From bea4c64d85a147fad0c6bb53883beb99ffc19cbd Mon Sep 17 00:00:00 2001
From: Alexander Rose <alexander.rose@weirdbyte.de>
Date: Fri, 17 Apr 2020 11:42:59 -0700
Subject: [PATCH] use asset-manager for custom-properties
- obtain function needs to return a value and assets
- assets are stored per descriptor in model/structure
- assets shold be released via customProperties.dispose()
---
src/examples/basic-wrapper/coloring.ts | 2 +-
.../proteopedia-wrapper/annotation.ts | 11 ++---
src/extensions/cellpack/model.ts | 2 +-
src/extensions/cellpack/property.ts | 4 +-
.../pdbe/structure-quality-report/prop.ts | 16 ++++----
.../rcsb/assembly-symmetry/behavior.ts | 8 ++--
src/extensions/rcsb/assembly-symmetry/prop.ts | 18 +++++----
.../rcsb/validation-report/behavior.ts | 6 +--
src/extensions/rcsb/validation-report/prop.ts | 25 ++++++------
.../common/custom-element-property.ts | 3 +-
.../common/custom-model-property.ts | 7 +++-
src/mol-model-props/common/custom-property.ts | 7 ++--
.../common/custom-structure-property.ts | 7 +++-
.../computed/accessible-surface-area.ts | 2 +-
src/mol-model-props/computed/interactions.ts | 2 +-
.../computed/secondary-structure.ts | 4 +-
src/mol-model-props/computed/valence-model.ts | 2 +-
.../cross-link-restraint/property.ts | 2 +-
.../structure/common/custom-property.ts | 28 ++++++++++---
src/mol-plugin-state/builder/structure.ts | 2 +-
.../helpers/structure-selection-query.ts | 2 +-
src/mol-plugin-state/transforms/model.ts | 37 ++++++++++++++++-
.../transforms/representation.ts | 6 +--
src/mol-util/graphql-client.ts | 40 +++++++------------
src/tests/browser/render-structure.ts | 4 +-
25 files changed, 151 insertions(+), 96 deletions(-)
diff --git a/src/examples/basic-wrapper/coloring.ts b/src/examples/basic-wrapper/coloring.ts
index 0b5fe352b..024783c2f 100644
--- a/src/examples/basic-wrapper/coloring.ts
+++ b/src/examples/basic-wrapper/coloring.ts
@@ -18,7 +18,7 @@ export const StripedResidues = CustomElementProperty.create<number>({
for (let i = 0, _i = model.atomicHierarchy.atoms._rowCount; i < _i; i++) {
map.set(i as ElementIndex, residueIndex[i] % 2);
}
- return map;
+ return { value: map };
},
coloring: {
getColor(e) { return e === 0 ? Color(0xff0000) : Color(0x0000ff); },
diff --git a/src/examples/proteopedia-wrapper/annotation.ts b/src/examples/proteopedia-wrapper/annotation.ts
index 647d0f603..1d158075e 100644
--- a/src/examples/proteopedia-wrapper/annotation.ts
+++ b/src/examples/proteopedia-wrapper/annotation.ts
@@ -9,6 +9,7 @@ import { CustomElementProperty } from '../../mol-model-props/common/custom-eleme
import { Model, ElementIndex, ResidueIndex } from '../../mol-model/structure';
import { Color } from '../../mol-util/color';
import { CustomProperty } from '../../mol-model-props/common/custom-property';
+import { Asset } from '../../mol-util/assets';
const EvolutionaryConservationPalette: Color[] = [
[255, 255, 129], // insufficient
@@ -30,9 +31,9 @@ export const EvolutionaryConservation = CustomElementProperty.create<number>({
type: 'static',
async getData(model: Model, ctx: CustomProperty.Context) {
const id = model.entryId.toLowerCase();
- const url = `https://proteopedia.org/cgi-bin/cnsrf?${id}`;
- const json = await ctx.fetch({ url, type: 'json' }).runInContext(ctx.runtime);
- const annotations = (json && json.residueAnnotations) || [];
+ const url = Asset.getUrlAsset(ctx.assetManager, `https://proteopedia.org/cgi-bin/cnsrf?${id}`);
+ const json = await ctx.assetManager.resolve(url, 'json').runInContext(ctx.runtime);
+ const annotations = json.data?.residueAnnotations || [];
const conservationMap = new Map<string, number>();
@@ -58,7 +59,7 @@ export const EvolutionaryConservation = CustomElementProperty.create<number>({
}
}
- return map;
+ return { value: map, assets: [json] };
},
coloring: {
getColor(e: number) {
@@ -68,7 +69,7 @@ export const EvolutionaryConservation = CustomElementProperty.create<number>({
defaultColor: EvolutionaryConservationDefaultColor
},
getLabel(e) {
- if (e === 10) return `Evolutionary Conservation: InsufficientData`;
+ if (e === 10) return `Evolutionary Conservation: Insufficient Data`;
return e ? `Evolutionary Conservation: ${e}` : void 0;
}
});
\ No newline at end of file
diff --git a/src/extensions/cellpack/model.ts b/src/extensions/cellpack/model.ts
index 06e0a9718..072850175 100644
--- a/src/extensions/cellpack/model.ts
+++ b/src/extensions/cellpack/model.ts
@@ -463,7 +463,7 @@ async function loadPackings(plugin: PluginContext, runtime: RuntimeContext, stat
const structure = packing.obj?.data;
if (structure) {
- await CellPackInfoProvider.attach({ fetch: plugin.fetch, runtime }, structure, {
+ await CellPackInfoProvider.attach({ runtime, assetManager: plugin.managers.asset }, structure, {
info: { packingsCount: packings.length, packingIndex: i }
});
}
diff --git a/src/extensions/cellpack/property.ts b/src/extensions/cellpack/property.ts
index 71c2e622f..700776fea 100644
--- a/src/extensions/cellpack/property.ts
+++ b/src/extensions/cellpack/property.ts
