diff --git a/src/apps/cif2bcif/converter.ts b/src/apps/cif2bcif/converter.ts
index 1a3a08221bdb79e9808e69dad4651aa141e2cd21..d885b3f62f6359211b63a31382feefbf6fd2a043 100644
--- a/src/apps/cif2bcif/converter.ts
+++ b/src/apps/cif2bcif/converter.ts
@@ -9,11 +9,10 @@ import CIF, { Category } from 'mol-io/reader/cif'
import * as Encoder from 'mol-io/writer/cif'
import * as fs from 'fs'
import classify from './field-classifier'
-import { Run } from 'mol-task'
async function getCIF(path: string) {
const str = fs.readFileSync(path, 'utf8');
- const parsed = await Run(CIF.parseText(str));
+ const parsed = await CIF.parseText(str).run();
if (parsed.isError) {
throw new Error(parsed.toString());
}
diff --git a/src/apps/combine-mmcif/index.ts b/src/apps/combine-mmcif/index.ts
index d107f81132f4110c1c4d01152711ba7f8a9155c5..205c55c11c748d752dd12033405a524fd6102b22 100644
--- a/src/apps/combine-mmcif/index.ts
+++ b/src/apps/combine-mmcif/index.ts
@@ -13,7 +13,7 @@ require('util.promisify').shim();
const readFile = util.promisify(fs.readFile);
const writeFile = util.promisify(fs.writeFile);
-import { Run, Progress } from 'mol-task'
+import { Progress } from 'mol-task'
import { Database, Table, DatabaseCollection } from 'mol-data/db'
import CIF from 'mol-io/reader/cif'
// import { CCD_Schema } from 'mol-io/reader/cif/schema/ccd'
@@ -78,7 +78,7 @@ export async function getBIRD() {
async function parseCif(data: string|Uint8Array) {
const comp = CIF.parse(data);
console.time('parse cif');
- const parsed = await Run(comp, p => console.log(Progress.format(p)), 250);
+ const parsed = await comp.run(p => console.log(Progress.format(p)), 250);
console.timeEnd('parse cif');
if (parsed.isError) throw parsed;
return parsed
diff --git a/src/apps/render-test/state.ts b/src/apps/render-test/state.ts
index 58f3404e7347b1632c2885754c8a57a20b0c865f..656074ce584ddfcb78843a2752810f7e1ff8891a 100644
--- a/src/apps/render-test/state.ts
+++ b/src/apps/render-test/state.ts
@@ -16,11 +16,10 @@ import Viewer from 'mol-view/viewer'
import Spacefill, { SpacefillProps } from 'mol-geo/representation/structure/spacefill'
import Point, { PointProps } from 'mol-geo/representation/structure/point'
-import { Run } from 'mol-task'
import { StructureSymmetry, Structure, Model } from 'mol-model/structure'
// import mcubes from './utils/mcubes'
-import { getModelFromPdbId, getModelFromFile, log, Volume, getVolumeFromEmdId } from './utils'
+import { getModelFromPdbId, getModelFromFile, runTask, Volume, getVolumeFromEmdId } from './utils'
import { StructureRepresentation } from 'mol-geo/representation/structure';
import { Color } from 'mol-util/color';
import Surface, { SurfaceProps } from 'mol-geo/representation/volume/surface';
@@ -110,7 +109,7 @@ export default class State {
let structure: Structure
const assemblies = model.symmetry.assemblies
if (assemblies.length) {
- structure = await Run(StructureSymmetry.buildAssembly(Structure.ofModel(model), assembly || '1'), log, 500)
+ structure = await runTask(StructureSymmetry.buildAssembly(Structure.ofModel(model), assembly || '1'));
} else {
structure = Structure.ofModel(model)
}
@@ -128,11 +127,11 @@ export default class State {
if (!structure) return
this.pointRepr = StructureRepresentation(Point)
- await Run(this.pointRepr.create(structure, this.getPointProps()), log, 500)
+ await runTask(this.pointRepr.create(structure, this.getPointProps()))
viewer.add(this.pointRepr)
this.spacefillRepr = StructureRepresentation(Spacefill)
- await Run(this.spacefillRepr.create(structure, this.getSpacefillProps()), log, 500)
+ await runTask(this.spacefillRepr.create(structure, this.getSpacefillProps()))
viewer.add(this.spacefillRepr)
this.updateVisibility()
@@ -160,13 +159,13 @@ export default class State {
if (this.surfaceRepr) this.viewer.remove(this.surfaceRepr)
this.surfaceRepr = VolumeRepresentation(Surface)
- await Run(this.surfaceRepr.create(v.volume, {
+ await runTask(this.surfaceRepr.create(v.volume, {
isoValue: VolumeIsoValue.relative(v.volume.dataStats, 3.0),
alpha: 0.5,
flatShaded: false,
flipSided: true,
doubleSided: true
- }), log, 500)
+ }))
viewer.add(this.surfaceRepr)
viewer.requestDraw()
@@ -197,8 +196,8 @@ export default class State {
async update () {
if (!this.spacefillRepr) return
- await Run(this.spacefillRepr.update(this.getSpacefillProps()), log, 500)
- await Run(this.pointRepr.update(this.getPointProps()), log, 500)
