diff --git a/src/mol-model/structure/query/context.ts b/src/mol-model/structure/query/context.ts
index 846e84377e14c66e5be41ad9a0d208e7100a2d27..7541c8ac2bb2b35476830dd45d163b6c4098da3b 100644
--- a/src/mol-model/structure/query/context.ts
+++ b/src/mol-model/structure/query/context.ts
@@ -5,6 +5,7 @@
*/
import { Structure, StructureElement } from '../structure';
+import { now } from 'mol-task';
export interface QueryContextView {
readonly element: StructureElement;
@@ -14,6 +15,8 @@ export interface QueryContextView {
export class QueryContext implements QueryContextView {
private currentElementStack: StructureElement[] = [];
private currentStructureStack: Structure[] = [];
+ private timeCreated = now();
+ private timeoutMs: number;
readonly inputStructure: Structure;
@@ -40,8 +43,18 @@ export class QueryContext implements QueryContextView {
else (this.currentStructure as Structure) = void 0 as any;
}
- constructor(structure: Structure) {
+ throwIfTimedOut() {
+ if (this.timeoutMs === 0) return;
+ if (now() - this.timeCreated > this.timeoutMs) {
+ throw new Error(`The query took too long to execute (> ${this.timeoutMs / 1000}s).`);
+ }
+ }
+
+ // todo timeout
+
+ constructor(structure: Structure, timeoutMs = 0) {
this.inputStructure = structure;
+ this.timeoutMs = timeoutMs;
}
}
diff --git a/src/mol-model/structure/query/queries/combinators.ts b/src/mol-model/structure/query/queries/combinators.ts
index 7bcf70406da68f04a13562fa50006c616588464b..854c54726292a58380805bf3578da5e8fb8414fe 100644
--- a/src/mol-model/structure/query/queries/combinators.ts
+++ b/src/mol-model/structure/query/queries/combinators.ts
@@ -11,8 +11,9 @@ export function merge(queries: ArrayLike<StructureQuery>): StructureQuery {
return ctx => {
const ret = StructureSelection.UniqueBuilder(ctx.inputStructure);
for (let i = 0; i < queries.length; i++) {
- StructureSelection.forEach(queries[i](ctx), s => {
+ StructureSelection.forEach(queries[i](ctx), (s, j) => {
ret.add(s);
+ if (i % 100) ctx.throwIfTimedOut();
});
}
return ret.getSelection();
diff --git a/src/mol-model/structure/query/queries/filters.ts b/src/mol-model/structure/query/queries/filters.ts
index 6d7363123cf450d8cf0be06e276fdb86504601d2..49ca5dc201f31af2bb1cf9575f7bde6453b10313 100644
--- a/src/mol-model/structure/query/queries/filters.ts
+++ b/src/mol-model/structure/query/queries/filters.ts
@@ -16,9 +16,10 @@ export function pick(query: StructureQuery, pred: QueryPredicate): StructureQuer
const sel = query(ctx);
const ret = StructureSelection.LinearBuilder(ctx.inputStructure);
ctx.pushCurrentElement();
- StructureSelection.forEach(sel, s => {
+ StructureSelection.forEach(sel, (s, i) => {
ctx.currentStructure = s;
if (pred(ctx)) ret.add(s);
+ if (i % 100) ctx.throwIfTimedOut();
});
ctx.popCurrentStructure();
return ret.getSelection();
@@ -44,6 +45,8 @@ export function getCurrentStructureProperties(ctx: QueryContext, props: UnitType
l.element = elements[j];
set.add(fn(ctx));
}
+
+ ctx.throwIfTimedOut();
}
ctx.popCurrentElement();
return set;
@@ -54,9 +57,11 @@ function getSelectionProperties(ctx: QueryContext, query: StructureQuery, props:
const sel = query(ctx);
ctx.pushCurrentElement();
- StructureSelection.forEach(sel, s => {
+ StructureSelection.forEach(sel, (s, i) => {
ctx.currentStructure = s;
getCurrentStructureProperties(ctx, props, set);
+
+ if (i % 10) ctx.throwIfTimedOut();
});
ctx.popCurrentElement();
return set;
@@ -69,12 +74,14 @@ export function withSameAtomProperties(query: StructureQuery, propertySource: St