@@ -27,6 +27,8 @@ export const CellPackInfoProvider: CustomStructureProperty.Provider<typeof CellP
getParams: (data: Structure) => CellPackInfoParams,
isApplicable: (data: Structure) => true,
obtain: async (ctx: CustomProperty.Context, data: Structure, props: CellPackInfoParams) => {
- return { ...CellPackInfoParams.info.defaultValue, ...props.info };
+ return {
+ value: { ...CellPackInfoParams.info.defaultValue, ...props.info }
+ };
}
});
\ No newline at end of file
diff --git a/src/extensions/pdbe/structure-quality-report/prop.ts b/src/extensions/pdbe/structure-quality-report/prop.ts
index 8121efa07..fa020b940 100644
--- a/src/extensions/pdbe/structure-quality-report/prop.ts
+++ b/src/extensions/pdbe/structure-quality-report/prop.ts
@@ -21,6 +21,7 @@ import { MmcifFormat } from '../../../mol-model-formats/structure/mmcif';
import { PropertyWrapper } from '../../../mol-model-props/common/wrapper';
import { CustomProperty } from '../../../mol-model-props/common/custom-property';
import { CustomModelProperty } from '../../../mol-model-props/common/custom-model-property';
+import { Asset } from '../../../mol-util/assets';
export { StructureQualityReport };
@@ -67,12 +68,12 @@ namespace StructureQualityReport {
return { info, data: issueMap };
}
- export async function fromServer(ctx: CustomProperty.Context, model: Model, props: StructureQualityReportProps): Promise<StructureQualityReport> {
- const url = getEntryUrl(model.entryId, props.serverUrl);
- const json = await ctx.fetch({ url, type: 'json' }).runInContext(ctx.runtime);
- const data = json[model.entryId.toLowerCase()];
+ export async function fromServer(ctx: CustomProperty.Context, model: Model, props: StructureQualityReportProps): Promise<CustomProperty.Data<StructureQualityReport>> {
+ const url = Asset.getUrlAsset(ctx.assetManager, getEntryUrl(model.entryId, props.serverUrl));
+ const json = await ctx.assetManager.resolve(url, 'json').runInContext(ctx.runtime);
+ const data = json.data[model.entryId.toLowerCase()];
if (!data) throw new Error('missing data');
- return fromJson(model, data);
+ return { value: fromJson(model, data), assets: [json] };
}
export function fromCif(ctx: CustomProperty.Context, model: Model, props: StructureQualityReportProps): StructureQualityReport | undefined {
@@ -83,8 +84,9 @@ namespace StructureQualityReport {
return { info, data: issueMap };
}
- export async function fromCifOrServer(ctx: CustomProperty.Context, model: Model, props: StructureQualityReportProps): Promise<StructureQualityReport> {
- return fromCif(ctx, model, props) || fromServer(ctx, model, props);
+ export async function fromCifOrServer(ctx: CustomProperty.Context, model: Model, props: StructureQualityReportProps): Promise<CustomProperty.Data<StructureQualityReport>> {
+ const cif = fromCif(ctx, model, props);
+ return cif ? { value: cif } : fromServer(ctx, model, props);
}
const _emptyArray: string[] = [];
diff --git a/src/extensions/rcsb/assembly-symmetry/behavior.ts b/src/extensions/rcsb/assembly-symmetry/behavior.ts
index 01c9f16c6..bebc5e868 100644
--- a/src/extensions/rcsb/assembly-symmetry/behavior.ts
+++ b/src/extensions/rcsb/assembly-symmetry/behavior.ts
@@ -80,7 +80,7 @@ export const InitAssemblySymmetry3D = StateAction.build({
isApplicable: (a) => AssemblySymmetry.isApplicable(a.data)
})(({ a, ref, state }, plugin: PluginContext) => Task.create('Init Assembly Symmetry', async ctx => {
try {
- const propCtx = { runtime: ctx, fetch: plugin.fetch };
+ const propCtx = { runtime: ctx, assetManager: plugin.managers.asset };
await AssemblySymmetryDataProvider.attach(propCtx, a.data);
const assemblySymmetryData = AssemblySymmetryDataProvider.get(a.data).value;
const symmetryIndex = assemblySymmetryData ? AssemblySymmetry.firstNonC1(assemblySymmetryData) : -1;
@@ -116,7 +116,7 @@ const AssemblySymmetry3D = PluginStateTransform.BuiltIn({
},
apply({ a, params }, plugin: PluginContext) {
return Task.create('Assembly Symmetry', async ctx => {
- await AssemblySymmetryProvider.attach({ runtime: ctx, fetch: plugin.fetch }, a.data);
+ await AssemblySymmetryProvider.attach({ runtime: ctx, assetManager: plugin.managers.asset }, a.data);
const assemblySymmetry = AssemblySymmetryProvider.get(a.data).value;
if (!assemblySymmetry || assemblySymmetry.symbol === 'C1') {
return StateObject.Null;
@@ -129,7 +129,7 @@ const AssemblySymmetry3D = PluginStateTransform.BuiltIn({
},
update({ a, b, newParams }, plugin: PluginContext) {
return Task.create('Assembly Symmetry', async ctx => {
- await AssemblySymmetryProvider.attach({ runtime: ctx, fetch: plugin.fetch }, a.data);
+ await AssemblySymmetryProvider.attach({ runtime: ctx, assetManager: plugin.managers.asset }, a.data);
const assemblySymmetry = AssemblySymmetryProvider.get(a.data).value;
if (!assemblySymmetry || assemblySymmetry.symbol === 'C1') {
// this should NOT be StateTransformer.UpdateResult.Null
@@ -172,7 +172,7 @@ export const AssemblySymmetryPreset = StructureRepresentationPresetProvider({
if (!AssemblySymmetryDataProvider.get(structure).value) {
await plugin.runTask(Task.create('Assembly Symmetry', async runtime => {
