diff --git a/src/servers/model/properties/pdbe.ts b/src/servers/model/properties/pdbe.ts
index 61d968f9c0ab694b93b9c9b4adb29b728f1c19bc..aafc6675c22ccd12fdd7e0ef9af03bb51f1ed228 100644
--- a/src/servers/model/properties/pdbe.ts
+++ b/src/servers/model/properties/pdbe.ts
@@ -8,10 +8,10 @@
import { Model } from 'mol-model/structure';
import { PDBe_structureQualityReport } from './providers/pdbe';
-export function attachModelProperties(model: Model): Promise<any>[] {
+export function attachModelProperties(model: Model, cache: object): Promise<any>[] {
// return a list of promises that start attaching the props in parallel
// (if there are downloads etc.)
return [
- PDBe_structureQualityReport(model)
+ PDBe_structureQualityReport(model, cache)
];
}
\ 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 cbc60c8c7e328914f61110adc18cf2d8563ebf0b..14a2119aa7321ceaa21b4a26b096ccdfb63c821e 100644
--- a/src/servers/model/properties/providers/pdbe.ts
+++ b/src/servers/model/properties/providers/pdbe.ts
@@ -7,12 +7,20 @@
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';
-export function PDBe_structureQualityReport(model: Model) {
+const cacheKey = UUID.create();
+export function PDBe_structureQualityReport(model: Model, cache: any) {
return StructureQualityReport.attachFromCifOrApi(model, {
PDBe_apiSourceJson: async model => {
+ if (cache[cacheKey]) {
+ console.log('cache hit');
+ return cache[cacheKey];
+ }
const rawData = await fetchRetry(`https://www.ebi.ac.uk/pdbe/api/validation/residuewise_outlier_summary/entry/${model.label.toLowerCase()}`, 1500, 5);
- return await rawData.json();
+ const json = await rawData.json();
+ cache[cacheKey] = json;
+ return json;
}
});
}
\ No newline at end of file
diff --git a/src/servers/model/property-provider.ts b/src/servers/model/property-provider.ts
index a2789b49055a4232f3273c0381f8e99e7cdbbc50..95f463e31ac90a3dd794cda97c36f8b62c739ca8 100644
--- a/src/servers/model/property-provider.ts
+++ b/src/servers/model/property-provider.ts
@@ -7,7 +7,7 @@
import { Model } from 'mol-model/structure';
import Config from './config';
-export type ModelPropertiesProvider = (model: Model) => Promise<any>[]
+export type ModelPropertiesProvider = (model: Model, cache: object) => Promise<any>[]
export function createModelPropertiesProviderFromConfig(): ModelPropertiesProvider {
if (!Config.customPropertyProviders || Config.customPropertyProviders.length === 0) return () => [];
@@ -17,10 +17,10 @@ export function createModelPropertiesProviderFromConfig(): ModelPropertiesProvid
ps.push(require(p).attachModelProperties);
}
- return model => {
+ return (model, cache) => {
const ret: Promise<any>[] = [];
for (const p of ps) {
- for (const e of p(model)) ret.push(e);
+ for (const e of p(model, cache)) ret.push(e);
}
return ret;
}
diff --git a/src/servers/model/server/query.ts b/src/servers/model/server/query.ts
index 35159b5dc3f4754618aca8e7933b8fdc5a53d373..ad0a649e2466a6c70cf4756e74f2a4df7de8a775 100644
--- a/src/servers/model/server/query.ts
+++ b/src/servers/model/server/query.ts
@@ -6,7 +6,7 @@
import { Column } from 'mol-data/db';
import { CifWriter } from 'mol-io/writer/cif';
-import { StructureQuery, StructureSelection } from 'mol-model/structure';
+import { StructureQuery, StructureSelection, Structure } from 'mol-model/structure';
import { encode_mmCIF_categories } from 'mol-model/structure/export/mmcif';
import { now, Progress } from 'mol-task';
import { ConsoleLogger } from 'mol-util/console-logger';
@@ -14,7 +14,7 @@ import { PerformanceMonitor } from 'mol-util/performance-monitor';
import Config from '../config';
import Version from '../version';
import { Job } from './jobs';
-import { createStructureWrapperFromJob, StructureWrapper, resolveStructure } from './structure-wrapper';
+import { createStructureWrapperFromJob, StructureWrapper, resolveStructures } from './structure-wrapper';
import CifField = CifWriter.Field
import { createModelPropertiesProviderFromConfig } from '../property-provider';
@@ -35,13 +35,23 @@ export async function resolveJob(job: Job): Promise<CifWriter.Encoder<any>> {