+ await runTask(this.spacefillRepr.update(this.getSpacefillProps()))
+ await runTask(this.pointRepr.update(this.getPointProps()))
this.viewer.add(this.spacefillRepr)
this.viewer.add(this.pointRepr)
this.viewer.update()
diff --git a/src/apps/render-test/utils/index.ts b/src/apps/render-test/utils/index.ts
index b5eb271c7a63815185263d5e7185934d33b4ed12..db2b732afdeee394a0d026b6ee8010800834f9db 100644
--- a/src/apps/render-test/utils/index.ts
+++ b/src/apps/render-test/utils/index.ts
@@ -5,7 +5,7 @@
*/
import CIF from 'mol-io/reader/cif'
-import { Run, Progress } from 'mol-task'
+import { Progress, Task } from 'mol-task'
import { Model } from 'mol-model/structure'
import { VolumeData, parseDensityServerData } from 'mol-model/volume'
import { DensityServer_Data_Database } from 'mol-io/reader/cif/schema/density-server';
@@ -15,6 +15,10 @@ export function log(progress: Progress) {
console.log(`${p.message} ${(p.current/p.max*100).toFixed(2)}%`)
}
+export function runTask<T>(task: Task<T>) {
+ return task.run(log, 500);
+}
+
export async function downloadCif(url: string, isBinary: boolean) {
const data = await fetch(url);
return parseCif(isBinary ? new Uint8Array(await data.arrayBuffer()) : await data.text());
@@ -22,14 +26,14 @@ export async function downloadCif(url: string, isBinary: boolean) {
export async function parseCif(data: string|Uint8Array) {
const comp = CIF.parse(data)
- const parsed = await Run(comp, log, 500);
+ const parsed = await comp.run(log, 500);
if (parsed.isError) throw parsed;
return parsed.result
}
export async function getModelFromPdbId(pdbid: string) {
const cif = await downloadCif(`https://files.rcsb.org/download/${pdbid}.cif`, false)
- return Run(Model.create({ kind: 'mmCIF', data: CIF.schema.mmCIF(cif.blocks[0]) }))
+ return Model.create({ kind: 'mmCIF', data: CIF.schema.mmCIF(cif.blocks[0]) }).run();
}
const readFileAsText = (file: File) => {
@@ -46,7 +50,7 @@ const readFileAsText = (file: File) => {
export async function getModelFromFile(file: File) {
const cif = await parseCif(await readFileAsText(file))
- return Run(Model.create({ kind: 'mmCIF', data: CIF.schema.mmCIF(cif.blocks[0]) }))
+ return Model.create({ kind: 'mmCIF', data: CIF.schema.mmCIF(cif.blocks[0]) }).run();
}
export type Volume = { source: DensityServer_Data_Database, volume: VolumeData }
@@ -54,5 +58,5 @@ export type Volume = { source: DensityServer_Data_Database, volume: VolumeData }
export async function getVolumeFromEmdId(emdid: string): Promise<Volume> {
const cif = await downloadCif(`https://webchem.ncbr.muni.cz/DensityServer/em/emd-${emdid}/cell?detail=4`, true)
const data = CIF.schema.densityServer(cif.blocks[1])
- return { source: data, volume: await Run(parseDensityServerData(data)) }
+ return { source: data, volume: await parseDensityServerData(data).run() }
}
\ No newline at end of file
diff --git a/src/apps/render-test/utils/mcubes.ts b/src/apps/render-test/utils/mcubes.ts
index 92905c7b6f5d111486ee7a1bd6fab7b95a5cd5e6..f74859d8b157afd0675a51a4c8deb2c0a8571b16 100644
--- a/src/apps/render-test/utils/mcubes.ts
+++ b/src/apps/render-test/utils/mcubes.ts
@@ -4,7 +4,6 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { Run } from 'mol-task'
import { computeMarchingCubes } from 'mol-geo/util/marching-cubes/algorithm'
import { Mesh } from 'mol-geo/shape/mesh'
import { Tensor, Mat4, Vec3 } from 'mol-math/linear-algebra'
@@ -38,11 +37,11 @@ export default async function computeSurface(f: (x: number, y: number, z: number
const min = Vec3.create(-1.1, -1.1, -1.1), max = Vec3.create(1.1, 1.1, 1.1);
fillField(field, f, min, max);
- const surface = await Run(computeMarchingCubes({
+ const surface = await computeMarchingCubes({
scalarField: field,
isoLevel: 0,
oldSurface: data ? data.surface : void 0
- }));
+ }).run();
const translation = Mat4.fromTranslation(Mat4.zero(), min);
const grid = Vec3.zero();
diff --git a/src/apps/schema-generator/schema-from-mmcif-dic.ts b/src/apps/schema-generator/schema-from-mmcif-dic.ts
index a6fc5fed2b9cc9a0a022055f77ded38923d5e82e..c9149a2c8f29a56d3f4468db23dc5a3dbe7b59a0 100644
--- a/src/apps/schema-generator/schema-from-mmcif-dic.ts
+++ b/src/apps/schema-generator/schema-from-mmcif-dic.ts
@@ -14,15 +14,14 @@ import CIF, { Frame } from 'mol-io/reader/cif'
import { generateSchema } from './util/cif-dic'
import { generate } from './util/generate'
import { Filter } from './util/json-schema'
-import { Run } from 'mol-task'
