molstar
Version:
A comprehensive macromolecular library.
526 lines (525 loc) • 21.5 kB
JavaScript
/**
* Copyright (c) 2018-2024 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>
* @author Neli Fonseca <neli@ebi.ac.uk>
*/
import * as CCP4 from '../../mol-io/reader/ccp4/parser';
import { CIF } from '../../mol-io/reader/cif';
import * as DSN6 from '../../mol-io/reader/dsn6/parser';
import * as PLY from '../../mol-io/reader/ply/parser';
import { parsePsf } from '../../mol-io/reader/psf/parser';
import { StateObject, StateTransformer } from '../../mol-state';
import { Task } from '../../mol-task';
import { ajaxGetMany } from '../../mol-util/data-source';
import { ParamDefinition as PD } from '../../mol-util/param-definition';
import { PluginStateObject as SO, PluginStateTransform } from '../objects';
import { Asset } from '../../mol-util/assets';
import { parseCube } from '../../mol-io/reader/cube/parser';
import { parseDx } from '../../mol-io/reader/dx/parser';
import { ColorNames } from '../../mol-util/color/names';
import { assertUnreachable } from '../../mol-util/type-helpers';
import { parsePrmtop } from '../../mol-io/reader/prmtop/parser';
import { parseTop } from '../../mol-io/reader/top/parser';
import { ungzip } from '../../mol-util/zip/zip';
import { StringLike } from '../../mol-io/common/string-like';
import { utf8ReadLong } from '../../mol-io/common/utf8';
export { Download };
export { DownloadBlob };
export { DeflateData };
export { RawData };
export { ReadFile };
export { ParseBlob };
export { ParseCif };
export { ParseCube };
export { ParsePsf };
export { ParsePrmtop };
export { ParseTop };
export { ParsePly };
export { ParseCcp4 };
export { ParseDsn6 };
export { ParseDx };
export { ImportString };
export { ImportJson };
export { ParseJson };
export { LazyVolume };
const Download = PluginStateTransform.BuiltIn({
name: 'download',
display: { name: 'Download', description: 'Download string or binary data from the specified URL' },
from: [SO.Root],
to: [SO.Data.String, SO.Data.Binary],
params: {
url: PD.Url('https://www.ebi.ac.uk/pdbe/static/entry/1cbs_updated.cif', { description: 'Resource URL. Must be the same domain or support CORS.' }),
label: PD.Optional(PD.Text('')),
isBinary: PD.Optional(PD.Boolean(false, { description: 'If true, download data as binary (string otherwise)' }))
}
})({
apply({ params: p, cache }, plugin) {
return Task.create('Download', async (ctx) => {
const url = Asset.getUrlAsset(plugin.managers.asset, p.url);
const asset = await plugin.managers.asset.resolve(url, p.isBinary ? 'binary' : 'string').runInContext(ctx);
cache.asset = asset;
return p.isBinary
? new SO.Data.Binary(asset.data, { label: p.label ? p.label : url.url })
: new SO.Data.String(asset.data, { label: p.label ? p.label : url.url });
});
},
dispose({ cache }) {
var _a;
(_a = cache === null || cache === void 0 ? void 0 : cache.asset) === null || _a === void 0 ? void 0 : _a.dispose();
},
update({ oldParams, newParams, b }) {
if (oldParams.url !== newParams.url || oldParams.isBinary !== newParams.isBinary)
return StateTransformer.UpdateResult.Recreate;
if (oldParams.label !== newParams.label) {
b.label = newParams.label || ((typeof newParams.url === 'string') ? newParams.url : newParams.url.url);
return StateTransformer.UpdateResult.Updated;
}
return StateTransformer.UpdateResult.Unchanged;
}
});
const DownloadBlob = PluginStateTransform.BuiltIn({
name: 'download-blob',
display: { name: 'Download Blob', description: 'Download multiple string or binary data from the specified URLs.' },