- const propCtx = { runtime, fetch: plugin.fetch };
+ const propCtx = { runtime, assetManager: plugin.managers.asset };
await AssemblySymmetryDataProvider.attach(propCtx, structure);
const assemblySymmetryData = AssemblySymmetryDataProvider.get(structure).value;
const symmetryIndex = assemblySymmetryData ? AssemblySymmetry.firstNonC1(assemblySymmetryData) : -1;
diff --git a/src/extensions/rcsb/assembly-symmetry/prop.ts b/src/extensions/rcsb/assembly-symmetry/prop.ts
index e4128ab3d..7bd128644 100644
--- a/src/extensions/rcsb/assembly-symmetry/prop.ts
+++ b/src/extensions/rcsb/assembly-symmetry/prop.ts
@@ -57,21 +57,23 @@ export namespace AssemblySymmetry {
);
}
- export async function fetch(ctx: CustomProperty.Context, structure: Structure, props: AssemblySymmetryDataProps): Promise<AssemblySymmetryDataValue> {
- if (!isApplicable(structure)) return [];
+ export async function fetch(ctx: CustomProperty.Context, structure: Structure, props: AssemblySymmetryDataProps): Promise<CustomProperty.Data<AssemblySymmetryDataValue>> {
+ if (!isApplicable(structure)) return { value: [] };
- const client = new GraphQLClient(props.serverUrl, ctx.fetch);
+ const client = new GraphQLClient(props.serverUrl, ctx.assetManager);
const variables: AssemblySymmetryQueryVariables = {
assembly_id: structure.units[0].conformation.operator.assembly?.id || 'deposited',
entry_id: structure.units[0].model.entryId
};
- const result = await client.request<AssemblySymmetryQuery>(ctx.runtime, query, variables);
+ const result = await client.request(ctx.runtime, query, variables);
+ let value: AssemblySymmetryDataValue = [];
- if (!result.assembly?.rcsb_struct_symmetry) {
+ if (!result.data.assembly?.rcsb_struct_symmetry) {
console.error('expected `rcsb_struct_symmetry` field');
- return [];
+ } else {
+ value = result.data.assembly.rcsb_struct_symmetry as AssemblySymmetryDataValue;
}
- return result.assembly.rcsb_struct_symmetry as AssemblySymmetryDataValue;
+ return { value, assets: [result] };
}
/** Returns the index of the first non C1 symmetry or -1 */
@@ -194,6 +196,6 @@ export const AssemblySymmetryProvider: CustomStructureProperty.Provider<Assembly
const assemblySymmetryData = AssemblySymmetryDataProvider.get(data).value;
const assemblySymmetry = assemblySymmetryData?.[p.symmetryIndex];
if (!assemblySymmetry) new Error(`No assembly symmetry found for index ${p.symmetryIndex}`);
- return assemblySymmetry;
+ return { value: assemblySymmetry };
}
});
\ No newline at end of file
diff --git a/src/extensions/rcsb/validation-report/behavior.ts b/src/extensions/rcsb/validation-report/behavior.ts
index fed94bf7b..00b9d38fc 100644
--- a/src/extensions/rcsb/validation-report/behavior.ts
+++ b/src/extensions/rcsb/validation-report/behavior.ts
@@ -314,7 +314,7 @@ export const ValidationReportGeometryQualityPreset = StructureRepresentationPres
if (!structureCell || !model) return {};
await plugin.runTask(Task.create('Validation Report', async runtime => {
- await ValidationReportProvider.attach({ fetch: plugin.fetch, runtime }, model);
+ await ValidationReportProvider.attach({ runtime, assetManager: plugin.managers.asset }, model);
}));
const colorTheme = GeometryQualityColorThemeProvider.name as any;
@@ -350,7 +350,7 @@ export const ValidationReportDensityFitPreset = StructureRepresentationPresetPro
if (!structureCell || !model) return {};
await plugin.runTask(Task.create('Validation Report', async runtime => {
- await ValidationReportProvider.attach({ fetch: plugin.fetch, runtime }, model);
+ await ValidationReportProvider.attach({ runtime, assetManager: plugin.managers.asset }, model);
}));
const colorTheme = DensityFitColorThemeProvider.name as any;
@@ -374,7 +374,7 @@ export const ValidationReportRandomCoilIndexPreset = StructureRepresentationPres
if (!structureCell || !model) return {};
await plugin.runTask(Task.create('Validation Report', async runtime => {
- await ValidationReportProvider.attach({ fetch: plugin.fetch, runtime }, model);
+ await ValidationReportProvider.attach({ runtime, assetManager: plugin.managers.asset }, model);
}));
const colorTheme = RandomCoilIndexColorThemeProvider.name as any;
diff --git a/src/extensions/rcsb/validation-report/prop.ts b/src/extensions/rcsb/validation-report/prop.ts
index 7e4fa8cfe..355da3089 100644
--- a/src/extensions/rcsb/validation-report/prop.ts
+++ b/src/extensions/rcsb/validation-report/prop.ts
@@ -10,7 +10,6 @@ import { CustomProperty } from '../../../mol-model-props/common/custom-property'
import { CustomModelProperty } from '../../../mol-model-props/common/custom-model-property';
import { Model, ElementIndex, ResidueIndex } from '../../../mol-model/structure/model';
import { IntAdjacencyGraph } from '../../../mol-math/graph';
-import { readFromFile } from '../../../mol-util/data-source';
import { CustomStructureProperty } from '../../../mol-model-props/common/custom-structure-property';
import { InterUnitGraph } from '../../../mol-math/graph/inter-unit-graph';