const ret = StructureSelection.LinearBuilder(ctx.inputStructure);
ctx.pushCurrentStructure();
- StructureSelection.forEach(sel, s => {
+ StructureSelection.forEach(sel, (s, i) => {
ctx.currentStructure = s;
const currentProps = getCurrentStructureProperties(ctx, props, new Set());
if (isSuperset(currentProps, propSet)) {
ret.add(s);
}
+
+ if (i % 10) ctx.throwIfTimedOut();
});
ctx.popCurrentStructure();
return ret.getSelection();
@@ -86,8 +93,9 @@ export function areIntersectedBy(query: StructureQuery, by: StructureQuery): Str
const mask = StructureSelection.unionStructure(by(ctx));
const ret = StructureSelection.LinearBuilder(ctx.inputStructure);
- StructureSelection.forEach(query(ctx), s => {
+ StructureSelection.forEach(query(ctx), (s, i) => {
if (structureAreIntersecting(mask, s)) ret.add(s);
+ if (i % 10) ctx.throwIfTimedOut();
});
return ret.getSelection();
};
diff --git a/src/mol-model/structure/query/queries/generators.ts b/src/mol-model/structure/query/queries/generators.ts
index ef9da1a1863010b8935be8d901ca28c9c74be8d3..c7e7d770e41dd544afeb30d9485fb92383c5d56a 100644
--- a/src/mol-model/structure/query/queries/generators.ts
+++ b/src/mol-model/structure/query/queries/generators.ts
@@ -60,6 +60,8 @@ function atomGroupsLinear(atomTest: QueryPredicate): StructureQuery {
if (atomTest(ctx)) builder.addElement(l.element);
}
builder.commitUnit();
+
+ ctx.throwIfTimedOut();
}
ctx.popCurrentElement();
return StructureSelection.Singletons(inputStructure, builder.getStructure());
@@ -105,6 +107,8 @@ function atomGroupsSegmented({ entityTest, chainTest, residueTest, atomTest }: A
}
}
builder.commitUnit();
+
+ ctx.throwIfTimedOut();
}
ctx.popCurrentElement();
return StructureSelection.Singletons(inputStructure, builder.getStructure());
@@ -146,6 +150,8 @@ function atomGroupsGrouped({ entityTest, chainTest, residueTest, atomTest, group
}
}
}
+
+ ctx.throwIfTimedOut();
}
ctx.popCurrentElement();
return builder.getSelection();
diff --git a/src/mol-model/structure/query/queries/modifiers.ts b/src/mol-model/structure/query/queries/modifiers.ts
index ba3404e3482e13d001030543a4a47b99131ed122..f6add3bbec78f401ac461fec32b2ef36767e429b 100644
--- a/src/mol-model/structure/query/queries/modifiers.ts
+++ b/src/mol-model/structure/query/queries/modifiers.ts
@@ -10,8 +10,9 @@ import { StructureQuery } from '../query';
import { StructureSelection } from '../selection';
import { UniqueStructuresBuilder } from '../utils/builders';
import { StructureUniqueSubsetBuilder } from '../../structure/util/unique-subset-builder';
+import { QueryContext } from '../context';
-function getWholeResidues(source: Structure, structure: Structure) {
+function getWholeResidues(ctx: QueryContext, source: Structure, structure: Structure) {
const builder = source.subsetBuilder(true);
for (const unit of structure.units) {
if (unit.kind !== Unit.Kind.Atomic) {
@@ -32,6 +33,8 @@ function getWholeResidues(source: Structure, structure: Structure) {
}
}
builder.commitUnit();
+
+ ctx.throwIfTimedOut();
}
return builder.getStructure();
}
@@ -40,11 +43,11 @@ export function wholeResidues(query: StructureQuery, isFlat: boolean): Structure
return ctx => {
const inner = query(ctx);
if (StructureSelection.isSingleton(inner)) {
- return StructureSelection.Singletons(ctx.inputStructure, getWholeResidues(ctx.inputStructure, inner.structure));
+ return StructureSelection.Singletons(ctx.inputStructure, getWholeResidues(ctx, ctx.inputStructure, inner.structure));
} else {
const builder = new UniqueStructuresBuilder(ctx.inputStructure);
