molstar
Version:
A comprehensive macromolecular library.
191 lines • 8.53 kB
JavaScript
;
/**
* 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.initWebApi = exports.createResultWriter = void 0;
var tslib_1 = require("tslib");
var fs = (0, tslib_1.__importStar)(require("fs"));
var path = (0, tslib_1.__importStar)(require("path"));
var bodyParser = (0, tslib_1.__importStar)(require("body-parser"));
var config_1 = require("../config");
var console_logger_1 = require("../../../mol-util/console-logger");
var query_1 = require("./query");
var jobs_1 = require("./jobs");
var api_1 = require("./api");
var api_schema_1 = require("./api-schema");
var swagger_ui_1 = require("../../common/swagger-ui");
var api_web_multiple_1 = require("./api-web-multiple");
var writer_1 = require("../utils/writer");
var string_1 = require("../../../mol-util/string");
function makePath(p) {
return config_1.ModelServerConfig.apiPrefix + '/' + p;
}
var responseMap = new Map();
function processNextJob() {
return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
var job, writer, e_1;
return (0, tslib_1.__generator)(this, function (_a) {
switch (_a.label) {
case 0:
if (!jobs_1.JobManager.hasNext())
return [2 /*return*/];
job = jobs_1.JobManager.getNext();
responseMap.delete(job.id);
writer = job.writer;
_a.label = 1;
case 1:
_a.trys.push([1, 3, 4, 5]);
return [4 /*yield*/, (0, query_1.resolveJob)(job)];
case 2:
_a.sent();
return [3 /*break*/, 5];
case 3:
e_1 = _a.sent();
console_logger_1.ConsoleLogger.errorId(job.id, '' + e_1);
writer.doError(404, '' + e_1);
return [3 /*break*/, 5];
case 4:
writer.end();
console_logger_1.ConsoleLogger.logId(job.id, 'Query', 'Finished.');
setImmediate(processNextJob);
return [7 /*endfinally*/];
case 5: return [2 /*return*/];
}
});
});
}
function createResultWriter(response, params) {
var filenameBase = params.entryId && params.queryName
? params.entryId + "_" + (0, string_1.splitCamelCase)(params.queryName.replace(/\s/g, '_'), '-').toLowerCase()
: "result";
return new writer_1.SimpleResponseResultWriter(params.filename || filenameBase + "." + params.encoding, response, params.encoding === 'bcif', params.download);
}
exports.createResultWriter = createResultWriter;
function mapQuery(app, queryName, queryDefinition) {
function createJob(queryParams, req, res) {
var entryId = req.params.id;
var commonParams = (0, api_1.normalizeRestCommonParams)(req.query);
var resultWriterParams = { encoding: commonParams.encoding, download: !!commonParams.download, filename: commonParams.filename, entryId: entryId, queryName: queryName };
var jobId = jobs_1.JobManager.add({
entries: [(0, jobs_1.JobEntry)({
sourceId: commonParams.data_source || config_1.ModelServerConfig.defaultSource,
entryId: entryId,
queryName: queryName,
queryParams: queryParams,
modelNums: commonParams.model_nums,
copyAllCategories: !!commonParams.copy_all_categories,
transform: commonParams.transform
})],
writer: createResultWriter(res, resultWriterParams),
options: { binary: commonParams.encoding === 'bcif', encoding: commonParams.encoding }
});
responseMap.set(jobId, res);
if (jobs_1.JobManager.size === 1)
processNextJob();
}
app.get(makePath('v1/:id/' + queryName), function (req, res) {
var queryParams = (0, api_1.normalizeRestQueryParams)(queryDefinition, req.query);
createJob(queryParams, req, res);
});
app.post(makePath('v1/:id/' + queryName), function (req, res) {