async function runGenerateSchema(name: string, fieldNamesPath?: string, typescript = false, out?: string) {
await ensureMmcifDicAvailable()
- const mmcifDic = await Run(CIF.parseText(fs.readFileSync(MMCIF_DIC_PATH, 'utf8')));
+ const mmcifDic = await CIF.parseText(fs.readFileSync(MMCIF_DIC_PATH, 'utf8')).run();
if (mmcifDic.isError) throw mmcifDic
await ensureIhmDicAvailable()
- const ihmDic = await Run(CIF.parseText(fs.readFileSync(IHM_DIC_PATH, 'utf8')));
+ const ihmDic = await CIF.parseText(fs.readFileSync(IHM_DIC_PATH, 'utf8')).run();
if (ihmDic.isError) throw ihmDic
const mmcifDicVersion = CIF.schema.dic(mmcifDic.result.blocks[0]).dictionary.version.value(0)
@@ -44,7 +43,7 @@ async function runGenerateSchema(name: string, fieldNamesPath?: string, typescri
async function getFieldNamesFilter(fieldNamesPath: string): Promise<Filter> {
const fieldNamesStr = fs.readFileSync(fieldNamesPath, 'utf8')
- const parsed = await Run(Csv(fieldNamesStr, { noColumnNames: true }));
+ const parsed = await Csv(fieldNamesStr, { noColumnNames: true }).run();
if (parsed.isError) throw parser.error
const csvFile = parsed.result;
diff --git a/src/apps/structure-info/helpers.ts b/src/apps/structure-info/helpers.ts
index 94095a99055759cdbab8d9b2c677345632520848..f4a86d9a67ac824988e4fbe0fffd13ced8b2aac5 100644
--- a/src/apps/structure-info/helpers.ts
+++ b/src/apps/structure-info/helpers.ts
@@ -10,7 +10,7 @@ import fetch from 'node-fetch'
require('util.promisify').shim();
import CIF from 'mol-io/reader/cif'
-import { Run, Progress } from 'mol-task'
+import { Progress } from 'mol-task'
const readFileAsync = util.promisify(fs.readFile);
@@ -27,7 +27,7 @@ async function readFile(path: string) {
async function parseCif(data: string|Uint8Array) {
const comp = CIF.parse(data);
- const parsed = await Run(comp, p => console.log(Progress.format(p)), 250);
+ const parsed = await comp.run(p => console.log(Progress.format(p)), 250);
if (parsed.isError) throw parsed;
return parsed.result;
}
diff --git a/src/apps/structure-info/model.ts b/src/apps/structure-info/model.ts
index 3f7957df85e57f94552e10188669cb6059f5d30d..ad61b5d13df2923b83ad95302ea505b80051542d 100644
--- a/src/apps/structure-info/model.ts
+++ b/src/apps/structure-info/model.ts
@@ -16,7 +16,6 @@ import { OrderedSet } from 'mol-data/int';
import { Table } from 'mol-data/db';
import { mmCIF_Database } from 'mol-io/reader/cif/schema/mmcif';
import { openCif, downloadCif } from './helpers';
-import { Run } from 'mol-task';
async function downloadFromPdb(pdb: string) {
@@ -118,7 +117,7 @@ export function printIHMModels(model: Model) {
}
async function run(mmcif: mmCIF_Database) {
- const models = await Run(Model.create({ kind: 'mmCIF', data: mmcif }));
+ const models = await Model.create({ kind: 'mmCIF', data: mmcif }).run();
const structure = Structure.ofModel(models[0]);
printSequence(models[0]);
printIHMModels(models[0]);
diff --git a/src/apps/structure-info/volume.ts b/src/apps/structure-info/volume.ts
index 325e268dd7779e311408fe7c72280b6a7acac48c..00dd391711eba424686f5825594056426ac04380 100644
--- a/src/apps/structure-info/volume.ts
+++ b/src/apps/structure-info/volume.ts
@@ -12,7 +12,6 @@ import { VolumeData, parseDensityServerData, VolumeIsoValue } from 'mol-model/vo
import { downloadCif } from './helpers'
import CIF from 'mol-io/reader/cif'
import { DensityServer_Data_Database } from 'mol-io/reader/cif/schema/density-server';
-import { Run } from 'mol-task';
import { Table } from 'mol-data/db';
import { computeVolumeSurface } from 'mol-geo/representation/volume/surface';
import { StringBuilder } from 'mol-util';
@@ -25,7 +24,7 @@ type Volume = { source: DensityServer_Data_Database, volume: VolumeData }
async function getVolume(url: string): Promise<Volume> {
const cif = await downloadCif(url, true);
const data = CIF.schema.densityServer(cif.blocks[1]);
- return { source: data, volume: await Run(parseDensityServerData(data)) };
+ return { source: data, volume: await parseDensityServerData(data).run() };
}
function print(data: Volume) {
@@ -38,7 +37,7 @@ function print(data: Volume) {
}
async function doMesh(data: Volume, filename: string) {
- const mesh = await Run(computeVolumeSurface(data.volume, VolumeIsoValue.relative(data.volume.dataStats, 1.5)));
+ const mesh = await computeVolumeSurface(data.volume, VolumeIsoValue.relative(data.volume.dataStats, 1.5)).run();
console.log({ vc: mesh.vertexCount, tc: mesh.triangleCount });
// Export the mesh in OBJ format.
