diff --git a/src/mol-model-props/pdbe/structure-quality-report.ts b/src/mol-model-props/pdbe/structure-quality-report.ts
index a517f8ee347ec07d7cc5623306401c40b3170c7e..137ea579d09ace454ac615cd4f767a65828b2a9b 100644
--- a/src/mol-model-props/pdbe/structure-quality-report.ts
+++ b/src/mol-model-props/pdbe/structure-quality-report.ts
@@ -27,7 +27,9 @@ const _Descriptor = ModelPropertyDescriptor({
prefix: 'pdbe',
categories: [{
name: 'pdbe_structure_quality_report',
- instance() {
+ instance(ctx) {
+ if (ctx.globalCache.pdbe_structure_quality_report) return CifWriter.Category.Empty;
+ ctx.globalCache.pdbe_structure_quality_report = true;
return { fields: _structure_quality_report_fields, rowCount: 1 }
}
}, {
@@ -122,9 +124,7 @@ export namespace StructureQualityReport {
const data = toTable(Schema.pdbe_structure_quality_report_issues, model.sourceData.frame.categories.pdbe_structure_quality_report);
issueMap = createIssueMapFromCif(model, data);
} else if (params.PDBe_apiSourceJson) {
- const id = model.label.toLowerCase();
- const json = await params.PDBe_apiSourceJson(model);
- const data = json[id];
+ const data = await params.PDBe_apiSourceJson(model);
if (!data) return false;
issueMap = createIssueMapFromJson(model, data);
} else {
diff --git a/src/mol-model/structure/export/mmcif.ts b/src/mol-model/structure/export/mmcif.ts
index 3f793d3d2a0634ba3a43e695d3a4b8ce51025408..bd774b605e6d3b3a1757c75b8be4cb51098fb3af 100644
--- a/src/mol-model/structure/export/mmcif.ts
+++ b/src/mol-model/structure/export/mmcif.ts
@@ -17,13 +17,16 @@ import { _pdbx_struct_mod_residue } from './categories/modified-residues';
export interface CifExportContext {
structure: Structure,
model: Model,
- cache: any
+ localCache: any,
+ /** useful when exporting multiple models at the same time */
+ globalCache: any
}
export namespace CifExportContext {
export function create(structures: Structure | Structure[]): CifExportContext[] {
- if (Array.isArray(structures)) return structures.map(structure => ({ structure, model: structure.models[0], cache: Object.create(null) }));
- return [{ structure: structures, model: structures.models[0], cache: Object.create(null) }];
+ const globalCache = Object.create(null);
+ if (Array.isArray(structures)) return structures.map(structure => ({ structure, model: structure.models[0], localCache: Object.create(null), globalCache }));
+ return [{ structure: structures, model: structures.models[0], localCache: Object.create(null), globalCache }];
}
}
diff --git a/src/mol-model/structure/model/properties/custom/residue.ts b/src/mol-model/structure/model/properties/custom/residue.ts
index 7c84a6b4065b00d9ea6e031b8660180246b1d37c..0b9b480b764c58fb64482610298618edf9db2722 100644
--- a/src/mol-model/structure/model/properties/custom/residue.ts
+++ b/src/mol-model/structure/model/properties/custom/residue.ts
@@ -26,7 +26,7 @@ export namespace ResidueCustomProperty {
};
function getExportCtx<T>(exportCtx: CifExportContext, prop: ResidueCustomProperty<T>): ExportCtx<T> {
- if (exportCtx.cache[prop.id]) return exportCtx.cache[prop.id];
+ if (exportCtx.localCache[prop.id]) return exportCtx.localCache[prop.id];
const residueIndex = exportCtx.model.atomicHierarchy.residueAtomSegments.index;
const elements = getStructureElements(exportCtx.structure, prop);
return {
diff --git a/src/mol-util/make-dir.ts b/src/mol-util/make-dir.ts
new file mode 100644
index 0000000000000000000000000000000000000000..051203d65191bfae0cd8c89b45409991b24119b7
--- /dev/null
+++ b/src/mol-util/make-dir.ts
@@ -0,0 +1,21 @@
+/**
+ * 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';
+
+export function makeDir(path: string, root?: string): boolean {
+ let dirs = path.split(/\/|\\/g),
+ dir = dirs.shift();
+
+ root = (root || '') + dir + '/';
+
+ try { fs.mkdirSync(root); }
+ catch (e) {
+ if (!fs.statSync(root).isDirectory()) throw new Error(e);
+ }
+
+ return !dirs.length || makeDir(dirs.join('/'), root);
+}
\ No newline at end of file
diff --git a/src/servers/model/properties/providers/pdbe.ts b/src/servers/model/properties/providers/pdbe.ts
index 2f2403a2013a926d4327bcc374121058a1bbcd5b..751bab2ea6fc56fdf99220976bb905aa930f1b86 100644