import { UnitIndex } from '../../../mol-model/structure/structure/element/element';
@@ -22,6 +21,7 @@ import { MmcifFormat } from '../../../mol-model-formats/structure/mmcif';
import { QuerySymbolRuntime } from '../../../mol-script/runtime/query/compiler';
import { CustomPropSymbol } from '../../../mol-script/language/symbol';
import Type from '../../../mol-script/language/type';
+import { Asset } from '../../../mol-util/assets';
export { ValidationReport };
@@ -104,20 +104,19 @@ namespace ValidationReport {
return parseValidationReportXml(xml, model);
}
- export async function fetch(ctx: CustomProperty.Context, model: Model, props: ServerSourceProps): Promise<ValidationReport> {
- const url = getEntryUrl(model.entryId, props.baseUrl);
- const xml = await ctx.fetch({ url, type: 'xml' }).runInContext(ctx.runtime);
- return fromXml(xml, model);
+ export async function fetch(ctx: CustomProperty.Context, model: Model, props: ServerSourceProps): Promise<CustomProperty.Data<ValidationReport>> {
+ const url = Asset.getUrlAsset(ctx.assetManager, getEntryUrl(model.entryId, props.baseUrl));
+ const xml = await ctx.assetManager.resolve(url, 'xml').runInContext(ctx.runtime);
+ return { value: fromXml(xml.data, model), assets: [xml] };
}
- export async function open(ctx: CustomProperty.Context, model: Model, props: FileSourceProps): Promise<ValidationReport> {
- // TODO: this should use the asset manager and release the file "somehow"
- if (!(props.input?.file instanceof File)) throw new Error('No file given');
- const xml = await readFromFile(props.input.file, 'xml').runInContext(ctx.runtime);
- return fromXml(xml, model);
+ export async function open(ctx: CustomProperty.Context, model: Model, props: FileSourceProps): Promise<CustomProperty.Data<ValidationReport>> {
+ if (props.input === null) throw new Error('No file given');
+ const xml = await ctx.assetManager.resolve(props.input, 'xml').runInContext(ctx.runtime);
+ return { value: fromXml(xml.data, model), assets: [xml] };
}
- export async function obtain(ctx: CustomProperty.Context, model: Model, props: ValidationReportProps): Promise<ValidationReport> {
+ export async function obtain(ctx: CustomProperty.Context, model: Model, props: ValidationReportProps): Promise<CustomProperty.Data<ValidationReport>> {
switch(props.source.name) {
case 'file': return open(ctx, model, props.source.params);
case 'server': return fetch(ctx, model, props.source.params);
@@ -319,7 +318,9 @@ export const ClashesProvider: CustomStructureProperty.Provider<{}, Clashes> = Cu
obtain: async (ctx: CustomProperty.Context, data: Structure) => {
await ValidationReportProvider.attach(ctx, data.models[0]);
const validationReport = ValidationReportProvider.get(data.models[0]).value!;
- return createClashes(data, validationReport.clashes);
+ return {
+ value: createClashes(data, validationReport.clashes)
+ };
}
});
diff --git a/src/mol-model-props/common/custom-element-property.ts b/src/mol-model-props/common/custom-element-property.ts
index 74d9da21c..a54b47798 100644
--- a/src/mol-model-props/common/custom-element-property.ts
+++ b/src/mol-model-props/common/custom-element-property.ts
@@ -27,11 +27,12 @@ interface CustomElementProperty<T> {
namespace CustomElementProperty {
export type Value<T> = Map<ElementIndex, T>
+ export type Data<T> = CustomProperty.Data<Value<T>>
export interface Builder<T> {
label: string
name: string
- getData(model: Model, ctx?: CustomProperty.Context): Value<T> | Promise<Value<T>>
+ getData(model: Model, ctx?: CustomProperty.Context): Data<T> | Promise<Data<T>>
coloring?: {
getColor: (p: T) => Color
defaultColor: Color
diff --git a/src/mol-model-props/common/custom-model-property.ts b/src/mol-model-props/common/custom-model-property.ts
index eea8c387f..2e8f14f4c 100644
--- a/src/mol-model-props/common/custom-model-property.ts
+++ b/src/mol-model-props/common/custom-model-property.ts
@@ -20,7 +20,7 @@ namespace CustomModelProperty {
readonly defaultParams: Params
readonly getParams: (data: Model) => Params
readonly isApplicable: (data: Model) => boolean
- readonly obtain: (ctx: CustomProperty.Context, data: Model, props: PD.Values<Params>) => Promise<Value>
+ readonly obtain: (ctx: CustomProperty.Context, data: Model, props: PD.Values<Params>) => Promise<CustomProperty.Data<Value>>
readonly type: 'static' | 'dynamic'
}
@@ -56,8 +56,9 @@ namespace CustomModelProperty {
const property = get(data);
const p = PD.merge(builder.defaultParams, property.props, props);
if (property.data.value && PD.areEqual(builder.defaultParams, property.props, p)) return;
- const value = await builder.obtain(ctx, data, p);
+ const { value, assets } = await builder.obtain(ctx, data, p);
data.customProperties.add(builder.descriptor);
+ data.customProperties.assets(builder.descriptor, assets);
set(data, p, value);
},
ref: (data: Model, add: boolean) => data.customProperties.reference(builder.descriptor, add),
@@ -68,6 +69,8 @@ namespace CustomModelProperty {
if (!PD.areEqual(builder.defaultParams, property.props, p)) {
// this invalidates property.value
set(data, p, undefined);
