molstar 3.0.0 → 3.0.1

package/lib/commonjs/servers/model/server/structure-wrapper.js

@@ -1,354 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.resolveStructures = exports.resolveStructure = exports.readStructureWrapper = exports.readDataAndFrame = exports.StructureCache = exports.createStructureWrapperFromJobEntry = exports.StructureSourceType = void 0;
-var tslib_1 = require("tslib");
-var structure_1 = require("../../../mol-model/structure");
-var performance_monitor_1 = require("../../../mol-util/performance-monitor");
-var cache_1 = require("./cache");
-var config_1 = require("../config");
-var cif_1 = require("../../../mol-io/reader/cif");
-var util = (0, tslib_1.__importStar)(require("util"));
-var fs = (0, tslib_1.__importStar)(require("fs"));
-var zlib = (0, tslib_1.__importStar)(require("zlib"));
-var console_logger_1 = require("../../../mol-util/console-logger");
-var mmcif_1 = require("../../../mol-model-formats/structure/mmcif");
-var fetch_retry_1 = require("../utils/fetch-retry");
-var mol_task_1 = require("../../../mol-task");
-require('util.promisify').shim();
-var StructureSourceType;
-(function (StructureSourceType) {
-    StructureSourceType[StructureSourceType["File"] = 0] = "File";
-    StructureSourceType[StructureSourceType["Cache"] = 1] = "Cache";
-})(StructureSourceType = exports.StructureSourceType || (exports.StructureSourceType = {}));
-function createStructureWrapperFromJobEntry(entry, propertyProvider, allowCache) {
-    if (allowCache === void 0) { allowCache = true; }
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        var ret_1, ret;
-        return (0, tslib_1.__generator)(this, function (_a) {
-            switch (_a.label) {
-                case 0:
-                    if (allowCache && config_1.ModelServerConfig.cacheMaxSizeInBytes > 0) {
-                        ret_1 = exports.StructureCache.get(entry.key);
-                        if (ret_1)
-                            return [2 /*return*/, ret_1];
-                    }
-                    return [4 /*yield*/, readStructureWrapper(entry.key, entry.sourceId, entry.entryId, entry.job.id, propertyProvider)];
-                case 1:
-                    ret = _a.sent();
-                    if (allowCache && config_1.ModelServerConfig.cacheMaxSizeInBytes > 0) {
-                        exports.StructureCache.add(ret);
-                    }
-                    return [2 /*return*/, ret];
-            }
-        });
-    });
-}
-exports.createStructureWrapperFromJobEntry = createStructureWrapperFromJobEntry;
-exports.StructureCache = new cache_1.Cache(function (s) { return s.key; }, function (s) { return s.approximateSize; });
-var perf = new performance_monitor_1.PerformanceMonitor();
-var readFileAsync = util.promisify(fs.readFile);
-var unzipAsync = util.promisify(zlib.unzip);
-function readFile(filename) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        var isGz, input, data, i, data, _a;
-        var _b;
-        return (0, tslib_1.__generator)(this, function (_c) {
-            switch (_c.label) {
-                case 0:
-                    isGz = /\.gz$/i.test(filename);
-                    if (!filename.match(/\.bcif/)) return [3 /*break*/, 4];
-                    return [4 /*yield*/, readFileAsync(filename)];
-                case 1:
-                    input = _c.sent();
-                    if (!isGz) return [3 /*break*/, 3];
-                    return [4 /*yield*/, unzipAsync(input)];
-                case 2:
-                    input = _c.sent();
-                    _c.label = 3;
-                case 3:
-                    data = new Uint8Array(input.byteLength);
-                    for (i = 0; i < input.byteLength; i++)
-                        data[i] = input[i];
-                    return [2 /*return*/, { data: data, isBinary: true }];
-                case 4:
-                    if (!isGz) return [3 /*break*/, 7];
-                    _a = unzipAsync;
-                    return [4 /*yield*/, readFileAsync(filename)];
-                case 5: return [4 /*yield*/, _a.apply(void 0, [_c.sent()])];
-                case 6:
-                    data = _c.sent();
-                    return [2 /*return*/, { data: data.toString('utf8'), isBinary: false }];
-                case 7:
-                    _b = {};
-                    return [4 /*yield*/, readFileAsync(filename, 'utf8')];
-                case 8: return [2 /*return*/, (_b.data = _c.sent(), _b.isBinary = false, _b)];
-            }
-        });
-    });
-}
-function parseCif(data) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        var comp, parsed;
-        return (0, tslib_1.__generator)(this, function (_a) {
-            switch (_a.label) {
-                case 0:
-                    comp = cif_1.CIF.parse(data);
-                    return [4 /*yield*/, comp.run()];
-                case 1:
-                    parsed = _a.sent();
-                    if (parsed.isError)
-                        throw parsed;
-                    return [2 /*return*/, parsed.result];
-            }
-        });
-    });
-}
-function readDataAndFrame(filename, key) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        var data, isBinary, read, e_1, frame;
-        return (0, tslib_1.__generator)(this, function (_a) {
-            switch (_a.label) {
