molstar
Version:
A comprehensive macromolecular library.
89 lines (88 loc) • 4.21 kB
JavaScript
/**
* Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
*/
import * as fs from 'fs';
import * as path from 'path';
import { StructureQualityReportProvider, StructureQualityReport } from '../../../../extensions/pdbe/structure-quality-report/prop';
import { fetchRetry } from '../../utils/fetch-retry';
import { UUID } from '../../../../mol-util';
import { PDBePreferredAssembly } from '../../../../extensions/pdbe/preferred-assembly';
import { PDBeStructRefDomain } from '../../../../extensions/pdbe/struct-ref-domain';
import { ConsoleLogger } from '../../../../mol-util/console-logger';
import { getParam } from '../../../common/util';
export const PDBe_structureQualityReport = async ({ model, params, cache }) => {
const PDBe_apiSourceJson = useFileSource(params)
? residuewise_outlier_summary.getDataFromAggregateFile(getFilePrefix(params, 'residuewise_outlier_summary'))
: apiQueryProvider(getApiUrl(params, 'residuewise_outlier_summary', StructureQualityReport.DefaultServerUrl), cache);
const data = StructureQualityReport.fromJson(model, await PDBe_apiSourceJson(model));
return StructureQualityReportProvider.set(model, { serverUrl: StructureQualityReport.DefaultServerUrl }, data);
};
export const PDBe_preferredAssembly = ({ model, params, cache }) => {
const PDBe_apiSourceJson = apiQueryProvider(getApiUrl(params, 'preferred_assembly', 'https://www.ebi.ac.uk/pdbe/api/pdb/entry/summary'), cache);
return PDBePreferredAssembly.attachFromCifOrApi(model, { PDBe_apiSourceJson });
};
export const PDBe_structRefDomain = ({ model, params, cache }) => {
const PDBe_apiSourceJson = apiQueryProvider(getApiUrl(params, 'struct_ref_domain', 'https://www.ebi.ac.uk/pdbe/api/mappings/sequence_domains'), cache);
return PDBeStructRefDomain.attachFromCifOrApi(model, { PDBe_apiSourceJson });
};
var residuewise_outlier_summary;
(function (residuewise_outlier_summary) {
const json = new Map();
function getDataFromAggregateFile(pathPrefix) {
// This is for "testing" purposes and should probably only read
// a single file with the appropriate prop in the "production" version.
return async (model) => {
const key = `${model.entryId[1]}${model.entryId[2]}`;
if (!json.has(key)) {
const fn = path.join(pathPrefix, `${key}.json`);
if (!fs.existsSync(fn))
json.set(key, {});
// TODO: use async readFile?
else
json.set(key, JSON.parse(fs.readFileSync(fn, 'utf8')));
}
return json.get(key)[model.entryId.toLowerCase()] || {};
};
}
residuewise_outlier_summary.getDataFromAggregateFile = getDataFromAggregateFile;
})(residuewise_outlier_summary || (residuewise_outlier_summary = {}));
function getApiUrl(params, name, fallback) {
const url = getParam(params, 'PDBe', 'API', name);
if (!url)
return fallback;
if (url[url.length - 1] === '/')
return url.substring(0, url.length - 1);
return url;
}
function getFilePrefix(params, name) {
const ret = getParam(params, 'PDBe', 'File', name);
if (!ret)
throw new Error(`PDBe file prefix '${name}' not set!`);
return ret;
}
function useFileSource(params) {
return !!getParam(params, 'PDBe', 'UseFileSource');
}
function apiQueryProvider(urlPrefix, cache) {
const cacheKey = UUID.create22();
return async (model) => {
try {
if (cache[cacheKey])
return cache[cacheKey];
const rawData = await fetchRetry(`${urlPrefix}/${model.entryId.toLowerCase()}`, 1500, 5);
// TODO: is this ok?
if (rawData.status !== 200)
return {};
const json = (await rawData.json())[model.entryId.toLowerCase()] || {};
cache[cacheKey] = json;
return json;
}
catch (e) {
// TODO: handle better
ConsoleLogger.warn('Props', `Could not retrieve prop @${`${urlPrefix}/${model.entryId.toLowerCase()}`}`);
return {};
}
};
}