+ // dispose of assets
+ data.customProperties.assets(builder.descriptor);
}
},
props: (data: Model) => get(data).props,
diff --git a/src/mol-model-props/common/custom-property.ts b/src/mol-model-props/common/custom-property.ts
index 80e40837d..5aafd392f 100644
--- a/src/mol-model-props/common/custom-property.ts
+++ b/src/mol-model-props/common/custom-property.ts
@@ -9,17 +9,18 @@ import { CustomPropertyDescriptor } from '../../mol-model/structure';
import { ParamDefinition as PD } from '../../mol-util/param-definition';
import { ValueBox } from '../../mol-util';
import { OrderedMap } from 'immutable';
-
-type AjaxTask = import('../../mol-util/data-source').AjaxTask
+import { AssetManager, Asset } from '../../mol-util/assets';
export { CustomProperty };
namespace CustomProperty {
export interface Context {
runtime: RuntimeContext
- fetch: AjaxTask
+ assetManager: AssetManager
}
+ export type Data<V> = { value: V, assets?: Asset.Wrapper[] }
+
export interface Container<P, V> {
readonly props: P
readonly data: ValueBox<V | undefined>
diff --git a/src/mol-model-props/common/custom-structure-property.ts b/src/mol-model-props/common/custom-structure-property.ts
index 8a5adb84b..fefa5f174 100644
--- a/src/mol-model-props/common/custom-structure-property.ts
+++ b/src/mol-model-props/common/custom-structure-property.ts
@@ -20,7 +20,7 @@ namespace CustomStructureProperty {
readonly defaultParams: Params
readonly getParams: (data: Structure) => Params
readonly isApplicable: (data: Structure) => boolean
- readonly obtain: (ctx: CustomProperty.Context, data: Structure, props: PD.Values<Params>) => Promise<Value>
+ readonly obtain: (ctx: CustomProperty.Context, data: Structure, props: PD.Values<Params>) => Promise<CustomProperty.Data<Value>>
readonly type: 'root' | 'local'
}
@@ -58,8 +58,9 @@ namespace CustomStructureProperty {
const property = get(data);
const p = PD.merge(builder.defaultParams, rootProps, props);
if (property.data.value && PD.areEqual(builder.defaultParams, property.props, p)) return;
- const value = await builder.obtain(ctx, data, p);
+ const { value, assets } = await builder.obtain(ctx, data, p);
data.customPropertyDescriptors.add(builder.descriptor);
+ data.customPropertyDescriptors.assets(builder.descriptor, assets);
set(data, p, value);
},
ref: (data: Structure, add: boolean) => data.customPropertyDescriptors.reference(builder.descriptor, add),
@@ -71,6 +72,8 @@ namespace CustomStructureProperty {
if (!PD.areEqual(builder.defaultParams, property.props, p)) {
// this invalidates property.value
set(data, p, value);
+ // dispose of assets
+ data.customPropertyDescriptors.assets(builder.descriptor);
}
},
props: (data: Structure) => get(data).props,
diff --git a/src/mol-model-props/computed/accessible-surface-area.ts b/src/mol-model-props/computed/accessible-surface-area.ts
index f691387ea..a12020eb6 100644
--- a/src/mol-model-props/computed/accessible-surface-area.ts
+++ b/src/mol-model-props/computed/accessible-surface-area.ts
@@ -54,6 +54,6 @@ export const AccessibleSurfaceAreaProvider: CustomStructureProperty.Provider<Acc
isApplicable: (data: Structure) => true,
obtain: async (ctx: CustomProperty.Context, data: Structure, props: Partial<AccessibleSurfaceAreaProps>) => {
const p = { ...PD.getDefaultValues(AccessibleSurfaceAreaParams), ...props };
- return await AccessibleSurfaceArea.compute(data, p).runInContext(ctx.runtime);
+ return { value: await AccessibleSurfaceArea.compute(data, p).runInContext(ctx.runtime) };
}
});
\ No newline at end of file
diff --git a/src/mol-model-props/computed/interactions.ts b/src/mol-model-props/computed/interactions.ts
index 88d67d898..bba29c192 100644
--- a/src/mol-model-props/computed/interactions.ts
+++ b/src/mol-model-props/computed/interactions.ts
@@ -30,6 +30,6 @@ export const InteractionsProvider: CustomStructureProperty.Provider<Interactions
isApplicable: (data: Structure) => true,
obtain: async (ctx: CustomProperty.Context, data: Structure, props: Partial<InteractionsProps>) => {
const p = { ...PD.getDefaultValues(InteractionsParams), ...props };
- return await computeInteractions(ctx, data, p);
+ return { value: await computeInteractions(ctx, data, p) };
}
});
\ No newline at end of file
diff --git a/src/mol-model-props/computed/secondary-structure.ts b/src/mol-model-props/computed/secondary-structure.ts
index 4ca57c396..383703dfb 100644
--- a/src/mol-model-props/computed/secondary-structure.ts
+++ b/src/mol-model-props/computed/secondary-structure.ts
@@ -57,8 +57,8 @@ export const SecondaryStructureProvider: CustomStructureProperty.Provider<Second
obtain: async (ctx: CustomProperty.Context, data: Structure, props: Partial<SecondaryStructureProps>) => {
const p = { ...PD.getDefaultValues(SecondaryStructureParams), ...props };
switch (p.type.name) {
- case 'dssp': return await computeDssp(data, p.type.params);
- case 'model': return await computeModel(data);
+ case 'dssp': return { value: await computeDssp(data, p.type.params) };
+ case 'model': return { value: await computeModel(data) };
}
}
});