-                case 0:
-                    perf.start('read');
-                    _a.label = 1;
-                case 1:
-                    _a.trys.push([1, 3, , 4]);
-                    return [4 /*yield*/, readFile(filename)];
-                case 2:
-                    read = _a.sent();
-                    data = read.data;
-                    isBinary = read.isBinary;
-                    return [3 /*break*/, 4];
-                case 3:
-                    e_1 = _a.sent();
-                    console_logger_1.ConsoleLogger.error(key || filename, '' + e_1);
-                    throw new Error("Could not read the file for '".concat(key || filename, "' from disk."));
-                case 4:
-                    perf.end('read');
-                    perf.start('parse');
-                    return [4 /*yield*/, parseCif(data)];
-                case 5:
-                    frame = (_a.sent()).blocks[0];
-                    perf.end('parse');
-                    return [2 /*return*/, { data: data, frame: frame, isBinary: isBinary }];
-            }
-        });
-    });
-}
-exports.readDataAndFrame = readDataAndFrame;
-function fetchDataAndFrame(jobId, uri, format, key) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        var isBinary, data, response, input, _a, i, _b, _c, e_2, frame;
-        return (0, tslib_1.__generator)(this, function (_d) {
-            switch (_d.label) {
-                case 0:
-                    perf.start('read');
-                    isBinary = format.startsWith('bcif');
-                    _d.label = 1;
-                case 1:
-                    _d.trys.push([1, 11, , 12]);
-                    console_logger_1.ConsoleLogger.logId(jobId, 'Fetch', "".concat(uri));
-                    return [4 /*yield*/, (0, fetch_retry_1.fetchRetry)(uri, 500, 3, function () { return console_logger_1.ConsoleLogger.logId(jobId, 'Fetch', "Retrying to fetch '".concat(uri, "'")); })];
-                case 2:
-                    response = _d.sent();
-                    if (!format.endsWith('.gz')) return [3 /*break*/, 5];
-                    _a = unzipAsync;
-                    return [4 /*yield*/, response.arrayBuffer()];
-                case 3: return [4 /*yield*/, _a.apply(void 0, [_d.sent()])];
-                case 4:
-                    input = _d.sent();
-                    if (isBinary) {
-                        data = new Uint8Array(input.byteLength);
-                        for (i = 0; i < input.byteLength; i++)
-                            data[i] = input[i];
-                    }
-                    else {
-                        data = input.toString('utf8');
-                    }
-                    return [3 /*break*/, 10];
-                case 5:
-                    if (!isBinary) return [3 /*break*/, 7];
-                    _c = Uint8Array.bind;
-                    return [4 /*yield*/, response.arrayBuffer()];
-                case 6:
-                    _b = new (_c.apply(Uint8Array, [void 0, _d.sent()]))();
-                    return [3 /*break*/, 9];
-                case 7: return [4 /*yield*/, response.text()];
-                case 8:
-                    _b = _d.sent();
-                    _d.label = 9;
-                case 9:
-                    data = _b;
-                    _d.label = 10;
-                case 10: return [3 /*break*/, 12];
-                case 11:
-                    e_2 = _d.sent();
-                    console_logger_1.ConsoleLogger.error(key || uri, '' + e_2);
-                    throw new Error("Could not fetch the file for '".concat(key || uri, "'."));
-                case 12:
-                    perf.end('read');
-                    perf.start('parse');
-                    return [4 /*yield*/, parseCif(data)];
-                case 13:
-                    frame = (_d.sent()).blocks[0];
-                    perf.end('parse');
-                    return [2 /*return*/, { data: data, frame: frame, isBinary: isBinary }];
-            }
-        });
-    });
-}
-function readOrFetch(jobId, key, sourceId, entryId) {
-    var mapped = sourceId === '_local_' ? [entryId] : (0, config_1.mapSourceAndIdToFilename)(sourceId, entryId);
-    if (!mapped)
-        throw new Error("Cound not map '".concat(key, "' for a resource."));
-    var uri = mapped[0].toLowerCase();
-    if (uri.startsWith('http://') || uri.startsWith('https://') || uri.startsWith('ftp://')) {
-        return fetchDataAndFrame(jobId, mapped[0], (mapped[1] || 'cif').toLowerCase(), key);
-    }
-    if (!fs.existsSync(mapped[0]))
-        throw new Error("Could not find source file for '".concat(key, "'."));
-    return readDataAndFrame(mapped[0], key);
-}
-function readStructureWrapper(key, sourceId, entryId, jobId, propertyProvider) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        var _a, data, frame, isBinary, trajectory, models, modelMap, i, m, ret;
-        return (0, tslib_1.__generator)(this, function (_b) {
-            switch (_b.label) {
-                case 0: return [4 /*yield*/, readOrFetch(jobId || '', key, sourceId, entryId)];
-                case 1:
-                    _a = _b.sent(), data = _a.data, frame = _a.frame, isBinary = _a.isBinary;
-                    perf.start('createModel');
-                    return [4 /*yield*/, (0, mmcif_1.trajectoryFromMmCIF)(frame).run()];
