From 31e92e4425bb2eab9d371394d59d53d82b30e736 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Thu, 26 Jul 2018 18:46:07 +0200
Subject: [PATCH] ModelServer JSON based web api
---
src/servers/model/properties.ts | 8 +-
.../properties/structure-quality-report.ts | 3 +-
src/servers/model/query/atoms.ts | 9 +-
src/servers/model/server/api-web.ts | 40 +++++----
src/servers/model/server/api.ts | 86 +++++++++----------
src/servers/model/server/query.ts | 2 +-
src/servers/model/server/structure-wrapper.ts | 13 ++-
7 files changed, 92 insertions(+), 69 deletions(-)
diff --git a/src/servers/model/properties.ts b/src/servers/model/properties.ts
index 3f35e2415..b3486a48d 100644
--- a/src/servers/model/properties.ts
+++ b/src/servers/model/properties.ts
@@ -7,6 +7,10 @@
import { Model } from 'mol-model/structure';
import { StructureQualityReport } from './properties/structure-quality-report';
-export async function attachModelProperties(model: Model) {
- await StructureQualityReport.attachFromPDBeApi(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 [
+ StructureQualityReport.attachFromPDBeApi(model)
+ ];
}
\ No newline at end of file
diff --git a/src/servers/model/properties/structure-quality-report.ts b/src/servers/model/properties/structure-quality-report.ts
index 0f57a6855..cc498b6f3 100644
--- a/src/servers/model/properties/structure-quality-report.ts
+++ b/src/servers/model/properties/structure-quality-report.ts
@@ -46,7 +46,6 @@ const _structure_quality_report_fields: CifField<ResidueIndex, ExportCtx>[] = [
CifField.int<ResidueIndex, ExportCtx>('auth_seq_id', (i, d) => P.residue.auth_seq_id(d.residues[i])),
CifField.str<ResidueIndex, ExportCtx>('auth_asym_id', (i, d) => P.chain.auth_asym_id(d.residues[i])),
-
CifField.str<ResidueIndex, ExportCtx>('issues', (i, d) => d.issues.get(d.residueIndex[d.residues[i].element])!.join(','))
];
@@ -106,7 +105,7 @@ export namespace StructureQualityReport {
if (model.customProperties.has(Descriptor)) return true;
const id = model.label.toLowerCase();
- const rawData = await fetch(`https://www.ebi.ac.uk/pdbe/api/validation/residuewise_outlier_summary/entry/${model.label.toLowerCase()}`);
+ const rawData = await fetch(`https://www.ebi.ac.uk/pdbe/api/validation/residuewise_outlier_summary/entry/${model.label.toLowerCase()}`, { timeout: 500 });
const json = await rawData.json();
const data = json[id];
if (!data) return false;
diff --git a/src/servers/model/query/atoms.ts b/src/servers/model/query/atoms.ts
index 3aca80108..524338e9f 100644
--- a/src/servers/model/query/atoms.ts
+++ b/src/servers/model/query/atoms.ts
@@ -8,6 +8,7 @@ import { QueryPredicate, StructureElement, StructureProperties as Props, Queries
import { AtomsQueryParams } from 'mol-model/structure/query/queries/generators';
export function getAtomsTests(params: any): Partial<AtomsQueryParams>[] {
+ if (!params) return [{ }];
if (Array.isArray(params)) {
return params.map(p => atomsTest(p));
} else {
@@ -25,12 +26,14 @@ function atomsTest(params: any): Partial<AtomsQueryParams> {
}
function entityTest(params: any): QueryPredicate | undefined {
- if (typeof params.entity_id === 'undefined') return void 0;
+ if (!params || typeof params.entity_id === 'undefined') return void 0;
const p = Props.entity.id, id = '' + params.label_entity_id;
return ctx => p(ctx.element) === id;
}
function chainTest(params: any): QueryPredicate | undefined {
+ if (!params) return void 0;
+
if (typeof params.label_asym_id !== 'undefined') {
const p = Props.chain.label_asym_id, id = '' + params.label_asym_id;
return ctx => p(ctx.element) === id;
