From 4ba3a5c811a606cebe8426f50ff61fcd52dc4810 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Mon, 24 Sep 2018 10:55:18 +0200
Subject: [PATCH] wip ModelServer multiple model support
---
src/servers/model/preprocess/preprocess.ts | 11 +++--
src/servers/model/server/query.ts | 10 ++--
src/servers/model/server/structure-wrapper.ts | 46 +++++++++++++++----
3 files changed, 48 insertions(+), 19 deletions(-)
diff --git a/src/servers/model/preprocess/preprocess.ts b/src/servers/model/preprocess/preprocess.ts
index cf45825df..f54468091 100644
--- a/src/servers/model/preprocess/preprocess.ts
+++ b/src/servers/model/preprocess/preprocess.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { readStructure } from '../server/structure-wrapper';
+import { readStructureWrapper, resolveStructure } from '../server/structure-wrapper';
import { classifyCif } from './converter';
// import { ConsoleLogger } from 'mol-util/console-logger';
import { Structure } from 'mol-model/structure';
@@ -24,18 +24,19 @@ export async function preprocessFile(filename: string, outputCif?: string, outpu
//const started = now();
//ConsoleLogger.log(`${linearId}`, `Reading '${filename}'...`);
// TODO: support the custom prop provider list here.
- const input = await readStructure('entry', '_local_', filename, void 0);
+ const input = await readStructureWrapper('entry', '_local_', filename, void 0);
+ const inputStructure = (await resolveStructure(input))!;
//ConsoleLogger.log(`${linearId}`, `Classifying CIF categories...`);
const categories = await classifyCif(input.cifFrame);
//clearLine();
- const exportCtx = CifExportContext.create(input.structure, input.structure.models[0]);
+ const exportCtx = CifExportContext.create(inputStructure, inputStructure.models[0]);
if (outputCif) {
//ConsoleLogger.log(`${linearId}`, `Encoding CIF...`);
const writer = wrapFileToWriter(outputCif);
const encoder = CifWriter.createEncoder({ binary: false });
- await encode(input.structure, input.cifFrame.header, categories, encoder, exportCtx, writer);
+ await encode(inputStructure, input.cifFrame.header, categories, encoder, exportCtx, writer);
// clearLine();
writer.end();
}
@@ -44,7 +45,7 @@ export async function preprocessFile(filename: string, outputCif?: string, outpu
// ConsoleLogger.log(`${linearId}`, `Encoding BinaryCIF...`);
const writer = wrapFileToWriter(outputBcif);
const encoder = CifWriter.createEncoder({ binary: true, binaryAutoClassifyEncoding: true });
- await encode(input.structure, input.cifFrame.header, categories, encoder, exportCtx, writer);
+ await encode(inputStructure, input.cifFrame.header, categories, encoder, exportCtx, writer);
//clearLine();
writer.end();
}
diff --git a/src/servers/model/server/query.ts b/src/servers/model/server/query.ts
index f4b699b99..50c04e0c9 100644
--- a/src/servers/model/server/query.ts
+++ b/src/servers/model/server/query.ts
@@ -14,7 +14,7 @@ import { PerformanceMonitor } from 'mol-util/performance-monitor';
import Config from '../config';
import Version from '../version';
import { Job } from './jobs';
-import { getStructure, StructureWrapper } from './structure-wrapper';
+import { createStructureWrapperFromJob, StructureWrapper, resolveStructure } from './structure-wrapper';
import CifField = CifWriter.Field
import { createModelPropertiesProviderFromConfig } from '../provider';
@@ -31,13 +31,15 @@ const propertyProvider = createModelPropertiesProviderFromConfig();
export async function resolveJob(job: Job): Promise<CifWriter.Encoder<any>> {
ConsoleLogger.logId(job.id, 'Query', 'Starting.');
- const wrappedStructure = await getStructure(job, propertyProvider);
+ const wrappedStructure = await createStructureWrapperFromJob(job, propertyProvider);
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, wrappedStructure.structure)
- : wrappedStructure.structure;
+ ? 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));