diff --git a/src/mol-model-props/computed/valence-model.ts b/src/mol-model-props/computed/valence-model.ts
index d2994f593..8fa1d24ba 100644
--- a/src/mol-model-props/computed/valence-model.ts
+++ b/src/mol-model-props/computed/valence-model.ts
@@ -30,6 +30,6 @@ export const ValenceModelProvider: CustomStructureProperty.Provider<ValenceModel
isApplicable: (data: Structure) => true,
obtain: async (ctx: CustomProperty.Context, data: Structure, props: Partial<ValenceModelProps>) => {
const p = { ...PD.getDefaultValues(ValenceModelParams), ...props };
- return await calcValenceModel(ctx.runtime, data, p);
+ return { value: await calcValenceModel(ctx.runtime, data, p) };
}
});
\ No newline at end of file
diff --git a/src/mol-model-props/integrative/cross-link-restraint/property.ts b/src/mol-model-props/integrative/cross-link-restraint/property.ts
index d68d94af5..8b7f07ee4 100644
--- a/src/mol-model-props/integrative/cross-link-restraint/property.ts
+++ b/src/mol-model-props/integrative/cross-link-restraint/property.ts
@@ -29,7 +29,7 @@ export const CrossLinkRestraintProvider: CustomStructureProperty.Provider<{}, Cr
getParams: (data: Structure) => ({}),
isApplicable: (data: Structure) => data.models.some(m => !!ModelCrossLinkRestraint.Provider.get(m)),
obtain: async (ctx: CustomProperty.Context, data: Structure, props: Partial<{}>) => {
- return extractCrossLinkRestraints(data);
+ return { value: extractCrossLinkRestraints(data) };
}
});
diff --git a/src/mol-model/structure/common/custom-property.ts b/src/mol-model/structure/common/custom-property.ts
index 8f69a41d8..3c6723d76 100644
--- a/src/mol-model/structure/common/custom-property.ts
+++ b/src/mol-model/structure/common/custom-property.ts
@@ -1,13 +1,15 @@
/**
- * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2020 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 { CifWriter } from '../../../mol-io/writer/cif';
import { CifExportContext } from '../export/mmcif';
import { QuerySymbolRuntime } from '../../../mol-script/runtime/query/compiler';
import { UUID } from '../../../mol-util';
+import { Asset } from '../../../mol-util/assets';
export { CustomPropertyDescriptor, CustomProperties };
@@ -42,6 +44,7 @@ class CustomProperties {
private _list: CustomPropertyDescriptor[] = [];
private _set = new Set<CustomPropertyDescriptor>();
private _refs = new Map<CustomPropertyDescriptor, number>();
+ private _assets = new Map<CustomPropertyDescriptor, Asset.Wrapper[]>();
get all(): ReadonlyArray<CustomPropertyDescriptor> {
return this._list;
@@ -55,11 +58,7 @@ class CustomProperties {
}
reference(desc: CustomPropertyDescriptor<any>, add: boolean) {
- let refs = this._refs.get(desc);
- if (refs === void 0) {
- refs = 0;
- this._refs.set(desc, refs);
- }
+ let refs = this._refs.get(desc) || 0;
refs += add ? 1 : -1;
this._refs.set(desc, Math.max(refs, 0));
}
@@ -71,4 +70,21 @@ class CustomProperties {
has(desc: CustomPropertyDescriptor<any>): boolean {
return this._set.has(desc);
}
+
+ /** Sets assets for a prop, disposes of existing assets for that prop */
+ assets(desc: CustomPropertyDescriptor<any>, assets?: Asset.Wrapper[]) {
+ const prevAssets = this._assets.get(desc);
+ if (prevAssets) {
+ for (const a of prevAssets) a.dispose();
+ }
+ if (assets) this._assets.set(desc, assets);
+ else this._assets.delete(desc);
+ }
+
+ /** Disposes of all assets of all props */
+ dispose() {
+ this._assets.forEach(assets => {
+ for (const a of assets) a.dispose();
+ });
+ }
}
\ No newline at end of file
diff --git a/src/mol-plugin-state/builder/structure.ts b/src/mol-plugin-state/builder/structure.ts
index 322d7ea8f..ba172758e 100644
--- a/src/mol-plugin-state/builder/structure.ts
+++ b/src/mol-plugin-state/builder/structure.ts
@@ -173,7 +173,7 @@ export class StructureBuilder {
};
if (selection.ensureCustomProperties) {
- await selection.ensureCustomProperties({ fetch: this.plugin.fetch, runtime: taskCtx }, structureData);
+ await selection.ensureCustomProperties({ runtime: taskCtx, assetManager: this.plugin.managers.asset }, structureData);
}
return this.tryCreateComponent(structure, transformParams, key, tags);
diff --git a/src/mol-plugin-state/helpers/structure-selection-query.ts b/src/mol-plugin-state/helpers/structure-selection-query.ts
index a53303356..d374b56b8 100644
--- a/src/mol-plugin-state/helpers/structure-selection-query.ts
+++ b/src/mol-plugin-state/helpers/structure-selection-query.ts
@@ -73,7 +73,7 @@ function StructureSelectionQuery(label: string, expression: Expression, props: S
const current = plugin.managers.structure.selection.getStructure(structure);
const currentSelection = current ? StructureSelection.Singletons(structure, current) : StructureSelection.Empty(structure);
if (props.ensureCustomProperties) {
- await props.ensureCustomProperties({ fetch: plugin.fetch, runtime }, structure);
+ await props.ensureCustomProperties({ runtime, assetManager: plugin.managers.asset }, structure);
}
if (!_query) _query = compile<StructureSelection>(expression);
return _query(new QueryContext(structure, { currentSelection }));