-                case 2:
-                    trajectory = _b.sent();
-                    perf.end('createModel');
-                    models = [];
-                    modelMap = new Map();
-                    i = 0;
-                    _b.label = 3;
-                case 3:
-                    if (!(i < trajectory.frameCount)) return [3 /*break*/, 6];
-                    return [4 /*yield*/, mol_task_1.Task.resolveInContext(trajectory.getFrameAtIndex(i))];
-                case 4:
-                    m = _b.sent();
-                    models.push(m);
-                    modelMap.set(m.modelNum, m);
-                    _b.label = 5;
-                case 5:
-                    i++;
-                    return [3 /*break*/, 3];
-                case 6:
-                    ret = {
-                        info: {
-                            sourceType: StructureSourceType.File,
-                            readTime: perf.time('read'),
-                            parseTime: perf.time('parse'),
-                            createModelTime: perf.time('createModel'),
-                            attachPropsTime: 0,
-                            sourceId: sourceId,
-                            entryId: entryId
-                        },
-                        isBinary: isBinary,
-                        key: key,
-                        approximateSize: typeof data === 'string' ? 2 * data.length : data.length,
-                        models: models,
-                        modelMap: modelMap,
-                        structureModelMap: new Map(),
-                        cifFrame: frame,
-                        propertyProvider: propertyProvider,
-                        cache: Object.create(null)
-                    };
-                    return [2 /*return*/, ret];
-            }
-        });
-    });
-}
-exports.readStructureWrapper = readStructureWrapper;
-function resolveStructure(wrapper, modelNum) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        var model, structure, modelProps, _i, modelProps_1, p;
-        return (0, tslib_1.__generator)(this, function (_a) {
-            switch (_a.label) {
-                case 0:
-                    if (typeof modelNum === 'undefined')
-                        modelNum = wrapper.models[0].modelNum;
-                    if (wrapper.structureModelMap.has(modelNum))
-                        return [2 /*return*/, wrapper.structureModelMap.get(modelNum)];
-                    if (!wrapper.modelMap.has(modelNum)) {
-                        return [2 /*return*/, void 0];
-                    }
-                    model = wrapper.modelMap.get(modelNum);
-                    structure = structure_1.Structure.ofModel(model);
-                    if (!wrapper.propertyProvider) return [3 /*break*/, 4];
-                    modelProps = wrapper.propertyProvider(model, wrapper.cache);
-                    _i = 0, modelProps_1 = modelProps;
-                    _a.label = 1;
-                case 1:
-                    if (!(_i < modelProps_1.length)) return [3 /*break*/, 4];
-                    p = modelProps_1[_i];
-                    return [4 /*yield*/, tryAttach(wrapper.key, p)];
-                case 2:
-                    _a.sent();
-                    _a.label = 3;
-                case 3:
-                    _i++;
-                    return [3 /*break*/, 1];
-                case 4: return [2 /*return*/, structure];
-            }
-        });
-    });
-}
-exports.resolveStructure = resolveStructure;
-function resolveStructures(wrapper, modelNums) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        var ret, _i, _a, n, s;
-        return (0, tslib_1.__generator)(this, function (_b) {
-            switch (_b.label) {
-                case 0:
-                    ret = [];
-                    _i = 0, _a = modelNums || wrapper.models.map(function (m) { return m.modelNum; });
-                    _b.label = 1;
-                case 1:
-                    if (!(_i < _a.length)) return [3 /*break*/, 4];
-                    n = _a[_i];
-                    return [4 /*yield*/, resolveStructure(wrapper, n)];
-                case 2:
-                    s = _b.sent();
-                    if (s)
-                        ret.push(s);
-                    _b.label = 3;
-                case 3:
-                    _i++;
-                    return [3 /*break*/, 1];
-                case 4: return [2 /*return*/, ret];
-            }
-        });
-    });
-}
-exports.resolveStructures = resolveStructures;
-function tryAttach(key, promise) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        var e_3;
-        return (0, tslib_1.__generator)(this, function (_a) {
-            switch (_a.label) {
-                case 0:
-                    _a.trys.push([0, 2, , 3]);
-                    return [4 /*yield*/, promise];
-                case 1:
-                    _a.sent();
-                    return [3 /*break*/, 3];
-                case 2:
-                    e_3 = _a.sent();
-                    console_logger_1.ConsoleLogger.errorId(key, 'Custom prop:' + e_3);
-                    return [3 /*break*/, 3];
-                case 3: return [2 /*return*/];
-            }
-        });
-    });
-}
-//# sourceMappingURL=structure-wrapper.js.map