@@ -43,6 +46,8 @@ function chainTest(params: any): QueryPredicate | undefined {
}
function residueTest(params: any): QueryPredicate | undefined {
+ if (!params) return void 0;
+
const props: StructureElement.Property<any>[] = [], values: any[] = [];
if (typeof params.label_seq_id !== 'undefined') {
@@ -74,6 +79,8 @@ function residueTest(params: any): QueryPredicate | undefined {
}
function atomTest(params: any): QueryPredicate | undefined {
+ if (!params) return void 0;
+
const props: StructureElement.Property<any>[] = [], values: any[] = [];
if (typeof params.label_atom_id !== 'undefined') {
diff --git a/src/servers/model/server/api-web.ts b/src/servers/model/server/api-web.ts
index ca96bbbe5..93332c55f 100644
--- a/src/servers/model/server/api-web.ts
+++ b/src/servers/model/server/api-web.ts
@@ -6,7 +6,6 @@
import * as express from 'express';
import Config from '../config';
-import { QueryDefinition, QueryList } from './api';
import { ConsoleLogger } from 'mol-util/console-logger';
import { resolveJob } from './query';
import { JobManager } from './jobs';
@@ -81,24 +80,35 @@ async function processNextJob() {
}
}
-function mapQuery(app: express.Express, queryName: string, queryDefinition: QueryDefinition) {
- app.get(makePath(':entryId/' + queryName), (req, res) => {
- ConsoleLogger.log('Server', `Query '${req.params.entryId}/${queryName}'...`);
+// function mapQuery(app: express.Express, queryName: string, queryDefinition: QueryDefinition) {
+// app.get(makePath(':entryId/' + queryName), (req, res) => {
+// ConsoleLogger.log('Server', `Query '${req.params.entryId}/${queryName}'...`);
- if (JobManager.size >= Config.maxQueueLength) {
- res.status(503).send('Too many queries, please try again later.');
- res.end();
- return;
- }
+// if (JobManager.size >= Config.maxQueueLength) {
+// res.status(503).send('Too many queries, please try again later.');
+// res.end();
+// return;
+// }
+
+// const jobId = JobManager.add('pdb', req.params.entryId, queryName, req.query);
+// responseMap.set(jobId, res);
+// if (JobManager.size === 1) processNextJob();
+// });
+// }
- const jobId = JobManager.add('pdb', req.params.entryId, queryName, req.query);
+export function initWebApi(app: express.Express) {
+ app.get(makePath('query'), (req, res) => {
+ const query = /\?(.*)$/.exec(req.url)![1];
+ const args = JSON.parse(decodeURIComponent(query));
+ const name = args.name;
+ const entryId = args.id;
+ const params = args.params || { };
+ const jobId = JobManager.add('pdb', entryId, name, params);
responseMap.set(jobId, res);
if (JobManager.size === 1) processNextJob();
});
-}
-export function initWebApi(app: express.Express) {
- for (const q of QueryList) {
- mapQuery(app, q.name, q.definition);
- }
+ // for (const q of QueryList) {
+ // mapQuery(app, q.name, q.definition);
+ // }
}
\ No newline at end of file
diff --git a/src/servers/model/server/api.ts b/src/servers/model/server/api.ts
index 44135d39d..93504ed29 100644
--- a/src/servers/model/server/api.ts
+++ b/src/servers/model/server/api.ts
@@ -34,18 +34,18 @@ export interface QueryDefinition {
structureTransform?: (params: any, s: Structure) => Promise<Structure>
}
-const AtomSiteParams = {
- entity_id: <QueryParamInfo>{ name: 'entity_id', type: QueryParamType.String, description: 'Corresponds to the \'_entity.id\' or \'*.label_entity_id\' field, depending on the context.' },
+// const AtomSiteParams = {
+// entity_id: <QueryParamInfo>{ name: 'entity_id', type: QueryParamType.String, description: 'Corresponds to the \'_entity.id\' or \'*.label_entity_id\' field, depending on the context.' },