diff --git a/src/mol-plugin-state/transforms/model.ts b/src/mol-plugin-state/transforms/model.ts
index 4738ae9b3..6ea005e21 100644
--- a/src/mol-plugin-state/transforms/model.ts
+++ b/src/mol-plugin-state/transforms/model.ts
@@ -304,6 +304,9 @@ const ModelFromTrajectory = PluginStateTransform.BuiltIn({
const label = `Model ${model.modelNum}`;
const description = a.data.length === 1 ? undefined : `of ${a.data.length}`;
return new SO.Molecule.Model(model, { label, description });
+ },
+ dispose({ b }) {
+ b?.data.customProperties.dispose();
}
});
@@ -320,6 +323,9 @@ const StructureFromTrajectory = PluginStateTransform.BuiltIn({
const props = { label: 'Ensemble', description: Structure.elementDescription(s) };
return new SO.Molecule.Structure(s, props);
});
+ },
+ dispose({ b }) {
+ b?.data.customPropertyDescriptors.dispose();
}
});
@@ -343,6 +349,9 @@ const StructureFromModel = PluginStateTransform.BuiltIn({
if (!b.data.models.includes(a.data)) return StateTransformer.UpdateResult.Recreate;
if (!deepEqual(oldParams, newParams)) return StateTransformer.UpdateResult.Recreate;
return StateTransformer.UpdateResult.Unchanged;
+ },
+ dispose({ b }) {
+ b?.data.customPropertyDescriptors.dispose();
}
});
@@ -439,6 +448,9 @@ const TransformStructureConformation = PluginStateTransform.BuiltIn({
const s = Structure.transform(a.data, transform);
return new SO.Molecule.Structure(s, { label: a.label, description: `${a.description} [Transformed]` });
+ },
+ dispose({ b }) {
+ b?.data.customPropertyDescriptors.dispose();
}
// interpolate(src, tar, t) {
// // TODO: optimize
@@ -489,6 +501,9 @@ const StructureSelectionFromExpression = PluginStateTransform.BuiltIn({
StructureQueryHelper.updateStructureObject(b, selection, newParams.label);
return StateTransformer.UpdateResult.Updated;
+ },
+ dispose({ b }) {
+ b?.data.customPropertyDescriptors.dispose();
}
});
@@ -650,6 +665,9 @@ const StructureSelectionFromScript = PluginStateTransform.BuiltIn({
const selection = StructureQueryHelper.updateStructure(entry, a.data);
StructureQueryHelper.updateStructureObject(b, selection, newParams.label);
return StateTransformer.UpdateResult.Updated;
+ },
+ dispose({ b }) {
+ b?.data.customPropertyDescriptors.dispose();
}
});
@@ -698,6 +716,9 @@ const StructureSelectionFromBundle = PluginStateTransform.BuiltIn({
b.description = Structure.elementDescription(s);
b.data = s;
return StateTransformer.UpdateResult.Updated;
+ },
+ dispose({ b }) {
+ b?.data.customPropertyDescriptors.dispose();
}
});
@@ -761,6 +782,9 @@ const StructureComplexElement = PluginStateTransform.BuiltIn({
if (s.elementCount === 0) return StateObject.Null;
return new SO.Molecule.Structure(s, { label, description: Structure.elementDescription(s) });
+ },
+ dispose({ b }) {
+ b?.data.customPropertyDescriptors.dispose();
}
});
@@ -777,6 +801,9 @@ const StructureComponent = PluginStateTransform.BuiltIn({
},
update: ({ a, b, oldParams, newParams, cache }) => {
return updateStructureComponent(a.data, b, oldParams, newParams, cache as any);
+ },
+ dispose({ b }) {
+ b?.data.customPropertyDescriptors.dispose();
}
});
@@ -810,10 +837,13 @@ const CustomModelProperties = PluginStateTransform.BuiltIn({
await attachModelProps(a.data, ctx, taskCtx, newParams);
return StateTransformer.UpdateResult.Updated;
});
+ },
+ dispose({ b }) {
+ b?.data.customProperties.dispose();
}
});
async function attachModelProps(model: Model, ctx: PluginContext, taskCtx: RuntimeContext, params: ReturnType<CustomModelProperties['createDefaultParams']>) {
- const propertyCtx = { runtime: taskCtx, fetch: ctx.fetch };
+ const propertyCtx = { runtime: taskCtx, assetManager: ctx.managers.asset };
const { autoAttach, properties } = params;
for (const name of Object.keys(properties)) {
const property = ctx.customModelProperties.get(name);
@@ -860,10 +890,13 @@ const CustomStructureProperties = PluginStateTransform.BuiltIn({
await attachStructureProps(a.data.root, ctx, taskCtx, newParams);
return StateTransformer.UpdateResult.Updated;
});
+ },
+ dispose({ b }) {
+ b?.data.customPropertyDescriptors.dispose();
}
});
async function attachStructureProps(structure: Structure, ctx: PluginContext, taskCtx: RuntimeContext, params: ReturnType<CustomStructureProperties['createDefaultParams']>) {
- const propertyCtx = { runtime: taskCtx, fetch: ctx.fetch };
+ const propertyCtx = { runtime: taskCtx, assetManager: ctx.managers.asset };
const { autoAttach, properties } = params;
for (const name of Object.keys(properties)) {
const property = ctx.customStructureProperties.get(name);
diff --git a/src/mol-plugin-state/transforms/representation.ts b/src/mol-plugin-state/transforms/representation.ts
index fb49d9b30..0aee3349c 100644
--- a/src/mol-plugin-state/transforms/representation.ts
+++ b/src/mol-plugin-state/transforms/representation.ts
@@ -120,7 +120,7 @@ const StructureRepresentation3D = PluginStateTransform.BuiltIn({
},
apply({ a, params, cache }, plugin: PluginContext) {
return Task.create('Structure Representation', async ctx => {
- const propertyCtx = { runtime: ctx, fetch: plugin.fetch };