perf.end('query');
diff --git a/src/servers/model/server/structure-wrapper.ts b/src/servers/model/server/structure-wrapper.ts
index cf3506a13..d7ffc7f2d 100644
--- a/src/servers/model/server/structure-wrapper.ts
+++ b/src/servers/model/server/structure-wrapper.ts
@@ -36,20 +36,22 @@ export interface StructureInfo {
export interface StructureWrapper {
info: StructureInfo,
-
isBinary: boolean,
key: string,
approximateSize: number,
- structure: Structure,
+ models: ArrayLike<Model>,
+ modelMap: Map<number, Model>,
+ structureModelMap: Map<number, Structure>,
+ propertyProvider: ModelPropertiesProvider | undefined,
cifFrame: CifFrame
}
-export async function getStructure(job: Job, propertyProvider: ModelPropertiesProvider | undefined, allowCache = true): Promise<StructureWrapper> {
+export async function createStructureWrapperFromJob(job: Job, propertyProvider: ModelPropertiesProvider | undefined, allowCache = true): Promise<StructureWrapper> {
if (allowCache && Config.cacheParams.useCache) {
const ret = StructureCache.get(job.key);
if (ret) return ret;
}
- const ret = await readStructure(job.key, job.sourceId, job.entryId, propertyProvider);
+ const ret = await readStructureWrapper(job.key, job.sourceId, job.entryId, propertyProvider);
if (allowCache && Config.cacheParams.useCache) {
StructureCache.add(ret);
}
@@ -86,7 +88,7 @@ async function parseCif(data: string|Uint8Array) {
return parsed.result;
}
-export async function readStructure(key: string, sourceId: string | '_local_', entryId: string, propertyProvider: ModelPropertiesProvider | undefined) {
+export async function readStructureWrapper(key: string, sourceId: string | '_local_', entryId: string, propertyProvider: ModelPropertiesProvider | undefined) {
const filename = sourceId === '_local_' ? entryId : Config.mapFile(sourceId, entryId);
if (!filename) throw new Error(`Cound not map '${key}' to a valid filename.`);
if (!fs.existsSync(filename)) throw new Error(`Could not find source file for '${key}'.`);
@@ -108,6 +110,11 @@ export async function readStructure(key: string, sourceId: string | '_local_', e
const models = await Model.create(Format.mmCIF(frame)).run();
perf.end('createModel');
+ const modelMap = new Map<number, Model>();
+ for (const m of models) {
+ modelMap.set(m.modelNum, m);
+ }
+
perf.start('attachProps');
if (propertyProvider) {
const modelProps = propertyProvider(models[0]);
@@ -117,28 +124,47 @@ export async function readStructure(key: string, sourceId: string | '_local_', e
}
perf.end('attachProps');
- const structure = Structure.ofModel(models[0]);
-
const ret: StructureWrapper = {
info: {
sourceType: StructureSourceType.File,
readTime: perf.time('read'),
parseTime: perf.time('parse'),
createModelTime: perf.time('createModel'),
- attachPropsTime: perf.time('attachProps'),
+ attachPropsTime: 0, // perf.time('attachProps'),
sourceId,
entryId
},
isBinary: /\.bcif/.test(filename),
key,
approximateSize: typeof data === 'string' ? 2 * data.length : data.length,
- structure,
- cifFrame: frame
+ models,
+ modelMap,
+ structureModelMap: new Map(),
+ cifFrame: frame,
+ propertyProvider
};
return ret;
}
+export async function resolveStructure(wrapper: StructureWrapper, modelNum?: number) {
+ if (typeof modelNum === 'undefined') modelNum = wrapper.models[0].modelNum;
+ if (wrapper.structureModelMap.has(modelNum)) return wrapper.structureModelMap.get(modelNum)!;
+ if (!wrapper.modelMap.has(modelNum)) {
+ return void 0;
+ }
+
+ const model = wrapper.modelMap.get(modelNum)!;
+ const structure = Structure.ofModel(model);
+ if (wrapper.propertyProvider) {
+ const modelProps = wrapper.propertyProvider(model);
+ for (const p of modelProps) {
+ await tryAttach(wrapper.key, p);
+ }
+ }
+ return structure;
+}
+
async function tryAttach(key: string, promise: Promise<any>) {
try {
await promise;
--
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