From 4dfafb531b0c39ab2b0ab2ef63190fa1e67e0383 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Tue, 18 Sep 2018 13:12:35 +0200
Subject: [PATCH] ModelServer: custom property providers defined by config file
---
src/servers/model/config.ts | 8 ++++++
src/servers/model/preprocess/preprocess.ts | 3 +-
src/servers/model/properties.ts | 19 -------------
src/servers/model/properties/pdbe.ts | 19 ++++++-------
.../model/properties/providers/pdbe.ts | 18 ++++++++++++
.../model/properties/providers/rcsb.ts | 12 ++++++++
src/servers/model/properties/rcsb.ts | 11 ++++++--
src/servers/model/provider.ts | 28 +++++++++++++++++++
src/servers/model/server/query.ts | 5 +++-
src/servers/model/server/structure-wrapper.ts | 16 ++++++-----
10 files changed, 98 insertions(+), 41 deletions(-)
delete mode 100644 src/servers/model/properties.ts
create mode 100644 src/servers/model/properties/providers/pdbe.ts
create mode 100644 src/servers/model/properties/providers/rcsb.ts
create mode 100644 src/servers/model/provider.ts
diff --git a/src/servers/model/config.ts b/src/servers/model/config.ts
index b53d12de2..8ae2425e7 100644
--- a/src/servers/model/config.ts
+++ b/src/servers/model/config.ts
@@ -47,6 +47,14 @@ const config = {
/** Maximum number of requests before "server busy" */
maxQueueLength: 30,
+ /**
+ * Paths (relative to the root directory of the model server) to JavaScript files that specify custom properties
+ */
+ customPropertyProviders: [
+ './properties/pdbe',
+ './properties/rcsb'
+ ],
+
/**
* Maps a request identifier to a filename.
*
diff --git a/src/servers/model/preprocess/preprocess.ts b/src/servers/model/preprocess/preprocess.ts
index bc6b5abca..cf45825df 100644
--- a/src/servers/model/preprocess/preprocess.ts
+++ b/src/servers/model/preprocess/preprocess.ts
@@ -23,7 +23,8 @@ export async function preprocessFile(filename: string, outputCif?: string, outpu
//const started = now();
//ConsoleLogger.log(`${linearId}`, `Reading '${filename}'...`);
- const input = await readStructure('entry', '_local_', filename);
+ // TODO: support the custom prop provider list here.
+ const input = await readStructure('entry', '_local_', filename, void 0);
//ConsoleLogger.log(`${linearId}`, `Classifying CIF categories...`);
const categories = await classifyCif(input.cifFrame);
//clearLine();
diff --git a/src/servers/model/properties.ts b/src/servers/model/properties.ts
deleted file mode 100644
index 5f2922238..000000000
--- a/src/servers/model/properties.ts
+++ /dev/null
@@ -1,19 +0,0 @@
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-import { Model } from 'mol-model/structure';
-//import { PDBe_structureQualityReport } from './properties/pdbe';
-//import { RCSB_assemblySymmetry } from './properties/rcsb';
-
-export function attachModelProperties(model: Model): Promise<any>[] {
- // return a list of promises that start attaching the props in parallel
- // (if there are downloads etc.)
- return [
- //PDBe_structureQualityReport(model),
- //RCSB_assemblySymmetry(model)
- ];
-}
\ No newline at end of file
diff --git a/src/servers/model/properties/pdbe.ts b/src/servers/model/properties/pdbe.ts
index acda123fe..61d968f9c 100644
--- a/src/servers/model/properties/pdbe.ts
+++ b/src/servers/model/properties/pdbe.ts
@@ -2,17 +2,16 @@
* Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
- import { Model } from 'mol-model/structure';
-import { StructureQualityReport } from 'mol-model-props/pdbe/structure-quality-report';
-import { fetchRetry } from '../utils/fetch-retry';
+import { Model } from 'mol-model/structure';
+import { PDBe_structureQualityReport } from './providers/pdbe';
-export function PDBe_structureQualityReport(model: Model) {
- return StructureQualityReport.attachFromCifOrApi(model, {
- PDBe_apiSourceJson: async model => {
- 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();
- }
- });
+export function attachModelProperties(model: Model): Promise<any>[] {
+ // return a list of promises that start attaching the props in parallel
+ // (if there are downloads etc.)