for (const s of inner.structures) {
- builder.add(getWholeResidues(ctx.inputStructure, s));
+ builder.add(getWholeResidues(ctx, ctx.inputStructure, s));
}
return builder.getSelection();
}
@@ -60,7 +63,7 @@ export interface IncludeSurroundingsParams {
wholeResidues?: boolean
}
-function getIncludeSurroundings(source: Structure, structure: Structure, params: IncludeSurroundingsParams) {
+function getIncludeSurroundings(ctx: QueryContext, source: Structure, structure: Structure, params: IncludeSurroundingsParams) {
const builder = new StructureUniqueSubsetBuilder(source);
const lookup = source.lookup3d;
const r = params.radius;
@@ -72,21 +75,23 @@ function getIncludeSurroundings(source: Structure, structure: Structure, params:
const e = elements[i];
lookup.findIntoBuilder(x(e), y(e), z(e), r, builder);
}
+
+ ctx.throwIfTimedOut();
}
- return !!params.wholeResidues ? getWholeResidues(source, builder.getStructure()) : builder.getStructure();
+ return !!params.wholeResidues ? getWholeResidues(ctx, source, builder.getStructure()) : builder.getStructure();
}
export function includeSurroundings(query: StructureQuery, params: IncludeSurroundingsParams): StructureQuery {
return ctx => {
const inner = query(ctx);
if (StructureSelection.isSingleton(inner)) {
- const surr = getIncludeSurroundings(ctx.inputStructure, inner.structure, params);
+ const surr = getIncludeSurroundings(ctx, ctx.inputStructure, inner.structure, params);
const ret = StructureSelection.Singletons(ctx.inputStructure, surr);
return ret;
} else {
const builder = new UniqueStructuresBuilder(ctx.inputStructure);
for (const s of inner.structures) {
- builder.add(getIncludeSurroundings(ctx.inputStructure, s, params));
+ builder.add(getIncludeSurroundings(ctx, ctx.inputStructure, s, params));
}
return builder.getSelection();
}
diff --git a/src/mol-model/structure/query/query.ts b/src/mol-model/structure/query/query.ts
index 98f8ab4d71b559f1fe9acc4d390f618a8daf1d1d..4283b6b73029bf88d6c793253fb6871f6657ed60 100644
--- a/src/mol-model/structure/query/query.ts
+++ b/src/mol-model/structure/query/query.ts
@@ -10,8 +10,8 @@ import { QueryContext } from './context';
interface StructureQuery { (ctx: QueryContext): StructureSelection }
namespace StructureQuery {
- export function run(query: StructureQuery, structure: Structure) {
- return query(new QueryContext(structure))
+ export function run(query: StructureQuery, structure: Structure, timeoutMs = 0) {
+ return query(new QueryContext(structure, timeoutMs));
}
}
diff --git a/src/servers/model/server/query.ts b/src/servers/model/server/query.ts
index 908f16dc833fc56c814b2691d3df213265f9c093..13a1816935f010f35d9627c23a576133f631fe05 100644
--- a/src/servers/model/server/query.ts
+++ b/src/servers/model/server/query.ts
@@ -32,11 +32,12 @@ export async function resolveJob(job: Job, writer: Writer) {
const wrappedStructure = await getStructure(job);
perf.start('query');
+ // TODO: encode errors that happen past this point as CIF rather than just 404
const structure = job.queryDefinition.structureTransform
? await job.queryDefinition.structureTransform(job.normalizedParams, wrappedStructure.structure)
: wrappedStructure.structure;
const query = job.queryDefinition.query(job.normalizedParams, structure);
- const result = StructureSelection.unionStructure(StructureQuery.run(query, structure));
+ const result = StructureSelection.unionStructure(StructureQuery.run(query, structure, Config.maxQueryTimeInMs));
perf.end('query');
ConsoleLogger.logId(job.id, 'Query', 'Query finished.');