diff --git a/src/examples/task.ts b/src/examples/task.ts
index 41025f042c48eb1252f14483ba94e1f10c771470..64143cfb7da152845fa702b6854eb0c5f677c018 100644
--- a/src/examples/task.ts
+++ b/src/examples/task.ts
@@ -4,11 +4,11 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { Task, Run, Progress, Scheduler, now, MultistepTask, chunkedSubtask } from 'mol-task'
+import { Task, Progress, Scheduler, now, MultistepTask, chunkedSubtask } from 'mol-task'
export async function test1() {
const t = Task.create('test', async () => 1);
- const r = await Run(t);
+ const r = await t.run();
console.log(r);
}
@@ -53,9 +53,9 @@ export function testTree() {
if (ctx.shouldUpdate) await ctx.update('hi! 3');
// ctx.update('Running children...', true);
- const c1 = ctx.runChild(createTask(250, 1));
- const c2 = ctx.runChild(createTask(500, 2));
- const c3 = ctx.runChild(createTask(750, 3));
+ const c1 = createTask(250, 1).runAsChild(ctx);
+ const c2 = createTask(500, 2).runAsChild(ctx);
+ const c3 = createTask(750, 3).runAsChild(ctx);
//await ctx.runChild(abortAfter(350));
@@ -87,8 +87,8 @@ export const ms = MultistepTask('ms-task', ['step 1', 'step 2', 'step 3'], async
const s = await chunkedSubtask(ctx, 25, { i: 0, current: 0, total: 125 }, processChunk, (ctx, s, p) => ctx.update('chunk test ' + p))
return s.i;
});
-
- await ctx.runChild(child);
+
+ await child.runAsChild(ctx);
await Scheduler.delay(250);
await step(1);
await chunkedSubtask(ctx, 25, { i: 0, current: 0, total: 80 }, processChunk, (ctx, s, p) => ctx.update('chunk test ' + p))
@@ -114,7 +114,7 @@ async function test() {
//const r = await Run(testTree(), abortingObserver, 250);
//console.log(r);
- const m = await Run(ms({ i: 10 }), logP);
+ const m = await ms({ i: 10 }).run(logP);
console.log(m);
} catch (e) {
console.error(e);
diff --git a/src/mol-geo/representation/structure/index.ts b/src/mol-geo/representation/structure/index.ts
index 774ea8b077f18059c09e50f7563221a9392d4540..363e1771ed7ff49ddb907967511e6123f4769410 100644
--- a/src/mol-geo/representation/structure/index.ts
+++ b/src/mol-geo/representation/structure/index.ts
@@ -42,7 +42,7 @@ export function StructureRepresentation<P>(reprCtor: () => UnitsRepresentation<P
const group = groups[i];
const repr = reprCtor()
groupReprs.push({ repr, group })
- await ctx.runChild(repr.create(group, props), { message: 'Building structure unit representations...', current: i, max: groups.length });
+ await repr.create(group, props).runAsChild(ctx, { message: 'Building structure unit representations...', current: i, max: groups.length });
renderObjects.push(...repr.renderObjects)
}
});
@@ -55,8 +55,8 @@ export function StructureRepresentation<P>(reprCtor: () => UnitsRepresentation<P
const groupRepr = groupReprs[i]
const { repr, group } = groupRepr
const state = { message: 'Updating structure unit representations...', current: i, max: il };
- if (!await ctx.runChild(repr.update(props), state)) {
- await ctx.runChild(repr.create(group, props), state)
+ if (!await repr.update(props).runAsChild(ctx, state)) {
+ await repr.create(group, props).runAsChild(ctx, state)
}
renderObjects.push(...repr.renderObjects)
}
diff --git a/src/mol-geo/representation/structure/spacefill.ts b/src/mol-geo/representation/structure/spacefill.ts
index db82405148603f4167fc66e3a9f7deaba9f872f4..7f2b7ab722ffe1911b2cb70cc8de332bb98fb8b1 100644
--- a/src/mol-geo/representation/structure/spacefill.ts
+++ b/src/mol-geo/representation/structure/spacefill.ts
@@ -83,8 +83,7 @@ export default function Spacefill(): UnitsRepresentation<SpacefillProps> {
const { detail, colorTheme, alpha, visible, doubleSided } = { ...DefaultSpacefillProps, ...props }
- await ctx.update('Computing spacefill mesh');
- const mesh = await ctx.runChild(createSpacefillMesh(group.units[0], detail))
+ const mesh = await createSpacefillMesh(group.units[0], detail).runAsChild(ctx, 'Computing spacefill mesh')
// console.log(mesh)
const vertexMap = VertexMap.fromMesh(mesh)
diff --git a/src/mol-geo/representation/volume/index.ts b/src/mol-geo/representation/volume/index.ts
index 84aee724fff635612391ba5d63db2f2df2e8f55e..779c05940b96e083a7e308479f76d010deaa7e79 100644
--- a/src/mol-geo/representation/volume/index.ts
+++ b/src/mol-geo/representation/volume/index.ts
@@ -29,8 +29,7 @@ export function VolumeRepresentation<P>(reprCtor: () => VolumeElementRepresentat
create(volumeData: VolumeData, props: P = {} as P) {