from: SO.Root,
to: SO.Data.Blob,
params: {
sources: PD.ObjectList({
id: PD.Text('', { label: 'Unique ID' }),
url: PD.Url('https://www.ebi.ac.uk/pdbe/static/entry/1cbs_updated.cif', { description: 'Resource URL. Must be the same domain or support CORS.' }),
isBinary: PD.Optional(PD.Boolean(false, { description: 'If true, download data as binary (string otherwise)' })),
canFail: PD.Optional(PD.Boolean(false, { description: 'Indicate whether the download can fail and not be included in the blob as a result.' }))
}, e => `${e.id}: ${e.url}`),
maxConcurrency: PD.Optional(PD.Numeric(4, { min: 1, max: 12, step: 1 }, { description: 'The maximum number of concurrent downloads.' }))
}
})({
apply({ params, cache }, plugin) {
return Task.create('Download Blob', async (ctx) => {
const entries = [];
const data = await ajaxGetMany(ctx, plugin.managers.asset, params.sources, params.maxConcurrency || 4);
const assets = [];
for (let i = 0; i < data.length; i++) {
const r = data[i], src = params.sources[i];
if (r.kind === 'error')
plugin.log.warn(`Download ${r.id} (${src.url}) failed: ${r.error}`);
else {
assets.push(r.result);
entries.push(src.isBinary
? { id: r.id, kind: 'binary', data: r.result.data }
: { id: r.id, kind: 'string', data: r.result.data });
}
}
cache.assets = assets;
return new SO.Data.Blob(entries, { label: 'Data Blob', description: `${entries.length} ${entries.length === 1 ? 'entry' : 'entries'}` });
});
},
dispose({ cache }, plugin) {
const assets = cache === null || cache === void 0 ? void 0 : cache.assets;
if (!assets)
return;
for (const a of assets) {
a.dispose();
}
}
// TODO: ??
// update({ oldParams, newParams, b }) {
// return 0 as any;
// // if (oldParams.url !== newParams.url || oldParams.isBinary !== newParams.isBinary) return StateTransformer.UpdateResult.Recreate;
// // if (oldParams.label !== newParams.label) {
// // (b.label as string) = newParams.label || newParams.url;
// // return StateTransformer.UpdateResult.Updated;
// // }
// // return StateTransformer.UpdateResult.Unchanged;
// }
});
const DeflateData = PluginStateTransform.BuiltIn({
name: 'defalate-data',
display: { name: 'Deflate', description: 'Deflate compressed data' },
params: {
method: PD.Select('gzip', [['gzip', 'gzip']]), // later on we might have to add say brotli
isString: PD.Boolean(false),
stringEncoding: PD.Optional(PD.Select('utf-8', [['utf-8', 'UTF8']])),
label: PD.Optional(PD.Text(''))
},
from: [SO.Data.Binary],
to: [SO.Data.Binary, SO.Data.String]
})({
apply({ a, params }, plugin) {
return Task.create('Gzip', async (ctx) => {
const decompressedData = await ungzip(ctx, a.data);
const label = params.label ? params.label : a.label;
// handle decoding based on stringEncoding param
if (params.isString) {
const textData = utf8ReadLong(decompressedData);
return new SO.Data.String(textData, { label });
}
return new SO.Data.Binary(decompressedData, { label });
});
}
});
const RawData = PluginStateTransform.BuiltIn({
name: 'raw-data',
display: { name: 'Raw Data', description: 'Raw data supplied by value.' },
from: [SO.Root],
to: [SO.Data.String, SO.Data.Binary],
params: {
data: PD.Value('', { isHidden: true }),
label: PD.Optional(PD.Text(''))
}
})({
apply({ params: p }) {
return Task.create('Raw Data', async () => {
if (typeof p.data === 'string') {
return new SO.Data.String(p.data, { label: p.label ? p.label : 'String' });
}
else if (Array.isArray(p.data)) {
return new SO.Data.Binary(new Uint8Array(p.data), { label: p.label ? p.label : 'Binary' });
}
else if (p.data instanceof ArrayBuffer) {