package/lib/commonjs/servers/model/server.js

@@ -1,66 +0,0 @@
-#!/usr/bin/env node
-"use strict";
-/**
- * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-Object.defineProperty(exports, "__esModule", { value: true });
-var tslib_1 = require("tslib");
-var compression_1 = (0, tslib_1.__importDefault)(require("compression"));
-var express_1 = (0, tslib_1.__importDefault)(require("express"));
-var console_logger_1 = require("../../mol-util/console-logger");
-var performance_monitor_1 = require("../../mol-util/performance-monitor");
-var config_1 = require("./config");
-var api_web_1 = require("./server/api-web");
-var version_1 = require("./version");
-function setupShutdown() {
-    if (config_1.ModelServerConfig.shutdownTimeoutVarianceMinutes > config_1.ModelServerConfig.shutdownTimeoutMinutes) {
-        console_logger_1.ConsoleLogger.log('Server', 'Shutdown timeout variance is greater than the timer itself, ignoring.');
-    }
-    else {
-        var tVar = 0;
-        if (config_1.ModelServerConfig.shutdownTimeoutVarianceMinutes > 0) {
-            tVar = 2 * (Math.random() - 0.5) * config_1.ModelServerConfig.shutdownTimeoutVarianceMinutes;
-        }
-        var tMs = (config_1.ModelServerConfig.shutdownTimeoutMinutes + tVar) * 60 * 1000;
-        console.log("----------------------------------------------------------------------------");
-        console.log("  The server will shut down in ".concat(performance_monitor_1.PerformanceMonitor.format(tMs), " to prevent slow performance."));
-        console.log("  Please make sure a daemon is running that will automatically restart it.");
-        console.log("----------------------------------------------------------------------------");
-        console.log();
-        setTimeout(function () {
-            // if (WebApi.ApiState.pendingQueries > 0) {
-            //     WebApi.ApiState.shutdownOnZeroPending = true;
-            // } else {
-            console_logger_1.ConsoleLogger.log('Server', "Shut down due to timeout.");
-            process.exit(0);
-            // }
-        }, tMs);
-    }
-}
-(0, config_1.configureServer)();
-function startServer() {
-    var app = (0, express_1.default)();
-    app.use((0, compression_1.default)({
-        level: 6, memLevel: 9, chunkSize: 16 * 16384,
-        filter: function (req, res) {
-            var ct = res.getHeader('Content-Type');
-            if (typeof ct === 'string' && ct.indexOf('tar+gzip') > 0)
-                return false;
-            return true;
-        }
-    }));
-    (0, api_web_1.initWebApi)(app);
-    var port = process.env.port || config_1.ModelServerConfig.defaultPort;
-    app.listen(port).setTimeout(config_1.ModelServerConfig.requestTimeoutMs);
-    console.log("Mol* ModelServer ".concat(version_1.VERSION));
-    console.log("");
-    console.log("The server is running on port ".concat(port, "."));
-    console.log("");
-}
-startServer();
-if (config_1.ModelServerConfig.shutdownTimeoutMinutes > 0) {
-    setupShutdown();
-}
-//# sourceMappingURL=server.js.map