return Task.create('VolumeRepresentation.create', async ctx => {
const repr = reprCtor()
- await ctx.update({ message: 'Building volume representation...', current: 0, max: 1 });
- await ctx.runChild(repr.create(volumeData, props));
+ await repr.create(volumeData, props).runAsChild(ctx, { message: 'Building volume representation...', current: 0, max: 1 });
renderObjects.push(...repr.renderObjects)
});
},
diff --git a/src/mol-geo/representation/volume/surface.ts b/src/mol-geo/representation/volume/surface.ts
index a2de1a61d10cef902ee848ee9efb6ddab6572ead..bc9531ead7527fed500969d8bf22aa1a966c2c9f 100644
--- a/src/mol-geo/representation/volume/surface.ts
+++ b/src/mol-geo/representation/volume/surface.ts
@@ -20,10 +20,10 @@ export function computeVolumeSurface(volume: VolumeData, isoValue: VolumeIsoValu
return Task.create<Mesh>('Volume Surface', async ctx => {
ctx.update({ message: 'Marching cubes...' });
- const mesh = await ctx.runChild(computeMarchingCubes({
+ const mesh = await computeMarchingCubes({
isoLevel: VolumeIsoValue.toAbsolute(isoValue).absoluteValue,
scalarField: volume.data
- }));
+ }).runAsChild(ctx);
const transform = VolumeData.getGridToCartesianTransform(volume);
ctx.update({ message: 'Transforming mesh...' });
@@ -56,7 +56,7 @@ export default function Surface(): VolumeElementRepresentation<SurfaceProps> {
curProps = { ...DefaultSurfaceProps, ...props }
const { alpha, visible, flatShaded, flipSided, doubleSided } = curProps
- const mesh = await ctx.runChild(computeVolumeSurface(volume, curProps.isoValue))
+ const mesh = await computeVolumeSurface(volume, curProps.isoValue).runAsChild(ctx)
if (!flatShaded) {
Mesh.computeNormalsImmediate(mesh)
}
diff --git a/src/mol-io/reader/_spec/csv.spec.ts b/src/mol-io/reader/_spec/csv.spec.ts
index b074b5bc7d51a2df190180065852e4f7dec8c75d..0802bc7491fedc90c702ef6bc24d7fa653746895 100644
--- a/src/mol-io/reader/_spec/csv.spec.ts
+++ b/src/mol-io/reader/_spec/csv.spec.ts
@@ -5,7 +5,6 @@
*/
import Csv from '../csv/parser'
-import { Run } from 'mol-task';
const csvStringBasic = `StrCol,IntCol,FloatCol
# comment
@@ -24,7 +23,7 @@ string2\t42\t2.44`
describe('csv reader', () => {
it('basic', async () => {
- const parsed = await Run(Csv(csvStringBasic));
+ const parsed = await Csv(csvStringBasic).run();
if (parsed.isError) return;
const csvFile = parsed.result;
@@ -46,7 +45,7 @@ describe('csv reader', () => {
});
it('advanced', async () => {
- const parsed = await Run(Csv(csvStringAdvanced));
+ const parsed = await Csv(csvStringAdvanced).run();
if (parsed.isError) return;
const csvFile = parsed.result;
@@ -63,7 +62,7 @@ describe('csv reader', () => {
});
it('tabs', async () => {
- const parsed = await Run(Csv(tabString, { delimiter: '\t' }));
+ const parsed = await Csv(tabString, { delimiter: '\t' }).run();;
if (parsed.isError) return;
const csvFile = parsed.result;
diff --git a/src/mol-io/reader/_spec/gro.spec.ts b/src/mol-io/reader/_spec/gro.spec.ts
index 6254be8f9d45d287f643e2d50993e8b62eb11bbe..055e4e61b227a58a86c5a1b4b6317c996558ec98 100644
--- a/src/mol-io/reader/_spec/gro.spec.ts
+++ b/src/mol-io/reader/_spec/gro.spec.ts
@@ -6,7 +6,6 @@
*/
import Gro from '../gro/parser'
-import { Run } from 'mol-task';
const groString = `MD of 2 waters, t= 4.2
6
@@ -27,7 +26,7 @@ const groStringHighPrecision = `Generated by trjconv : 2168 system t= 15.00000
describe('gro reader', () => {
it('basic', async () => {
- const parsed = await Run(Gro(groString));
+ const parsed = await Gro(groString).run();
if (parsed.isError) {
console.log(parsed)
@@ -58,7 +57,7 @@ describe('gro reader', () => {
});
it('high precision', async () => {
- const parsed = await Run(Gro(groStringHighPrecision));
+ const parsed = await Gro(groStringHighPrecision).run();
if (parsed.isError) {
console.log(parsed)
diff --git a/src/mol-io/reader/_spec/mol2.spec.ts b/src/mol-io/reader/_spec/mol2.spec.ts
index 43244780636af6fbcd75010522ba9405b75ca2ff..dc88b16043caf6777ca6571656f2c3cfab6eb38f 100644
--- a/src/mol-io/reader/_spec/mol2.spec.ts
+++ b/src/mol-io/reader/_spec/mol2.spec.ts
@@ -1,6 +1,5 @@
import Mol2 from '../mol2/parser'
-import { Run } from 'mol-task';
const Mol2String = `@<TRIPOS>MOLECULE
5816
@@ -247,7 +246,7 @@ GASTEIGER
describe('mol2 reader', () => {
it('basic', async () => {
- const parsed = await Run(Mol2(Mol2String));
+ const parsed = await Mol2(Mol2String).run();
if (parsed.isError) {
throw new Error(parsed.message);
}