try {
perf.start('query');
- const sourceStructure = await resolveStructure(wrappedStructure);
- if (!sourceStructure) throw new Error('Model not available');
- const structure = job.queryDefinition.structureTransform
- ? await job.queryDefinition.structureTransform(job.normalizedParams, sourceStructure)
- : sourceStructure;
- const query = job.queryDefinition.query(job.normalizedParams, structure);
- const result = await StructureSelection.unionStructure(StructureQuery.run(query, structure, Config.maxQueryTimeInMs));
+ const sourceStructures = await resolveStructures(wrappedStructure);
+ if (!sourceStructures.length) throw new Error('Model not available');
+
+ let structures: Structure[] = sourceStructures;
+
+ if (job.queryDefinition.structureTransform) {
+ structures = [];
+ for (const s of sourceStructures) {
+ structures.push(await job.queryDefinition.structureTransform(job.normalizedParams, s));
+ }
+ }
+
+ const queries = structures.map(s => job.queryDefinition.query(job.normalizedParams, s));
+ const result: Structure[] = [];
+ for (let i = 0; i < structures.length; i++) {
+ result.push(await StructureSelection.unionStructure(StructureQuery.run(queries[i], structures[i], Config.maxQueryTimeInMs)));
+ }
perf.end('query');
const encoder = CifWriter.createEncoder({
@@ -54,7 +64,7 @@ export async function resolveJob(job: Job): Promise<CifWriter.Encoder<any>> {
ConsoleLogger.logId(job.id, 'Query', 'Query finished.');
perf.start('encode');
- encoder.startDataBlock(structure.models[0].label.toUpperCase());
+ encoder.startDataBlock(sourceStructures[0].models[0].label.toUpperCase());
encoder.writeCategory(_model_server_result, [job]);
encoder.writeCategory(_model_server_params, [job]);
diff --git a/src/servers/model/server/structure-wrapper.ts b/src/servers/model/server/structure-wrapper.ts
index 60275ddc5f2a514cefd9243f536c0e752bc811cf..7c8bb1b255ddf845a0c86ac861332e39bd681755 100644
--- a/src/servers/model/server/structure-wrapper.ts
+++ b/src/servers/model/server/structure-wrapper.ts
@@ -43,7 +43,8 @@ export interface StructureWrapper {
modelMap: Map<number, Model>,
structureModelMap: Map<number, Structure>,
propertyProvider: ModelPropertiesProvider | undefined,
- cifFrame: CifFrame
+ cifFrame: CifFrame,
+ cache: object
}
export async function createStructureWrapperFromJob(job: Job, propertyProvider: ModelPropertiesProvider | undefined, allowCache = true): Promise<StructureWrapper> {
@@ -115,15 +116,6 @@ export async function readStructureWrapper(key: string, sourceId: string | '_loc
modelMap.set(m.modelNum, m);
}
- perf.start('attachProps');
- if (propertyProvider) {
- const modelProps = propertyProvider(models[0]);
- for (const p of modelProps) {
- await tryAttach(key, p);
- }
- }
- perf.end('attachProps');
-
const ret: StructureWrapper = {
info: {
sourceType: StructureSourceType.File,
@@ -141,7 +133,8 @@ export async function readStructureWrapper(key: string, sourceId: string | '_loc
modelMap,
structureModelMap: new Map(),
cifFrame: frame,
- propertyProvider
+ propertyProvider,
+ cache: Object.create(null)
};
return ret;
@@ -157,7 +150,7 @@ export async function resolveStructure(wrapper: StructureWrapper, modelNum?: num
const model = wrapper.modelMap.get(modelNum)!;
const structure = Structure.ofModel(model);
if (wrapper.propertyProvider) {
- const modelProps = wrapper.propertyProvider(model);
+ const modelProps = wrapper.propertyProvider(model, wrapper.cache);
for (const p of modelProps) {
await tryAttach(wrapper.key, p);
}
@@ -165,6 +158,15 @@ export async function resolveStructure(wrapper: StructureWrapper, modelNum?: num
return structure;
}
+export async function resolveStructures(wrapper: StructureWrapper, modelNums?: number[]) {
+ const ret: Structure[] = [];
+ for (const n of modelNums || (wrapper.models as Model[]).map(m => m.modelNum)) {
+ const s = await resolveStructure(wrapper, n);
+ if (s) ret.push(s);
+ }
+ return ret;
+}
+
async function tryAttach(key: string, promise: Promise<any>) {
try {
await promise;