package/lib/commonjs/servers/model/test.js

@@ -1,82 +0,0 @@
-"use strict";
-// import { resolveJob } from './server/query';
-// import * as fs from 'fs'
-// import * as path from 'path'
-// import { StructureCache } from './server/structure-wrapper';
-// import { createJob } from './server/jobs';
-// function wrapFile(fn: string) {
-//     const w = {
-//         open(this: any) {
-//             if (this.opened) return;
-//             this.file = fs.openSync(fn, 'w');
-//             this.opened = true;
-//         },
-//         writeBinary(this: any, data: Uint8Array) {
-//             this.open();
-//             fs.writeSync(this.file, Buffer.from(data));
-//             return true;
-//         },
-//         writeString(this: any, data: string) {
-//             this.open();
-//             fs.writeSync(this.file, data);
-//             return true;
-//         },
-//         end(this: any) {
-//             if (!this.opened || this.ended) return;
-//             fs.close(this.file, function () { });
-//             this.ended = true;
-//         },
-//         file: 0,
-//         ended: false,
-//         opened: false
-//     };
-//     return w;
-// }
-// export const basePath = path.join(__dirname, '..', '..', '..', '..')
-// export const examplesPath = path.join(basePath, 'examples')
-// export const outPath = path.join(basePath, 'build', 'test')
-// if (!fs.existsSync(outPath)) fs.mkdirSync(outPath);
-// async function run() {
-//     try {
-//         // const testFile = '1crn.cif'
-//         // const testFile = '1grm_updated.cif'
-//         // const testFile = 'C:/Projects/mol-star/molstar/build/test/in/1grm_updated.cif'
-//         // const request = createJob({
-//         //     entryId: testFile,
-//         //     queryName: 'full',
-//         //     queryParams: { },
-//         // });
-//         const testFile = '1cbs_updated.cif'
-//         const request = createJob({
-//             entryId: path.join(examplesPath, testFile),
-//             queryName: 'full',
-//             queryParams: { }
-//         });
-//         // const request = createJob({
-//         //     entryId: path.join(examplesPath, testFile),
-//         //     queryName: 'atoms',
-//         //     queryParams: {
-//         //         atom_site: { label_comp_id: 'ALA' }
-//         //     }
-//         // });
-//         // const request = createJob({
-//         //     entryId: path.join(examplesPath, testFile),
-//         //     queryName: 'residueInteraction',
-//         //     queryParams: {
-//         //         atom_site: { label_comp_id: 'REA' },
-//         //         radius: 5
-//         //     }
-//         // });
-//         const encoder = await resolveJob(request);
-//         const writer = wrapFile(path.join(outPath, testFile));
-//         // const writer = wrapFile(path.join(outPath, '1grm_test.cif'));
-//         encoder.writeTo(writer);
-//         writer.end();
-//     } catch (e) {
-//         console.error(e)
-//     } finally {
-//         StructureCache.expireAll();
-//     }
-// }
-// run();
-//# sourceMappingURL=test.js.map

package/lib/commonjs/servers/model/utils/fetch-props-pdbe.d.ts

@@ -1,6 +0,0 @@
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-export {};