+ const propertyCtx = { runtime: ctx, assetManager: plugin.managers.asset };
const provider = plugin.representation.structure.registry.get(params.type.name);
if (provider.ensureCustomProperties) await provider.ensureCustomProperties.attach(propertyCtx, a.data);
const props = params.type.params || {};
@@ -149,7 +149,7 @@ const StructureRepresentation3D = PluginStateTransform.BuiltIn({
Theme.releaseDependencies(plugin.representation.structure.themes, { structure: a.data }, oldParams);
const provider = plugin.representation.structure.registry.get(newParams.type.name);
- const propertyCtx = { runtime: ctx, fetch: plugin.fetch };
+ const propertyCtx = { runtime: ctx, assetManager: plugin.managers.asset };
if (provider.ensureCustomProperties) await provider.ensureCustomProperties.attach(propertyCtx, a.data);
const props = { ...b.data.repr.props, ...newParams.type.params };
await Theme.ensureDependencies(propertyCtx, plugin.representation.structure.themes, { structure: a.data }, newParams);
@@ -524,7 +524,7 @@ const VolumeRepresentation3D = PluginStateTransform.BuiltIn({
},
apply({ a, params }, plugin: PluginContext) {
return Task.create('Volume Representation', async ctx => {
- const propertyCtx = { runtime: ctx, fetch: plugin.fetch };
+ const propertyCtx = { runtime: ctx, assetManager: plugin.managers.asset };
const provider = plugin.representation.volume.registry.get(params.type.name);
if (provider.ensureCustomProperties) await provider.ensureCustomProperties.attach(propertyCtx, a.data);
const props = params.type.params || {};
diff --git a/src/mol-util/graphql-client.ts b/src/mol-util/graphql-client.ts
index 9fc1708a2..0e2f5eac7 100644
--- a/src/mol-util/graphql-client.ts
+++ b/src/mol-util/graphql-client.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*
@@ -7,6 +7,7 @@
*/
import { RuntimeContext } from '../mol-task';
+import { AssetManager, Asset } from './assets';
type Variables = { [key: string]: any }
@@ -42,44 +43,33 @@ export class ClientError extends Error {
this.request = request;
// this is needed as Safari doesn't support .captureStackTrace
- /* tslint:disable-next-line */
if (typeof Error.captureStackTrace === 'function') {
Error.captureStackTrace(this, ClientError);
}
}
private static extractMessage (response: GraphQLResponse): string {
- try {
- return response.errors![0].message;
- } catch (e) {
- return `GraphQL Error (Code: ${response.status})`;
- }
+ return response.errors ? response.errors[0].message : `GraphQL Error (Code: ${response.status})`;
}
}
export class GraphQLClient {
- constructor(private url: string, private fetch: import('../mol-util/data-source').AjaxTask) {
- this.url = url;
- }
-
- async request<T extends any>(ctx: RuntimeContext, query: string, variables?: Variables): Promise<T> {
+ constructor(private url: string, private assetManager: AssetManager) { }
- const body = JSON.stringify({
- query,
- variables: variables ? variables : undefined,
- });
+ async request(ctx: RuntimeContext, query: string, variables?: Variables): Promise<Asset.Wrapper<'json'>> {
- const resultStr = await this.fetch({ url: this.url, body }).runInContext(ctx);
- const result = JSON.parse(resultStr);
+ const body = JSON.stringify({ query, variables }, null, 2);
+ const url = Asset.getUrlAsset(this.assetManager, this.url, body);
+ const result = await this.assetManager.resolve(url, 'json').runInContext(ctx);
- if (!result.errors && result.data) {
- return result.data;
+ if (!result.data.errors && result.data.data) {
+ return {
+ data: result.data.data,
+ dispose: result.dispose
+ };
} else {
- const errorResult = typeof result === 'string' ? { error: result } : result;
- throw new ClientError(
- { ...errorResult },
- { query, variables },
- );
+ const errorResult = typeof result.data === 'string' ? { error: result.data } : result.data;
+ throw new ClientError({ ...errorResult }, { query, variables });
}
}
}
\ No newline at end of file
diff --git a/src/tests/browser/render-structure.ts b/src/tests/browser/render-structure.ts
index 4969c910f..e57e5ba87 100644
--- a/src/tests/browser/render-structure.ts
+++ b/src/tests/browser/render-structure.ts
@@ -25,7 +25,7 @@ import { InteractionsRepresentationProvider } from '../../mol-model-props/comput
import { InteractionsProvider } from '../../mol-model-props/computed/interactions';
import { SecondaryStructureProvider } from '../../mol-model-props/computed/secondary-structure';
import { SyncRuntimeContext } from '../../mol-task/execution/synchronous';
-import { ajaxGet } from '../../mol-util/data-source';
+import { AssetManager } from '../../mol-util/assets';
const parent = document.getElementById('app')!;
parent.style.width = '100%';
@@ -117,7 +117,7 @@ function getGaussianSurfaceRepr() {
}
async function init() {
- const ctx = { runtime: SyncRuntimeContext, fetch: ajaxGet };
+ const ctx = { runtime: SyncRuntimeContext, assetManager: new AssetManager() };
const cif = await downloadFromPdb('3pqr');
const models = await getModels(cif);
--
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