- label_asym_id: <QueryParamInfo>{ name: 'label_asym_id', type: QueryParamType.String, description: 'Corresponds to the \'_atom_site.label_asym_id\' field.' },
- auth_asym_id: <QueryParamInfo>{ name: 'auth_asym_id', type: QueryParamType.String, exampleValue: 'A', description: 'Corresponds to the \'_atom_site.auth_asym_id\' field.' },
+// label_asym_id: <QueryParamInfo>{ name: 'label_asym_id', type: QueryParamType.String, description: 'Corresponds to the \'_atom_site.label_asym_id\' field.' },
+// auth_asym_id: <QueryParamInfo>{ name: 'auth_asym_id', type: QueryParamType.String, exampleValue: 'A', description: 'Corresponds to the \'_atom_site.auth_asym_id\' field.' },
- label_seq_id: <QueryParamInfo>{ name: 'label_seq_id', type: QueryParamType.Integer, description: 'Residue seq. number. Corresponds to the \'_atom_site.label_seq_id\' field.' },
- auth_seq_id: <QueryParamInfo>{ name: 'auth_seq_id', type: QueryParamType.Integer, exampleValue: '200', description: 'Author residue seq. number. Corresponds to the \'_atom_site.auth_seq_id\' field.' },
- label_comp_id: <QueryParamInfo>{ name: 'label_comp_id', type: QueryParamType.String, description: 'Residue name. Corresponds to the \'_atom_site.label_comp_id\' field.' },
- auth_comp_id: <QueryParamInfo>{ name: 'auth_comp_id', type: QueryParamType.String, exampleValue: 'REA', description: 'Author residue name. Corresponds to the \'_atom_site.auth_comp_id\' field.' },
- pdbx_PDB_ins_code: <QueryParamInfo>{ name: 'pdbx_PDB_ins_code', type: QueryParamType.String, description: 'Corresponds to the \'_atom_site.pdbx_PDB_ins_code\' field.' },
-};
+// label_seq_id: <QueryParamInfo>{ name: 'label_seq_id', type: QueryParamType.Integer, description: 'Residue seq. number. Corresponds to the \'_atom_site.label_seq_id\' field.' },
+// auth_seq_id: <QueryParamInfo>{ name: 'auth_seq_id', type: QueryParamType.Integer, exampleValue: '200', description: 'Author residue seq. number. Corresponds to the \'_atom_site.auth_seq_id\' field.' },
+// label_comp_id: <QueryParamInfo>{ name: 'label_comp_id', type: QueryParamType.String, description: 'Residue name. Corresponds to the \'_atom_site.label_comp_id\' field.' },
+// auth_comp_id: <QueryParamInfo>{ name: 'auth_comp_id', type: QueryParamType.String, exampleValue: 'REA', description: 'Author residue name. Corresponds to the \'_atom_site.auth_comp_id\' field.' },
+// pdbx_PDB_ins_code: <QueryParamInfo>{ name: 'pdbx_PDB_ins_code', type: QueryParamType.String, description: 'Corresponds to the \'_atom_site.pdbx_PDB_ins_code\' field.' },
+// };
const AtomSiteTestParams: QueryParamInfo = {
name: 'atom_site',
@@ -99,10 +99,10 @@ const QueryMap: { [id: string]: Partial<QueryDefinition> } = {
}]
},
'residueInteraction': {
- niceName: 'Residues Inside a Sphere',
+ niceName: 'Residue Interaction',
description: 'Identifies all residues within the given radius from the source residue. Takes crystal symmetry into account.',
query(p) {
- const tests = getAtomsTests(p);
+ const tests = getAtomsTests(p.atom_site);
const center = Queries.combinators.merge(tests.map(test => Queries.generators.atoms({
...test,
entityTest: test.entityTest
@@ -114,17 +114,7 @@ const QueryMap: { [id: string]: Partial<QueryDefinition> } = {
structureTransform(p, s) {
return StructureSymmetry.builderSymmetryMates(s, p.radius).run();
},
- params: [
- AtomSiteParams.entity_id,
- AtomSiteParams.label_asym_id,
- AtomSiteParams.auth_asym_id,
- AtomSiteParams.label_comp_id,
- AtomSiteParams.auth_comp_id,
- AtomSiteParams.pdbx_PDB_ins_code,
- AtomSiteParams.label_seq_id,
- AtomSiteParams.auth_seq_id,