package/lib/commonjs/servers/model/utils/fetch-props-pdbe.js

@@ -1,118 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-Object.defineProperty(exports, "__esModule", { value: true });
-var tslib_1 = require("tslib");
-var node_fetch_1 = (0, tslib_1.__importDefault)(require("node-fetch"));
-var fs = (0, tslib_1.__importStar)(require("fs"));
-var path = (0, tslib_1.__importStar)(require("path"));
-var argparse = (0, tslib_1.__importStar)(require("argparse"));
-var make_dir_1 = require("../../../mol-util/make-dir");
-var now_1 = require("../../../mol-util/now");
-var performance_monitor_1 = require("../../../mol-util/performance-monitor");
-var cmdParser = new argparse.ArgumentParser({
-    add_help: true,
-    description: 'Download JSON data from PDBe API'
-});
-cmdParser.add_argument('--in', { help: 'Input folder', required: true });
-cmdParser.add_argument('--out', { help: 'Output folder', required: true });
-var cmdArgs = cmdParser.parse_args();
-function getPDBid(name) {
-    var idx = name.indexOf('_');
-    if (idx < 0)
-        idx = name.indexOf('.');
-    return name.substr(0, idx).toLowerCase();
-}
-function findEntries() {
-    var files = fs.readdirSync(cmdArgs.in);
-    var cifTest = /\.cif$/;
-    var groups = new Map();
-    var keys = [];
-    for (var _i = 0, files_1 = files; _i < files_1.length; _i++) {
-        var f = files_1[_i];
-        if (!cifTest.test(f))
-            continue;
-        var id = getPDBid(f);
-        var groupId = "".concat(id[1]).concat(id[2]);
-        if (groups.has(groupId))
-            groups.get(groupId).push(id);
-        else {
-            keys.push(groupId);
-            groups.set(groupId, [id]);
-        }
-    }
-    var ret = [];
-    for (var _a = 0, keys_1 = keys; _a < keys_1.length; _a++) {
-        var key = keys_1[_a];
-        ret.push({ key: key, entries: groups.get(key) });
-    }
-    return ret;
-}
-function process() {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        var entries, started, prog, _i, entries_1, e, ts, data, _a, _b, ee, query, _c, _d, e_1, time;
-        return (0, tslib_1.__generator)(this, function (_e) {
-            switch (_e.label) {
-                case 0:
-                    entries = findEntries();
-                    (0, make_dir_1.makeDir)(cmdArgs.out);
-                    started = (0, now_1.now)();
-                    prog = 0;
-                    _i = 0, entries_1 = entries;
-                    _e.label = 1;
-                case 1:
-                    if (!(_i < entries_1.length)) return [3 /*break*/, 12];
-                    e = entries_1[_i];
-                    ts = (0, now_1.now)();
-                    console.log("".concat(prog, "/").concat(entries.length, " ").concat(e.entries.length, " entries."));
-                    data = Object.create(null);
-                    _a = 0, _b = e.entries;
-                    _e.label = 2;
-                case 2:
-                    if (!(_a < _b.length)) return [3 /*break*/, 10];
-                    ee = _b[_a];
-                    return [4 /*yield*/, (0, node_fetch_1.default)("https://www.ebi.ac.uk/pdbe/api/validation/residuewise_outlier_summary/entry/".concat(ee))];
-                case 3:
-                    query = _e.sent();
-                    _e.label = 4;
-                case 4:
-                    _e.trys.push([4, 8, , 9]);
-                    if (!(query.status === 200)) return [3 /*break*/, 6];
-                    _c = data;
-                    _d = ee;
-                    return [4 /*yield*/, query.json()];
-                case 5:
-                    _c[_d] = (_e.sent())[ee] || {};
-                    return [3 /*break*/, 7];
-                case 6:
-                    console.error(ee, query.status);
-                    _e.label = 7;
-                case 7: return [3 /*break*/, 9];
-                case 8:
-                    e_1 = _e.sent();
-                    console.error(ee, '' + e_1);
-                    return [3 /*break*/, 9];
-                case 9:
-                    _a++;
-                    return [3 /*break*/, 2];
-                case 10:
-                    // const query = await fetch(`https://www.ebi.ac.uk/pdbe/api/validation/residuewise_outlier_summary/entry`, { method: 'POST', body });
-                    // console.log(query.status);
-                    // const data = await query.text();
-                    fs.writeFileSync(path.join(cmdArgs.out, e.key + '.json'), JSON.stringify(data));
-                    time = (0, now_1.now)() - started;
-                    console.log("".concat(++prog, "/").concat(entries.length, " in ").concat(performance_monitor_1.PerformanceMonitor.format(time), " (last ").concat(performance_monitor_1.PerformanceMonitor.format((0, now_1.now)() - ts), ", avg ").concat(performance_monitor_1.PerformanceMonitor.format(time / prog), ")"));
-                    _e.label = 11;
-                case 11:
-                    _i++;
-                    return [3 /*break*/, 1];
-                case 12: return [2 /*return*/];
-            }
-        });
-    });
-}
-process();
-//# sourceMappingURL=fetch-props-pdbe.js.map

package/lib/commonjs/servers/model/utils/fetch-retry.d.ts

@@ -1,7 +0,0 @@
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-import { Response } from 'node-fetch';
-export declare function fetchRetry(url: string, timeout: number, retryCount: number, onRetry?: () => void): Promise<Response>;