molstar
Version:
A comprehensive macromolecular library.
126 lines (125 loc) • 6.48 kB
JavaScript
;
/**
* 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 });
exports.PDBe_structRefDomain = exports.PDBe_preferredAssembly = exports.PDBe_structureQualityReport = void 0;
var tslib_1 = require("tslib");
var fs = tslib_1.__importStar(require("fs"));
var path = tslib_1.__importStar(require("path"));
var prop_1 = require("../../../../extensions/pdbe/structure-quality-report/prop");
var fetch_retry_1 = require("../../utils/fetch-retry");
var mol_util_1 = require("../../../../mol-util");
var preferred_assembly_1 = require("../../../../extensions/pdbe/preferred-assembly");
var struct_ref_domain_1 = require("../../../../extensions/pdbe/struct-ref-domain");
var console_logger_1 = require("../../../../mol-util/console-logger");
var util_1 = require("../../../common/util");
var PDBe_structureQualityReport = function (_a) {
var model = _a.model, params = _a.params, cache = _a.cache;
return tslib_1.__awaiter(void 0, void 0, void 0, function () {
var PDBe_apiSourceJson, data, _b, _c, _d;
return tslib_1.__generator(this, function (_e) {
switch (_e.label) {
case 0:
PDBe_apiSourceJson = useFileSource(params)
? residuewise_outlier_summary.getDataFromAggregateFile(getFilePrefix(params, 'residuewise_outlier_summary'))
: apiQueryProvider(getApiUrl(params, 'residuewise_outlier_summary', prop_1.StructureQualityReport.DefaultServerUrl), cache);
_c = (_b = prop_1.StructureQualityReport).fromJson;
_d = [model];
return [4 /*yield*/, PDBe_apiSourceJson(model)];
case 1:
data = _c.apply(_b, _d.concat([_e.sent()]));
return [2 /*return*/, prop_1.StructureQualityReportProvider.set(model, { serverUrl: prop_1.StructureQualityReport.DefaultServerUrl }, data)];
}
});
});
};
exports.PDBe_structureQualityReport = PDBe_structureQualityReport;
var PDBe_preferredAssembly = function (_a) {
var model = _a.model, params = _a.params, cache = _a.cache;
var PDBe_apiSourceJson = apiQueryProvider(getApiUrl(params, 'preferred_assembly', 'https://www.ebi.ac.uk/pdbe/api/pdb/entry/summary'), cache);
return preferred_assembly_1.PDBePreferredAssembly.attachFromCifOrApi(model, { PDBe_apiSourceJson: PDBe_apiSourceJson });
};
exports.PDBe_preferredAssembly = PDBe_preferredAssembly;
var PDBe_structRefDomain = function (_a) {
var model = _a.model, params = _a.params, cache = _a.cache;
var PDBe_apiSourceJson = apiQueryProvider(getApiUrl(params, 'struct_ref_domain', 'https://www.ebi.ac.uk/pdbe/api/mappings/sequence_domains'), cache);
return struct_ref_domain_1.PDBeStructRefDomain.attachFromCifOrApi(model, { PDBe_apiSourceJson: PDBe_apiSourceJson });
};
exports.PDBe_structRefDomain = PDBe_structRefDomain;
var residuewise_outlier_summary;
(function (residuewise_outlier_summary) {
var json = new Map();
function getDataFromAggregateFile(pathPrefix) {
var _this = this;
// This is for "testing" purposes and should probably only read
// a single file with the appropriate prop in the "production" version.
return function (model) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
var key, fn;
return tslib_1.__generator(this, function (_a) {
key = "".concat(model.entryId[1]).concat(model.entryId[2]);
if (!json.has(key)) {
fn = path.join(pathPrefix, "".concat(key, ".json"));
if (!fs.existsSync(fn))
json.set(key, {});
// TODO: use async readFile?
else
json.set(key, JSON.parse(fs.readFileSync(fn, 'utf8')));
}
return [2 /*return*/, json.get(key)[model.entryId.toLowerCase()] || {}];
});
}); };
}
residuewise_outlier_summary.getDataFromAggregateFile = getDataFromAggregateFile;
})(residuewise_outlier_summary || (residuewise_outlier_summary = {}));
function getApiUrl(params, name, fallback) {
var url = (0, util_1.getParam)(params, 'PDBe', 'API', name);
if (!url)
return fallback;
if (url[url.length - 1] === '/')
return url.substring(0, url.length - 1);
return url;
}
function getFilePrefix(params, name) {
var ret = (0, util_1.getParam)(params, 'PDBe', 'File', name);
if (!ret)
throw new Error("PDBe file prefix '".concat(name, "' not set!"));
return ret;
}
function useFileSource(params) {
return !!(0, util_1.getParam)(params, 'PDBe', 'UseFileSource');
}
function apiQueryProvider(urlPrefix, cache) {
var _this = this;
var cacheKey = mol_util_1.UUID.create22();
return function (model) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
var rawData, json, e_1;
return tslib_1.__generator(this, function (_a) {
switch (_a.label) {
case 0:
_a.trys.push([0, 3, , 4]);
if (cache[cacheKey])
return [2 /*return*/, cache[cacheKey]];
return [4 /*yield*/, (0, fetch_retry_1.fetchRetry)("".concat(urlPrefix, "/").concat(model.entryId.toLowerCase()), 1500, 5)];
case 1:
rawData = _a.sent();
// TODO: is this ok?
if (rawData.status !== 200)
return [2 /*return*/, {}];
return [4 /*yield*/, rawData.json()];
case 2:
json = (_a.sent())[model.entryId.toLowerCase()] || {};
cache[cacheKey] = json;
return [2 /*return*/, json];
case 3:
e_1 = _a.sent();
// TODO: handle better
console_logger_1.ConsoleLogger.warn('Props', "Could not retrieve prop @".concat("".concat(urlPrefix, "/").concat(model.entryId.toLowerCase())));
return [2 /*return*/, {}];
case 4: return [2 /*return*/];
}
});
}); };
}