@@ -298,7 +297,7 @@ describe('mol2 reader', () => {
});
it('multiblocks', async () => {
- const parsed = await Run(Mol2(Mol2StringMultiBlocks));
+ const parsed = await Mol2(Mol2StringMultiBlocks).run();
if (parsed.isError) {
throw new Error(parsed.message);
}
@@ -349,7 +348,7 @@ describe('mol2 reader', () => {
});
it('minimal', async () => {
- const parsed = await Run(Mol2(Mol2StringMinimal));
+ const parsed = await Mol2(Mol2StringMinimal).run();
if (parsed.isError) {
throw new Error(parsed.message);
}
diff --git a/src/mol-model/structure/structure/symmetry.ts b/src/mol-model/structure/structure/symmetry.ts
index bf17c9013887a9f910257183ee3a2bfc99870826..4a0abaf78eacd46439cbf61a69b5ad97b3ea19c6 100644
--- a/src/mol-model/structure/structure/symmetry.ts
+++ b/src/mol-model/structure/structure/symmetry.ts
@@ -26,7 +26,7 @@ namespace StructureSymmetry {
const assembler = Structure.Builder();
for (const g of assembly.operatorGroups) {
- const selection = await ctx.runChild(g.selector(structure));
+ const selection = await g.selector(structure).runAsChild(ctx);
if (Selection.structureCount(selection) === 0) {
continue;
}
diff --git a/src/mol-task/execution/observable.ts b/src/mol-task/execution/observable.ts
index 82d4e05a43917365d625115cdd1b13c072346d88..4f451628759827ebebb7fca9f2988f1727d45f11 100644
--- a/src/mol-task/execution/observable.ts
+++ b/src/mol-task/execution/observable.ts
@@ -10,13 +10,22 @@ import { Progress } from './progress'
import { now } from '../util/now'
import { Scheduler } from '../util/scheduler'
-function ExecuteObservable<T>(task: Task<T>, observer: Progress.Observer, updateRateMs = 250) {
+interface ExposedTask<T> extends Task<T> {
+ f: (ctx: RuntimeContext) => Promise<T>,
+ onAbort?: () => void
+}
+
+export function ExecuteObservable<T>(task: Task<T>, observer: Progress.Observer, updateRateMs = 250) {
const info = ProgressInfo(task, observer, updateRateMs);
const ctx = new ObservableRuntimeContext(info, info.root);
- return execute(task, ctx);
+ return execute(task as ExposedTask<T>, ctx);
+}
+
+export function ExecuteObservableChild<T>(ctx: RuntimeContext, task: Task<T>, progress?: string | Partial<RuntimeContext.ProgressUpdate>) {
+ return (ctx as ObservableRuntimeContext).runChild(task, progress);
}
-namespace ExecuteObservable {
+export namespace ExecuteObservable {
export let PRINT_ERRORS_TO_STD_ERR = false;
}
@@ -77,10 +86,10 @@ function snapshotProgress(info: ProgressInfo): Progress {
return { root: cloneTree(info.root), canAbort: canAbort(info.root), requestAbort: info.tryAbort };
}
-async function execute<T>(task: Task<T>, ctx: ObservableRuntimeContext) {
+async function execute<T>(task: ExposedTask<T>, ctx: ObservableRuntimeContext) {
ctx.node.progress.startedTime = now();
try {
- const ret = await task.__f(ctx);
+ const ret = await task.f(ctx);
if (ctx.info.abortToken.abortRequested) {
abort(ctx.info, ctx.node);
}
@@ -91,7 +100,7 @@ async function execute<T>(task: Task<T>, ctx: ObservableRuntimeContext) {
if (ctx.node.children.length > 0) {
await new Promise(res => { ctx.onChildrenFinished = res; });
}
- if (task.__onAbort) task.__onAbort();
+ if (task.onAbort) task.onAbort();
}
if (ExecuteObservable.PRINT_ERRORS_TO_STD_ERR) console.error(e);
throw e;
@@ -197,7 +206,7 @@ class ObservableRuntimeContext implements RuntimeContext {
children.push(node);
const ctx = new ObservableRuntimeContext(this.info, node);
try {
- return await execute(task, ctx);
+ return await execute(task as ExposedTask<T>, ctx);
} catch (e) {
if (Task.isAbort(e)) {
// need to catch the error here because otherwise
@@ -223,6 +232,4 @@ class ObservableRuntimeContext implements RuntimeContext {
this.node = node;
this.info = info;
}
-}
-
-export { ExecuteObservable }
\ No newline at end of file
+}
\ No newline at end of file
diff --git a/src/mol-task/execution/runtime-context.ts b/src/mol-task/execution/runtime-context.ts
index d2529a3eb3599d9ece65c7183b7a36cdc0117b33..d0469abcfe65c408f321087e40170791c19c4176 100644
--- a/src/mol-task/execution/runtime-context.ts
+++ b/src/mol-task/execution/runtime-context.ts
@@ -4,8 +4,6 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { Task } from '../task'
-
interface RuntimeContext {
readonly shouldUpdate: boolean,
readonly isSynchronous: boolean,
@@ -15,11 +13,7 @@ interface RuntimeContext {
//
// Alternatively, progress can be updated without notifying (and yielding) using update(progress, true).
