molstar
Version:
A comprehensive macromolecular library.
277 lines (276 loc) • 11.4 kB
JavaScript
;
/**
* Copyright (c) 2018-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.ModelServerConfigTemplate = exports.ModelServerConfig = exports.mapSourceAndIdToFilename = exports.ModelServerFetchFormats = void 0;
exports.configureServer = configureServer;
const tslib_1 = require("tslib");
const argparse = tslib_1.__importStar(require("argparse"));
const type_helpers_1 = require("../../mol-util/type-helpers");
const version_1 = require("./version");
const fs = tslib_1.__importStar(require("fs"));
const DefaultModelServerConfig = {
// 0 for off
cacheMaxSizeInBytes: 2 * 1014 * 1024 * 1024, // 2 GB
cacheEntryTimeoutMs: 10 * 60 * 1000, // 10 minutes
/**
* Node (V8) sometimes exhibits GC related issues that significantly slow down the execution
* (https://github.com/nodejs/node/issues/8670).
*
* Therefore an option is provided that automatically shuts down the server.
* For this to work, the server must be run using a deamon (i.e. forever.js on Linux
* or IISnode on Windows) so that the server is automatically restarted when the shutdown happens.
*/
// 0 for off, server will shut down after this amount of minutes.
shutdownTimeoutMinutes: 24 * 60, /* a day */
// modifies the shutdown timer by +/- timeoutVarianceMinutes (to avoid multiple instances shutting at the same time)
shutdownTimeoutVarianceMinutes: 60,
defaultPort: 1337,
/**
* Specify the prefix of the API, i.e.
* <host>/<apiPrefix>/<API queries>
*/
apiPrefix: '/ModelServer',
/**
* The maximum time the server dedicates to executing a query.
* Does not include the time it takes to read and export the data.
*/
queryTimeoutMs: 5 * 1000,
/**
* The maximum number of ms the server spends on a request
*/
requestTimeoutMs: 60 * 1000,
/** Maximum number of requests before "server busy" */
maxQueueLength: 30,
/** The maximum number of queries allowed by the query-many at a time */
maxQueryManyQueries: 50,
/**
* Provide a property config or a path a JSON file with the config.
*/
// TODO: finish customProperty support
customProperties: {
sources: [
// 'pdbe',
// 'rcsb',
// 'wwpdb'
],
params: {
// PDBe: {
// UseFileSource: false,
// API: {
// residuewise_outlier_summary: 'https://www.ebi.ac.uk/pdbe/api/validation/residuewise_outlier_summary/entry',
// preferred_assembly: 'https://www.ebi.ac.uk/pdbe/api/pdb/entry/summary',
// struct_ref_domain: 'https://www.ebi.ac.uk/pdbe/api/mappings/sequence_domains'
// },
// File: {
// residuewise_outlier_summary: 'e:/test/mol-star/model/props/'
// }
// },
// RCSB: {
// API: {
// assembly_symmetry: 'https://rest-staging.rcsb.org/graphql'
// }
// },
// wwPDB: {
// chemCompBondTablePath: '',
// chemCompAtomTablePath: ''
// }
}
},
/**
* Default source for fileMapping.
*/
defaultSource: 'pdb-cif',
/**
* Maps a request identifier to either:
* - filename [source, mapping]
* - URI [source, mapping, format]
*
* Mapping is provided 'source' and 'id' variables to interpolate.
*
* /static query uses 'pdb-cif' and 'pdb-bcif' source names.
*/
sourceMap: [
['pdb-cif', 'e:/test/quick/${id}_updated.cif'],
// ['pdb-bcif', 'e:/test/quick/${id}.bcif'],
],
/**
* Optionally point to files. The service health-check will assert that all are readable and fail otherwise.
*/
healthCheckPath: [],
};
exports.ModelServerFetchFormats = ['cif', 'bcif', 'cif.gz', 'bcif.gz'];
let mapSourceAndIdToFilename = () => {
throw new Error('call setupConfig & validateConfigAndSetupSourceMap to initialize this function');
};
exports.mapSourceAndIdToFilename = mapSourceAndIdToFilename;
function addServerArgs(parser) {
parser.add_argument('--apiPrefix', {
default: DefaultModelServerConfig.apiPrefix,
metavar: 'PREFIX',
help: `Specify the prefix of the API, i.e. <host>/<apiPrefix>/<API queries>`
});
parser.add_argument('--defaultPort', {
default: DefaultModelServerConfig.defaultPort,
metavar: 'PORT',
type: 'int',
help: `Specify the port the server is running on`
});
parser.add_argument('--cacheMaxSizeInBytes', {
default: DefaultModelServerConfig.cacheMaxSizeInBytes,
metavar: 'CACHE_SIZE',
type: 'int',
help: `0 for off.`
});
parser.add_argument('--cacheEntryTimeoutMs', {
default: DefaultModelServerConfig.cacheEntryTimeoutMs,
metavar: 'CACHE_TIMEOUT',
type: 'int',
help: `Specify in ms how long to keep entries in cache.`
});
parser.add_argument('--requestTimeoutMs', {
default: DefaultModelServerConfig.requestTimeoutMs,
metavar: 'REQUEST_TIMEOUT',
type: 'int',
help: `The maximum number of ms the server spends on a request.`
});
parser.add_argument('--queryTimeoutMs', {
default: DefaultModelServerConfig.queryTimeoutMs,
metavar: 'QUERY_TIMEOUT',
type: 'int',
help: `The maximum time the server dedicates to executing a query in ms.\nDoes not include the time it takes to read and export the data.`
});