return new SO.Data.Binary(new Uint8Array(p.data), { label: p.label ? p.label : 'Binary' });
}
else if (p.data instanceof Uint8Array) {
return new SO.Data.Binary(p.data, { label: p.label ? p.label : 'Binary' });
}
else {
assertUnreachable(p.data);
}
});
},
update({ oldParams, newParams, b }) {
if (oldParams.data !== newParams.data)
return StateTransformer.UpdateResult.Recreate;
if (oldParams.label !== newParams.label) {
b.label = newParams.label || b.label;
return StateTransformer.UpdateResult.Updated;
}
return StateTransformer.UpdateResult.Unchanged;
},
customSerialization: {
toJSON(p) {
if (typeof p.data === 'string' || Array.isArray(p.data)) {
return p;
}
else if (p.data instanceof ArrayBuffer) {
const v = new Uint8Array(p.data);
const data = new Array(v.length);
for (let i = 0, _i = v.length; i < _i; i++)
data[i] = v[i];
return { data, label: p.label };
}
else if (p.data instanceof Uint8Array) {
const data = new Array(p.data.length);
for (let i = 0, _i = p.data.length; i < _i; i++)
data[i] = p.data[i];
return { data, label: p.label };
}
},
fromJSON(data) {
return data;
}
}
});
const ReadFile = PluginStateTransform.BuiltIn({
name: 'read-file',
display: { name: 'Read File', description: 'Read string or binary data from the specified file' },
from: SO.Root,
to: [SO.Data.String, SO.Data.Binary],
params: {
file: PD.File(),
label: PD.Optional(PD.Text('')),
isBinary: PD.Optional(PD.Boolean(false, { description: 'If true, open file as as binary (string otherwise)' }))
}
})({
apply({ params: p, cache }, plugin) {
return Task.create('Open File', async (ctx) => {
if (p.file === null) {
plugin.log.error('No file(s) selected');
return StateObject.Null;
}
const asset = await plugin.managers.asset.resolve(p.file, p.isBinary ? 'binary' : 'string').runInContext(ctx);
cache.asset = asset;
const o = p.isBinary
? new SO.Data.Binary(asset.data, { label: p.label ? p.label : p.file.name })
: new SO.Data.String(asset.data, { label: p.label ? p.label : p.file.name });
return o;
});
},
dispose({ cache }) {
var _a;
(_a = cache === null || cache === void 0 ? void 0 : cache.asset) === null || _a === void 0 ? void 0 : _a.dispose();
},
update({ oldParams, newParams, b }) {
var _a;
if (oldParams.label !== newParams.label) {
b.label = newParams.label || ((_a = oldParams.file) === null || _a === void 0 ? void 0 : _a.name) || '';
return StateTransformer.UpdateResult.Updated;
}
return StateTransformer.UpdateResult.Unchanged;
},
isSerializable: () => ({ isSerializable: false, reason: 'Cannot serialize user loaded files.' })
});
const ParseBlob = PluginStateTransform.BuiltIn({
name: 'parse-blob',
display: { name: 'Parse Blob', description: 'Parse multiple data enties' },
from: SO.Data.Blob,
to: SO.Format.Blob,
params: {
formats: PD.ObjectList({
id: PD.Text('', { label: 'Unique ID' }),
format: PD.Select('cif', [['cif', 'cif']])
}, e => `${e.id}: ${e.format}`)
}
})({
apply({ a, params }, plugin) {
return Task.create('Parse Blob', async (ctx) => {
const map = new Map();
for (const f of params.formats)
map.set(f.id, f.format);
const entries = [];
for (const e of a.data) {
if (!map.has(e.id))
continue;
const parsed = await (e.kind === 'string' ? CIF.parse(e.data) : CIF.parseBinary(e.data)).runInContext(ctx);
if (parsed.isError)
throw new Error(`${e.id}: ${parsed.message}`);
entries.push({ id: e.id, kind: 'cif', data: parsed.result });
}
return new SO.Format.Blob(entries, { label: 'Format Blob', description: `${entries.length} ${entries.length === 1 ? 'entry' : 'entries'}` });
});
},
// TODO: ??