// This is useful for nested tasks.
- update(progress?: string | Partial<RuntimeContext.ProgressUpdate>, dontNotify?: boolean): Promise<void> | void,
-
- // Run a child task that adds a new node to the progress tree.
- // Allow to pass the progress so that the progress tree can be kept in a "good state" without having to separately call update.
- runChild<T>(task: Task<T>, progress?: string | Partial<RuntimeContext.ProgressUpdate>): Promise<T>
+ update(progress?: string | Partial<RuntimeContext.ProgressUpdate>, dontNotify?: boolean): Promise<void> | void
}
namespace RuntimeContext {
diff --git a/src/mol-task/execution/synchronous.ts b/src/mol-task/execution/synchronous.ts
index 4ca40a04a5ccc91024b08ca3bcf6093ac8643e34..5c729a61097f58d47d00619901f00487dcc282df 100644
--- a/src/mol-task/execution/synchronous.ts
+++ b/src/mol-task/execution/synchronous.ts
@@ -4,21 +4,12 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { Task } from '../task'
import { RuntimeContext } from './runtime-context'
class SynchronousRuntimeContext implements RuntimeContext {
shouldUpdate = false;
isSynchronous = true;
-
update(progress: string | Partial<RuntimeContext.ProgressUpdate>, dontNotify?: boolean): Promise<void> | void { }
- runChild<T>(task: Task<T>, progress?: string | Partial<RuntimeContext.ProgressUpdate>): Promise<T> { return ExecuteSynchronous(task); }
-}
-
-const SyncRuntimeInstance = new SynchronousRuntimeContext();
-
-function ExecuteSynchronous<T>(task: Task<T>) {
- return task.__f(SyncRuntimeInstance);
}
-export { ExecuteSynchronous }
\ No newline at end of file
+export const SyncRuntimeContext = new SynchronousRuntimeContext();
\ No newline at end of file
diff --git a/src/mol-task/index.ts b/src/mol-task/index.ts
index 830153c1cfaa3cd6512b083dd988b90b825bdb08..2ef6489c9fffe85d67739274d1aab599dae14de9 100644
--- a/src/mol-task/index.ts
+++ b/src/mol-task/index.ts
@@ -6,21 +6,10 @@
import { Task } from './task'
import { RuntimeContext } from './execution/runtime-context'
-import { ExecuteSynchronous } from './execution/synchronous'
-import { ExecuteObservable } from './execution/observable'
import { Progress } from './execution/progress'
import { now } from './util/now'
import { Scheduler } from './util/scheduler'
import { MultistepTask } from './util/multistep'
import { chunkedSubtask } from './util/chunked'
-// Run the task without the ability to observe its progress.
-function Run<T>(task: Task<T>): Promise<T>;
-// Run the task with the ability to observe its progress and request cancellation.
-function Run<T>(task: Task<T>, observer: Progress.Observer, updateRateMs?: number): Promise<T>;
-function Run<T>(task: Task<T>, observer?: Progress.Observer, updateRateMs?: number): Promise<T> {
- if (observer) return ExecuteObservable(task, observer, updateRateMs || 250);
- return ExecuteSynchronous(task);
-}
-
-export { Task, RuntimeContext, Progress, Run, now, Scheduler, MultistepTask, chunkedSubtask }
\ No newline at end of file
+export { Task, RuntimeContext, Progress, now, Scheduler, MultistepTask, chunkedSubtask }
\ No newline at end of file
diff --git a/src/mol-task/task.ts b/src/mol-task/task.ts
index 0ce5ca40bf65ef59de655b3ecdf39d4a2b12abec..34dc4556373cc1b7afb381f7d6b56dd7c100d1cf 100644
--- a/src/mol-task/task.ts
+++ b/src/mol-task/task.ts
@@ -5,25 +5,51 @@
*/
import { RuntimeContext } from './execution/runtime-context'
+import { Progress } from './execution/progress'
+import { ExecuteObservable, ExecuteObservableChild } from './execution/observable';
+import { SyncRuntimeContext } from 'mol-task/execution/synchronous';
// A "named function wrapper" with built in "computation tree progress tracking".
// Use Run(t, ?observer, ?updateRate) to execute
interface Task<T> {
+ // run the task without observation
+ run(): Promise<T>,
+ // run the task with the specified observer, default updateRate is 250ms
+ run(observer: Progress.Observer, updateRateMs?: number): Promise<T>,
+
+ // Run a child task that adds a new node to the progress tree.
+ // Allow to pass the progress so that the progress tree can be kept in a "good state" without having to separately call update.
+ runAsChild(ctx: RuntimeContext, progress?: string | Partial<RuntimeContext.ProgressUpdate>): Promise<T>
+
readonly id: number,
- readonly name: string,
- // Do not call this directly, use Run.
- readonly __f: (ctx: RuntimeContext) => Promise<T>,
- // Do not call this directly, use Run.