--- a/src/servers/model/properties/providers/pdbe.ts
+++ b/src/servers/model/properties/providers/pdbe.ts
@@ -4,20 +4,39 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
- import { Model } from 'mol-model/structure';
+import * as fs from 'fs'
+import { Model } from 'mol-model/structure';
import { StructureQualityReport } from 'mol-model-props/pdbe/structure-quality-report';
import { fetchRetry } from '../../utils/fetch-retry';
import { UUID } from 'mol-util';
-const cacheKey = UUID.create();
export function PDBe_structureQualityReport(model: Model, cache: any) {
return StructureQualityReport.attachFromCifOrApi(model, {
- PDBe_apiSourceJson: async model => {
+ PDBe_apiSourceJson: residuewise_outlier_summary.getDataFromFile
+ });
+}
+
+namespace residuewise_outlier_summary {
+ const json = new Map<string, any>();
+
+ export async function getDataFromFile(model: Model) {
+ const key = `${model.label[1]}${model.label[2]}`;
+ if (!json.has(key)) {
+ const fn = `e:/test/mol-star/model/props/${key}.json`;
+ if (!fs.existsSync(fn)) json.set(key, { });
+ else json.set(key, JSON.parse(fs.readFileSync(fn, 'utf8')));
+ }
+ return json.get(key)![model.label.toLowerCase()] || { };
+ }
+
+ export function getDataFromApiProvider(cache: any) {
+ const cacheKey = UUID.create();
+ return async (model: Model) => {
if (cache[cacheKey]) return cache[cacheKey];
const rawData = await fetchRetry(`https://www.ebi.ac.uk/pdbe/api/validation/residuewise_outlier_summary/entry/${model.label.toLowerCase()}`, 1500, 5);
- const json = await rawData.json();
+ const json = (await rawData.json())[model.label.toLowerCase()] || { };
cache[cacheKey] = json;
return json;
}
- });
+ }
}
\ No newline at end of file
diff --git a/src/servers/model/utils/fetch-props-pdbe.ts b/src/servers/model/utils/fetch-props-pdbe.ts
new file mode 100644
index 0000000000000000000000000000000000000000..0f3caf6350767b9c4d45e91be2074633f5ea58ba
--- /dev/null
+++ b/src/servers/model/utils/fetch-props-pdbe.ts
@@ -0,0 +1,80 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import fetch from 'node-fetch';
+import * as fs from 'fs'
+import * as path from 'path'
+import * as argparse from 'argparse'
+import { makeDir } from 'mol-util/make-dir';
+import { now } from 'mol-task';
+import { PerformanceMonitor } from 'mol-util/performance-monitor';
+
+const cmdParser = new argparse.ArgumentParser({
+ addHelp: true,
+ description: 'Download JSON data from PDBe API'
+});
+
+cmdParser.addArgument(['--in'], { help: 'Input folder', required: true });
+cmdParser.addArgument(['--out'], { help: 'Output folder', required: true });
+
+interface CmdArgs {
+ in: string,
+ out: string
+}
+
+const cmdArgs = cmdParser.parseArgs() as CmdArgs;
+
+function getPDBid(name: string) {
+ let idx = name.indexOf('_');
+ if (idx < 0) idx = name.indexOf('.');
+ return name.substr(0, idx).toLowerCase();
+}
+
+function findEntries() {
+ const files = fs.readdirSync(cmdArgs.in);
+ const cifTest = /\.cif$/;
+ const groups = new Map<string, string[]>();
+ const keys: string[] = [];
+
+ for (const f of files) {
+ if (!cifTest.test(f)) continue;
+ const id = getPDBid(f);
+ const groupId = `${id[1]}${id[2]}`;
+
+ if (groups.has(groupId)) groups.get(groupId)!.push(id);
+ else {
+ keys.push(groupId);
+ groups.set(groupId, [id]);
+ }
+ }
+
+ const ret: { key: string, entries: string[] }[] = [];
+ for (const key of keys) {
+ ret.push({ key, entries: groups.get(key)! })
+ }
+
+ return ret;
+}
+
+async function process() {
+ const entries = findEntries();
+ makeDir(cmdArgs.out);
+
+ const started = now();
+ let prog = 0;
+ for (const e of entries) {
+ const ts = now();
+ console.log(`${prog}/${entries.length} ${e.entries.length} entries.`)
+ const body = e.entries.join(',');
+ const query = await fetch(`https://www.ebi.ac.uk/pdbe/api/validation/residuewise_outlier_summary/entry`, { method: 'POST', body });
+ const data = await query.text();
+ fs.writeFileSync(path.join(cmdArgs.out, e.key + '.json'), data);
+ const time = now() - started;
+ console.log(`${++prog}/${entries.length} in ${PerformanceMonitor.format(time)} (last ${PerformanceMonitor.format(now() - ts)}, avg ${PerformanceMonitor.format(time / prog)})`);
+ }
+}
+
+process();
\ No newline at end of file