// update({ oldParams, newParams, b }) {
// return 0 as any;
// // if (oldParams.url !== newParams.url || oldParams.isBinary !== newParams.isBinary) return StateTransformer.UpdateResult.Recreate;
// // if (oldParams.label !== newParams.label) {
// // (b.label as string) = newParams.label || newParams.url;
// // return StateTransformer.UpdateResult.Updated;
// // }
// // return StateTransformer.UpdateResult.Unchanged;
// }
});
const ParseCif = PluginStateTransform.BuiltIn({
name: 'parse-cif',
display: { name: 'Parse CIF', description: 'Parse CIF from String or Binary data' },
from: [SO.Data.String, SO.Data.Binary],
to: SO.Format.Cif
})({
apply({ a }) {
return Task.create('Parse CIF', async (ctx) => {
const parsed = await (CIF.parse(a.data)).runInContext(ctx);
if (parsed.isError)
throw new Error(parsed.message);
if (parsed.result.blocks.length === 0)
return StateObject.Null;
return new SO.Format.Cif(parsed.result);
});
}
});
const ParseCube = PluginStateTransform.BuiltIn({
name: 'parse-cube',
display: { name: 'Parse Cube', description: 'Parse Cube from String data' },
from: SO.Data.String,
to: SO.Format.Cube
})({
apply({ a }) {
return Task.create('Parse Cube', async (ctx) => {
const parsed = await parseCube(a.data, a.label).runInContext(ctx);
if (parsed.isError)
throw new Error(parsed.message);
return new SO.Format.Cube(parsed.result);
});
}
});
const ParsePsf = PluginStateTransform.BuiltIn({
name: 'parse-psf',
display: { name: 'Parse PSF', description: 'Parse PSF from String data' },
from: [SO.Data.String],
to: SO.Format.Psf
})({
apply({ a }) {
return Task.create('Parse PSF', async (ctx) => {
const parsed = await parsePsf(a.data).runInContext(ctx);
if (parsed.isError)
throw new Error(parsed.message);
return new SO.Format.Psf(parsed.result);
});
}
});
const ParsePrmtop = PluginStateTransform.BuiltIn({
name: 'parse-prmtop',
display: { name: 'Parse PRMTOP', description: 'Parse PRMTOP from String data' },
from: [SO.Data.String],
to: SO.Format.Prmtop
})({
apply({ a }) {
return Task.create('Parse PRMTOP', async (ctx) => {
const parsed = await parsePrmtop(a.data).runInContext(ctx);
if (parsed.isError)
throw new Error(parsed.message);
return new SO.Format.Prmtop(parsed.result);
});
}
});
const ParseTop = PluginStateTransform.BuiltIn({
name: 'parse-top',
display: { name: 'Parse TOP', description: 'Parse TOP from String data' },
from: [SO.Data.String],
to: SO.Format.Top
})({
apply({ a }) {
return Task.create('Parse TOP', async (ctx) => {
const parsed = await parseTop(a.data).runInContext(ctx);
if (parsed.isError)
throw new Error(parsed.message);
return new SO.Format.Top(parsed.result);
});
}
});
const ParsePly = PluginStateTransform.BuiltIn({
name: 'parse-ply',
display: { name: 'Parse PLY', description: 'Parse PLY from String data' },
from: [SO.Data.String],
to: SO.Format.Ply
})({
apply({ a }) {
return Task.create('Parse PLY', async (ctx) => {
const parsed = await PLY.parsePly(a.data).runInContext(ctx);
if (parsed.isError)
throw new Error(parsed.message);
return new SO.Format.Ply(parsed.result, { label: parsed.result.comments[0] || 'PLY Data' });
});
}
});
const ParseCcp4 = PluginStateTransform.BuiltIn({
name: 'parse-ccp4',
display: { name: 'Parse CCP4/MRC/MAP', description: 'Parse CCP4/MRC/MAP from Binary data' },
from: [SO.Data.Binary],
to: SO.Format.Ccp4
})({
apply({ a }) {
return Task.create('Parse CCP4/MRC/MAP', async (ctx) => {
const parsed = await CCP4.parse(a.data, a.label).runInContext(ctx);
if (parsed.isError)
throw new Error(parsed.message);
return new SO.Format.Ccp4(parsed.result);
});
}
});
const ParseDsn6 = PluginStateTransform.BuiltIn({
name: 'parse-dsn6',
