buffer, length) => {
length = (0, mol_util_1.defaults)(length, buffer.length);
return fs.writeSync(file, buffer, 0, length, position);
},
close: () => {
try {
if (file !== void 0)
fs.close(file, mol_util_1.noop);
}
catch (e) {
}
}
};
}
/** Create a read-only file handle from a Google Cloud Storage URL (gs://bucket-name/file-name). */
function fileHandleFromGS(url, name) {
return {
name,
readBuffer: async (position, sizeOrBuffer, length, byteOffset) => {
let outBuffer;
if (typeof sizeOrBuffer === 'number') {
length = (0, mol_util_1.defaults)(length, sizeOrBuffer);
outBuffer = simple_buffer_1.SimpleBuffer.fromArrayBuffer(new ArrayBuffer(sizeOrBuffer));
}
else {
length = (0, mol_util_1.defaults)(length, sizeOrBuffer.length);
outBuffer = sizeOrBuffer;
}
let data;
try {
data = await (0, google_cloud_storage_1.downloadGs)(url, { decompress: false, start: position, end: position + length - 1 });
}
catch (err) {
err.isFileNotFound = true;
throw err;
}
const bytesRead = data.copy(outBuffer, byteOffset);
if (length !== bytesRead) {
console.warn(`byteCount ${length} and bytesRead ${bytesRead} differ`);
}
return { bytesRead, buffer: outBuffer };
},
writeBuffer: () => {
throw new Error('Writing to Google Cloud Storage file handle not supported');
},
writeBufferSync: () => {
throw new Error('Writing to Google Cloud Storage file handle not supported');
},
close: () => { },
};
}
/** Create a read-only file handle from a HTTP or HTTPS URL. */
function fileHandleFromHTTP(url, name) {
let innerHandle = undefined;
return {
name,
readBuffer: async (position, sizeOrBuffer, length, byteOffset) => {
if (!innerHandle) {
const response = await (0, node_fetch_1.default)(url);
if (response.ok) {
const buffer = await response.buffer();
innerHandle = file_handle_1.FileHandle.fromBuffer(buffer, name);
}
else {
const error = new Error(`fileHandleFromHTTP: Fetch failed with status code ${response.status}`);
error.isFileNotFound = true;
throw error;
}
}
return innerHandle.readBuffer(position, sizeOrBuffer, length, byteOffset);
},
writeBuffer: () => {
throw new Error('Writing to HTTP(S) file handle not supported');
},
writeBufferSync: () => {
throw new Error('Writing to HTTP(S) file handle not supported');
},
close: () => { },
};
}