+ return [
+ PDBe_structureQualityReport(model)
+ ];
}
\ No newline at end of file
diff --git a/src/servers/model/properties/providers/pdbe.ts b/src/servers/model/properties/providers/pdbe.ts
new file mode 100644
index 000000000..cbc60c8c7
--- /dev/null
+++ b/src/servers/model/properties/providers/pdbe.ts
@@ -0,0 +1,18 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+ import { Model } from 'mol-model/structure';
+import { StructureQualityReport } from 'mol-model-props/pdbe/structure-quality-report';
+import { fetchRetry } from '../../utils/fetch-retry';
+
+export function PDBe_structureQualityReport(model: Model) {
+ return StructureQualityReport.attachFromCifOrApi(model, {
+ PDBe_apiSourceJson: async model => {
+ 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();
+ }
+ });
+}
\ No newline at end of file
diff --git a/src/servers/model/properties/providers/rcsb.ts b/src/servers/model/properties/providers/rcsb.ts
new file mode 100644
index 000000000..fbc3347d3
--- /dev/null
+++ b/src/servers/model/properties/providers/rcsb.ts
@@ -0,0 +1,12 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Model } from 'mol-model/structure';
+import { AssemblySymmetry } from 'mol-model-props/rcsb/symmetry';
+
+export function RCSB_assemblySymmetry(model: Model) {
+ return AssemblySymmetry.attachFromCifOrAPI(model)
+}
\ No newline at end of file
diff --git a/src/servers/model/properties/rcsb.ts b/src/servers/model/properties/rcsb.ts
index fbc3347d3..9cfaaebcd 100644
--- a/src/servers/model/properties/rcsb.ts
+++ b/src/servers/model/properties/rcsb.ts
@@ -1,12 +1,17 @@
/**
* Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
+ * @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { Model } from 'mol-model/structure';
-import { AssemblySymmetry } from 'mol-model-props/rcsb/symmetry';
+import { RCSB_assemblySymmetry } from './providers/rcsb';
-export function RCSB_assemblySymmetry(model: Model) {
- return AssemblySymmetry.attachFromCifOrAPI(model)
+export function attachModelProperties(model: Model): Promise<any>[] {
+ // return a list of promises that start attaching the props in parallel
+ // (if there are downloads etc.)
+ return [
+ RCSB_assemblySymmetry(model)
+ ];
}
\ No newline at end of file
diff --git a/src/servers/model/provider.ts b/src/servers/model/provider.ts
new file mode 100644
index 000000000..a2789b490
--- /dev/null
+++ b/src/servers/model/provider.ts
@@ -0,0 +1,28 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { Model } from 'mol-model/structure';
+import Config from './config';
+
+export type ModelPropertiesProvider = (model: Model) => Promise<any>[]
+
+export function createModelPropertiesProviderFromConfig(): ModelPropertiesProvider {
+ if (!Config.customPropertyProviders || Config.customPropertyProviders.length === 0) return () => [];
+
+ const ps: ModelPropertiesProvider[] = [];
+ for (const p of Config.customPropertyProviders) {
+ ps.push(require(p).attachModelProperties);
+ }
+
+ return model => {
+ const ret: Promise<any>[] = [];
+ for (const p of ps) {
+ for (const e of p(model)) ret.push(e);
+ }
+ return ret;
+ }
+}
+
diff --git a/src/servers/model/server/query.ts b/src/servers/model/server/query.ts
index d71200a0c..f4b699b99 100644
--- a/src/servers/model/server/query.ts
+++ b/src/servers/model/server/query.ts
@@ -16,6 +16,7 @@ import Version from '../version';
import { Job } from './jobs';
import { getStructure, StructureWrapper } from './structure-wrapper';
import CifField = CifWriter.Field
+import { createModelPropertiesProviderFromConfig } from '../provider';
export interface Stats {
structure: StructureWrapper,
@@ -25,10 +26,12 @@ export interface Stats {
const perf = new PerformanceMonitor();
+const propertyProvider = createModelPropertiesProviderFromConfig();
+
export async function resolveJob(job: Job): Promise<CifWriter.Encoder<any>> {
ConsoleLogger.logId(job.id, 'Query', 'Starting.');
- const wrappedStructure = await getStructure(job);
+ const wrappedStructure = await getStructure(job, propertyProvider);
try {
perf.start('query');
diff --git a/src/servers/model/server/structure-wrapper.ts b/src/servers/model/server/structure-wrapper.ts
index a24aaffd9..cf3506a13 100644
--- a/src/servers/model/server/structure-wrapper.ts
+++ b/src/servers/model/server/structure-wrapper.ts
@@ -14,7 +14,7 @@ import * as fs from 'fs'
import * as zlib from 'zlib'
import { Job } from './jobs';
import { ConsoleLogger } from 'mol-util/console-logger';
-import { attachModelProperties } from '../properties';
+import { ModelPropertiesProvider } from '../provider';
require('util.promisify').shim();
@@ -44,12 +44,12 @@ export interface StructureWrapper {
cifFrame: CifFrame
}
-export async function getStructure(job: Job, allowCache = true): Promise<StructureWrapper> {
+export async function getStructure(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);
+ const ret = await readStructure(job.key, job.sourceId, job.entryId, propertyProvider);
if (allowCache && Config.cacheParams.useCache) {
StructureCache.add(ret);
}
@@ -86,7 +86,7 @@ async function parseCif(data: string|Uint8Array) {
return parsed.result;
}
-export async function readStructure(key: string, sourceId: string | '_local_', entryId: string) {
+export async function readStructure(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}'.`);
@@ -109,9 +109,11 @@ export async function readStructure(key: string, sourceId: string | '_local_', e
perf.end('createModel');
perf.start('attachProps');
- const modelProps = attachModelProperties(models[0]);
- for (const p of modelProps) {
- await tryAttach(key, p);
+ if (propertyProvider) {
+ const modelProps = propertyProvider(models[0]);
+ for (const p of modelProps) {
+ await tryAttach(key, p);
+ }
}
perf.end('attachProps');
--
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