- readonly __onAbort: (() => void) | undefined
+ readonly name: string
}
namespace Task {
+ class Impl<T> implements Task<T> {
+ readonly id: number;
+
+ run(observer?: Progress.Observer, updateRateMs?: number): Promise<T> {
+ if (observer) return ExecuteObservable(this, observer, updateRateMs as number || 250);
+ return this.f(SyncRuntimeContext);
+ }
+
+ runAsChild(ctx: RuntimeContext, progress?: string | Partial<RuntimeContext.ProgressUpdate>): Promise<T> {
+ if (ctx.isSynchronous) return this.f(SyncRuntimeContext);
+ return ExecuteObservableChild(ctx, this, progress as string | Partial<RuntimeContext.ProgressUpdate>);
+ }
+
+ constructor(public name: string, public f: (ctx: RuntimeContext) => Promise<T>, public onAbort?: () => void) {
+ this.id = nextId();
+ }
+ }
+
export interface Aborted { isAborted: true, reason: string }
export function isAbort(e: any): e is Aborted { return !!e && !!e.isAborted; }
export function Aborted(reason: string): Aborted { return { isAborted: true, reason }; }
export function create<T>(name: string, f: (ctx: RuntimeContext) => Promise<T>, onAbort?: () => void): Task<T> {
- return { id: nextId(), name, __f: f, __onAbort: onAbort };
+ return new Impl(name, f, onAbort);
}
export function constant<T>(name: string, value: T): Task<T> { return create(name, async ctx => value); }
diff --git a/src/perf-tests/lookup3d.ts b/src/perf-tests/lookup3d.ts
index 1245d80d4cf4f2509d15316fa9871aae83aa54e6..3b52eee9f0e027d48f6113ae3551a3d42e922038 100644
--- a/src/perf-tests/lookup3d.ts
+++ b/src/perf-tests/lookup3d.ts
@@ -4,7 +4,6 @@ import CIF from 'mol-io/reader/cif'
import { Structure, Model } from 'mol-model/structure'
-import { Run } from 'mol-task';
import { GridLookup3D } from 'mol-math/geometry';
// import { sortArray } from 'mol-data/util';
import { OrderedSet } from 'mol-data/int';
@@ -27,14 +26,14 @@ async function readData(path: string) {
export async function readCIF(path: string) {
const input = await readData(path)
const comp = typeof input === 'string' ? CIF.parseText(input) : CIF.parseBinary(input);
- const parsed = await Run(comp);
+ const parsed = await comp.run();
if (parsed.isError) {
throw parsed;
}
const data = parsed.result.blocks[0];
const mmcif = CIF.schema.mmCIF(data);
- const models = await Run(Model.create({ kind: 'mmCIF', data: mmcif }));
+ const models = await Model.create({ kind: 'mmCIF', data: mmcif }).run();
const structures = models.map(Structure.ofModel);
return { mmcif, models, structures };
diff --git a/src/perf-tests/structure.ts b/src/perf-tests/structure.ts
index e859ff78eb862628727f5d66f17d11a20195123e..2ad787c4ac9b2d1416a78fb73f5ac92cc3fdb44d 100644
--- a/src/perf-tests/structure.ts
+++ b/src/perf-tests/structure.ts
@@ -15,7 +15,6 @@ import { Structure, Model, Queries as Q, Element, Selection, StructureSymmetry,
//import { Segmentation, OrderedSet } from 'mol-data/int'
import to_mmCIF from 'mol-model/structure/export/mmcif'
-import { Run } from 'mol-task';
import { Vec3 } from 'mol-math/linear-algebra';
//import { EquivalenceClasses } from 'mol-data/util';
@@ -62,7 +61,7 @@ export async function readCIF(path: string) {
console.time('parse');
const comp = typeof input === 'string' ? CIF.parseText(input) : CIF.parseBinary(input);
- const parsed = await Run(comp);
+ const parsed = await comp.run();
console.timeEnd('parse');
if (parsed.isError) {
throw parsed;
@@ -74,7 +73,7 @@ export async function readCIF(path: string) {
console.timeEnd('schema')
console.time('buildModels')
- const models = await Run(Model.create({ kind: 'mmCIF', data: mmcif }));
+ const models = await Model.create({ kind: 'mmCIF', data: mmcif }).run();
console.timeEnd('buildModels')
const structures = models.map(Structure.ofModel);
@@ -292,7 +291,7 @@ export namespace PropertyAccess {
export async function testAssembly(id: string, s: Structure) {
console.time('assembly')
- const a = await Run(StructureSymmetry.buildAssembly(s, '1'));
+ const a = await StructureSymmetry.buildAssembly(s, '1').run();
//const auth_comp_id = Q.props.residue.auth_comp_id;
//const q1 = Query(Q.generators.atoms({ residueTest: l => auth_comp_id(l) === 'ALA' }));
//const alas = await query(q1, a);
@@ -305,7 +304,7 @@ export namespace PropertyAccess {
export async function testSymmetry(id: string, s: Structure) {
console.time('symmetry')
- const a = await Run(StructureSymmetry.buildSymmetryRange(s, Vec3.create(-1, -1, -1), Vec3.create(1, 1, 1)));
+ const a = await StructureSymmetry.buildSymmetryRange(s, Vec3.create(-1, -1, -1), Vec3.create(1, 1, 1)).run();
//const auth_comp_id = Q.props.residue.auth_comp_id;
//const q1 = Query(Q.generators.atoms({ residueTest: l => auth_comp_id(l) === 'ALA' }));
//const alas = await query(q1, a);
@@ -336,7 +335,7 @@ export namespace PropertyAccess {
// }
function query(q: Query, s: Structure) {
- return Run((q(s)));
+ return q(s).run();
}
export async function run() {