var queryParams = req.body;
createJob(queryParams, req, res);
});
}
function serveStatic(req, res) {
var source = req.params.source === 'bcif'
? 'pdb-bcif'
: req.params.source === 'cif'
? 'pdb-cif'
: req.params.source;
var id = req.params.id;
var _a = (0, config_1.mapSourceAndIdToFilename)(source, id), fn = _a[0], format = _a[1];
var binary = format === 'bcif' || fn.indexOf('.bcif') > 0;
if (!fn || !fs.existsSync(fn)) {
res.status(404);
res.end();
return;
}
fs.readFile(fn, function (err, data) {
if (err) {
res.status(404);
res.end();
return;
}
var f = path.parse(fn);
res.writeHead(200, {
'Content-Type': binary ? 'application/octet-stream' : 'text/plain; charset=utf-8',
'Access-Control-Allow-Origin': '*',
'Access-Control-Allow-Headers': 'X-Requested-With',
'Content-Disposition': "inline; filename=\"" + f.name + f.ext + "\""
});
res.write(data);
res.end();
});
}
function createMultiJob(spec, res) {
var _a;
var writer = spec.asTarGz
? new writer_1.TarballResponseResultWriter((0, api_web_multiple_1.getMultiQuerySpecFilename)(), res)
: createResultWriter(res, { encoding: spec.encoding, download: !!spec.download, filename: spec.filename });
if (spec.queries.length > config_1.ModelServerConfig.maxQueryManyQueries) {
writer.doError(400, "query-many queries limit (" + config_1.ModelServerConfig.maxQueryManyQueries + ") exceeded.");
return;
}
var jobId = jobs_1.JobManager.add({
entries: spec.queries.map(function (q) { return (0, jobs_1.JobEntry)({
sourceId: q.data_source || config_1.ModelServerConfig.defaultSource,
entryId: q.entryId,
queryName: q.query,
queryParams: q.params || {},
modelNums: q.model_nums,
copyAllCategories: !!q.copy_all_categories
}); }),
writer: writer,
options: { binary: ((_a = spec.encoding) === null || _a === void 0 ? void 0 : _a.toLowerCase()) === 'bcif', tarball: spec.asTarGz }
});
responseMap.set(jobId, res);
if (jobs_1.JobManager.size === 1)
processNextJob();
}
function initWebApi(app) {
app.use(bodyParser.json({ limit: '1mb' }));
app.get(makePath('static/:source/:id'), function (req, res) { return serveStatic(req, res); });
app.get(makePath('v1/static/:source/:id'), function (req, res) { return serveStatic(req, res); });
app.get(makePath('v1/query-many'), function (req, res) {
var query = /\?query=(.*)$/.exec(req.url)[1];
var params = JSON.parse(decodeURIComponent(query));
createMultiJob(params, res);
});
app.post(makePath('v1/query-many'), function (req, res) {
var params = req.body;
req.setTimeout;
createMultiJob(params, res);
});
app.use(bodyParser.json({ limit: '20mb' }));
for (var _i = 0, QueryList_1 = api_1.QueryList; _i < QueryList_1.length; _i++) {
var q = QueryList_1[_i];
mapQuery(app, q.name, q.definition);
}
var schema = (0, api_schema_1.getApiSchema)();
app.get(makePath('openapi.json'), function (req, res) {
res.writeHead(200, {
'Content-Type': 'application/json; charset=utf-8',
'Access-Control-Allow-Origin': '*',
'Access-Control-Allow-Headers': 'X-Requested-With'
});
res.end(JSON.stringify(schema));
});
app.use(makePath(''), (0, swagger_ui_1.swaggerUiAssetsHandler)());
app.get(makePath(''), (0, swagger_ui_1.swaggerUiIndexHandler)({
openapiJsonUrl: makePath('openapi.json'),
apiPrefix: config_1.ModelServerConfig.apiPrefix,
title: 'ModelServer API',
shortcutIconLink: api_schema_1.shortcutIconLink
}));
}
exports.initWebApi = initWebApi;
//# sourceMappingURL=api-web.js.map