parser.add_argument('--shutdownTimeoutMinutes', {
default: DefaultModelServerConfig.shutdownTimeoutMinutes,
metavar: 'TIME',
type: 'int',
help: `0 for off, server will shut down after this amount of minutes.`
});
parser.add_argument('--shutdownTimeoutVarianceMinutes', {
default: DefaultModelServerConfig.shutdownTimeoutVarianceMinutes,
metavar: 'VARIANCE',
type: 'int',
help: `modifies the shutdown timer by +/- timeoutVarianceMinutes (to avoid multiple instances shutting at the same time)`
});
parser.add_argument('--maxQueryManyQueries', {
default: DefaultModelServerConfig.maxQueryManyQueries,
metavar: 'QUERY_MANY_LIMIT',
type: 'int',
help: `maximum number of queries allowed by the query-many at a time`
});
parser.add_argument('--defaultSource', {
default: DefaultModelServerConfig.defaultSource,
metavar: 'DEFAULT_SOURCE',
help: `modifies which 'sourceMap' source to use by default`
});
parser.add_argument('--sourceMap', {
nargs: 2,
action: 'append',
metavar: ['SOURCE', 'PATH'],
help: [
'Map `id`s for a `source` to a file path.',
'Example: pdb-bcif \'../../data/bcif/${id}.bcif\' ',
'JS expressions can be used inside ${}, e.g. \'${id.substr(1, 2)}/${id}.mdb\'',
'Can be specified multiple times.',
'The `SOURCE` variable (e.g. `pdb-bcif`) is arbitrary and depends on how you plan to use the server.',
`Supported formats: ${exports.ModelServerFetchFormats.join(', ')}`
].join('\n'),
});
parser.add_argument('--sourceMapUrl', {
nargs: 3,
action: 'append',
metavar: ['SOURCE', 'PATH', 'SOURCE_MAP_FORMAT'],
help: [
'Same as --sourceMap but for URL. \'--sourceMapUrl src url format\'',
'Example: "pdb-cif \'https://www.ebi.ac.uk/pdbe/entry-files/download/${id}_updated.cif\' cif"',
`Supported formats: ${exports.ModelServerFetchFormats.join(', ')}. Supported protocols: http://, https://, gs://`
].join('\n'),
});
parser.add_argument('--healthCheckPath', {
default: DefaultModelServerConfig.healthCheckPath,
action: 'append',
metavar: 'PATH',
help: `File path(s) to use for health-checks. Will test if all files are accessible and report a failed health-check if that's not the case.`,
});
}
exports.ModelServerConfig = { ...DefaultModelServerConfig };
exports.ModelServerConfigTemplate = {
...DefaultModelServerConfig,
defaultSource: 'pdb-bcif',
sourceMap: [
['pdb-bcif', './path-to-binary-cif/${id.substr(1, 2)}/${id}.bcif'],
['pdb-cif', './path-to-text-cif/${id.substr(1, 2)}/${id}.cif'],
['pdb-updated', 'https://www.ebi.ac.uk/pdbe/entry-files/download/${id}_updated.cif', 'cif']
]
};
// TODO: include once properly supported
// cast to any to prevent "The operand of a 'delete' operator must be optional"
delete exports.ModelServerConfigTemplate.customProperties;
function addJsonConfigArgs(parser) {
parser.add_argument('--cfg', {
help: [
'JSON config file path',
'If a property is not specified, cmd line param/OS variable/default value are used.'
].join('\n'),
required: false,
});
parser.add_argument('--printCfg', { help: 'Print current config for validation and exit.', required: false, action: 'store_true' });
parser.add_argument('--cfgTemplate', { help: 'Prints default JSON config template to be modified and exits.', required: false, action: 'store_true' });
}
function setConfig(config) {
for (const k of (0, type_helpers_1.ObjectKeys)(exports.ModelServerConfig)) {
if (config[k] !== void 0)
exports.ModelServerConfig[k] = config[k];
}
if (config.sourceMapUrl) {
if (!exports.ModelServerConfig.sourceMap)
exports.ModelServerConfig.sourceMap = [];
exports.ModelServerConfig.sourceMap.push(...config.sourceMapUrl);
}
}
function validateConfigAndSetupSourceMap() {
if (!exports.ModelServerConfig.sourceMap || exports.ModelServerConfig.sourceMap.length === 0) {
throw new Error(`Please provide 'sourceMap' configuration. See [-h] for available options.`);
}
exports.mapSourceAndIdToFilename = new Function('source', 'id', [
'switch (source.toLowerCase()) {',
...exports.ModelServerConfig.sourceMap.map(([source, path, format]) => `case '${source.toLowerCase()}': return [\`${path}\`, '${format}'];`),
'}',
].join('\n'));
}
function parseConfigArguments() {
const parser = new argparse.ArgumentParser({
add_help: true,
description: `ModelServer ${version_1.VERSION}, (c) 2018-2020, Mol* contributors`
});
addJsonConfigArgs(parser);
addServerArgs(parser);
return parser.parse_args();
}
function configureServer() {
const config = parseConfigArguments();
if (!!config.cfgTemplate) {
console.log(JSON.stringify(exports.ModelServerConfigTemplate, null, 2));
process.exit(0);
}
try {
setConfig(config); // sets the config for global use
if (config.cfg) {
const cfg = JSON.parse(fs.readFileSync(config.cfg, 'utf8'));
setConfig(cfg);
}
if (!!config.printCfg) {
console.log(JSON.stringify(exports.ModelServerConfig, null, 2));
process.exit(0);
}
validateConfigAndSetupSourceMap();
}
catch (e) {
console.error('' + e);
process.exit(1);
}
}