- RadiusParam,
- ]
+ params: [ AtomSiteTestParams, RadiusParam ]
},
};
@@ -148,30 +138,32 @@ export const QueryList = (function () {
}
})();
-function _normalizeQueryParams(params: { [p: string]: string }, paramList: QueryParamInfo[]): { [p: string]: string | number | boolean } {
- const ret: any = {};
- for (const p of paramList) {
- const key = p.name;
- const value = params[key];
- if (typeof value === 'undefined' || (typeof value !== 'undefined' && value !== null && value['length'] === 0)) {
- if (p.required) {
- throw `The parameter '${key}' is required.`;
- }
- if (typeof p.defaultValue !== 'undefined') ret[key] = p.defaultValue;
- } else {
- switch (p.type) {
- case QueryParamType.String: ret[key] = value; break;
- case QueryParamType.Integer: ret[key] = parseInt(value); break;
- case QueryParamType.Float: ret[key] = parseFloat(value); break;
- }
-
- if (p.validation) p.validation(ret[key]);
- }
- }
-
- return ret;
-}
+// function _normalizeQueryParams(params: { [p: string]: string }, paramList: QueryParamInfo[]): { [p: string]: string | number | boolean } {
+// const ret: any = {};
+// for (const p of paramList) {
+// const key = p.name;
+// const value = params[key];
+// if (typeof value === 'undefined' || (typeof value !== 'undefined' && value !== null && value['length'] === 0)) {
+// if (p.required) {
+// throw `The parameter '${key}' is required.`;
+// }
+// if (typeof p.defaultValue !== 'undefined') ret[key] = p.defaultValue;
+// } else {
+// switch (p.type) {
+// case QueryParamType.JSON: ret[key] = JSON.parse(value); break;
+// case QueryParamType.String: ret[key] = value; break;
+// case QueryParamType.Integer: ret[key] = parseInt(value); break;
+// case QueryParamType.Float: ret[key] = parseFloat(value); break;
+// }
+
+// if (p.validation) p.validation(ret[key]);
+// }
+// }
+
+// return ret;
+// }
export function normalizeQueryParams(query: QueryDefinition, params: any) {
- return _normalizeQueryParams(params, query.params);
+ return params;
+ //return _normalizeQueryParams(params, query.params);
}
\ No newline at end of file
diff --git a/src/servers/model/server/query.ts b/src/servers/model/server/query.ts
index 92b01d622..3fce312b7 100644
--- a/src/servers/model/server/query.ts
+++ b/src/servers/model/server/query.ts
@@ -137,7 +137,7 @@ const _model_server_params: CifWriter.Category<Job> = {
instance(job) {
const params: string[][] = [];
for (const k of Object.keys(job.normalizedParams)) {
- params.push([k, '' + job.normalizedParams[k]]);
+ params.push([k, JSON.stringify(job.normalizedParams[k])]);
}
return {
data: params,
diff --git a/src/servers/model/server/structure-wrapper.ts b/src/servers/model/server/structure-wrapper.ts
index d70a75823..8774e578c 100644
--- a/src/servers/model/server/structure-wrapper.ts
+++ b/src/servers/model/server/structure-wrapper.ts
@@ -107,7 +107,10 @@ async function readStructure(key: string, sourceId: string, entryId: string) {
perf.end('createModel');
perf.start('attachProps');
- await attachModelProperties(models[0]);
+ const modelProps = attachModelProperties(models[0]);
+ for (const p of modelProps) {
+ await tryAttach(key, p);
+ }
perf.end('attachProps');
const structure = Structure.ofModel(models[0]);
@@ -128,4 +131,12 @@ async function readStructure(key: string, sourceId: string, entryId: string) {
};
return ret;
+}
+
+async function tryAttach(key: string, promise: Promise<any>) {
+ try {
+ await promise;
+ } catch (e) {
+ ConsoleLogger.errorId(key, 'Custom prop:' + e);
+ }
}
\ No newline at end of file
--
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