display: { name: 'Parse DSN6/BRIX', description: 'Parse CCP4/BRIX from Binary data' },
from: [SO.Data.Binary],
to: SO.Format.Dsn6
})({
apply({ a }) {
return Task.create('Parse DSN6/BRIX', async (ctx) => {
const parsed = await DSN6.parse(a.data, a.label).runInContext(ctx);
if (parsed.isError)
throw new Error(parsed.message);
return new SO.Format.Dsn6(parsed.result);
});
}
});
const ParseDx = PluginStateTransform.BuiltIn({
name: 'parse-dx',
display: { name: 'Parse DX', description: 'Parse DX from Binary/String data' },
from: [SO.Data.Binary, SO.Data.String],
to: SO.Format.Dx
})({
apply({ a }) {
return Task.create('Parse DX', async (ctx) => {
const parsed = await parseDx(a.data, a.label).runInContext(ctx);
if (parsed.isError)
throw new Error(parsed.message);
return new SO.Format.Dx(parsed.result);
});
}
});
const ImportString = PluginStateTransform.BuiltIn({
name: 'import-string',
display: { name: 'Import String', description: 'Import given data as a string' },
from: SO.Root,
to: SO.Data.String,
params: {
data: PD.Value(''),
label: PD.Optional(PD.Text('')),
}
})({
apply({ params: { data, label } }) {
return new SO.Data.String(data, { label: label || '' });
},
update({ oldParams, newParams, b }) {
if (oldParams.data !== newParams.data)
return StateTransformer.UpdateResult.Recreate;
if (oldParams.label !== newParams.label) {
b.label = newParams.label || '';
return StateTransformer.UpdateResult.Updated;
}
return StateTransformer.UpdateResult.Unchanged;
},
isSerializable: () => ({ isSerializable: false, reason: 'Cannot serialize user imported strings.' })
});
const ImportJson = PluginStateTransform.BuiltIn({
name: 'import-json',
display: { name: 'Import JSON', description: 'Import given data as a JSON' },
from: SO.Root,
to: SO.Format.Json,
params: {
data: PD.Value({}),
label: PD.Optional(PD.Text('')),
}
})({
apply({ params: { data, label } }) {
return new SO.Format.Json(data, { label: label || '' });
},
update({ oldParams, newParams, b }) {
if (oldParams.data !== newParams.data)
return StateTransformer.UpdateResult.Recreate;
if (oldParams.label !== newParams.label) {
b.label = newParams.label || '';
return StateTransformer.UpdateResult.Updated;
}
return StateTransformer.UpdateResult.Unchanged;
},
isSerializable: () => ({ isSerializable: false, reason: 'Cannot serialize user imported JSON.' })
});
const ParseJson = PluginStateTransform.BuiltIn({
name: 'parse-json',
display: { name: 'Parse JSON', description: 'Parse JSON from String data' },
from: [SO.Data.String],
to: SO.Format.Json
})({
apply({ a }) {
return Task.create('Parse JSON', async (ctx) => {
const json = await (new Response(StringLike.toString(a.data))).json(); // async JSON parsing via fetch API
return new SO.Format.Json(json);
});
}
});
const LazyVolume = PluginStateTransform.BuiltIn({
name: 'lazy-volume',
display: { name: 'Lazy Volume', description: 'A placeholder for lazy loaded volume representation' },
from: SO.Root,
to: SO.Volume.Lazy,
params: {
url: PD.Url(''),
isBinary: PD.Boolean(false),
format: PD.Text('ccp4'), // TODO: use Select based on available formats
entryId: PD.Value('', { isHidden: true }),
isovalues: PD.ObjectList({
type: PD.Text('relative'), // TODO: Select
value: PD.Numeric(0),
color: PD.Color(ColorNames.black),
alpha: PD.Numeric(1, { min: 0, max: 1, step: 0.01 }),
volumeIndex: PD.Numeric(0),
}, e => `${e.type} ${e.value}`)
}
})({
apply({ a, params }) {
return Task.create('Lazy Volume', async (ctx) => {
const entryId = Array.isArray(params.entryId) ? params.entryId.join(', ') : params.entryId;
return new SO.Volume.Lazy(params, { label: `${entryId || params.url}`, description: 'Lazy Volume' });
});
}
});