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/**
* 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 { isTypedArray } from '../../mol-data/db/column-helpers';
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 { PluginContext } from '../../mol-plugin/context';
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';
export { Download };
export { DownloadBlob };
export { RawData };
export { ReadFile };
export { ParseBlob };
export { ParseCif };
export { ParsePsf };
export { ParsePly };
export { ParseCcp4 };
export { ParseDsn6 };
export { ImportString };
export { ImportJson };
export { ParseJson };
type Download = typeof Download
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: PluginContext) {
return Task.create('Download', async ctx => {
let url = Asset.getUrlAsset(plugin.managers.asset, p.url);
const asset = await plugin.managers.asset.resolve(url, p.isBinary ? 'binary' : 'string').runInContext(ctx);
(cache as any).asset = asset;
return p.isBinary
? new SO.Data.Binary(asset.data as Uint8Array, { label: p.label ? p.label : url.url })
: new SO.Data.String(asset.data as string, { label: p.label ? p.label : url.url });
});
},
dispose({ cache }) {
((cache as any)?.asset as Asset.Wrapper | undefined)?.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;
}
});
type DownloadBlob = typeof DownloadBlob
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: PluginContext) {
return Task.create('Download Blob', async ctx => {
const entries: SO.Data.BlobEntry[] = [];
const data = await ajaxGetMany(ctx, plugin.managers.asset, params.sources, params.maxConcurrency || 4);
const assets: Asset.Wrapper[] = [];
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: ${r.error}`);
else {
assets.push(r.result);
entries.push(src.isBinary
? { id: r.id, kind: 'binary', data: r.result.data as Uint8Array }
: { id: r.id, kind: 'string', data: r.result.data as string });
}
}
(cache as any).assets = assets;
return new SO.Data.Blob(entries, { label: 'Data Blob', description: `${entries.length} ${entries.length === 1 ? 'entry' : 'entries'}` });
});
},
dispose({ cache }, plugin: PluginContext) {
const assets: Asset.Wrapper[] | undefined = (cache as any)?.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;
// }
});
type RawData = typeof RawData
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<string | number[]>('', { isHidden: true }),
label: PD.Optional(PD.Text(''))
}
})({
apply({ params: p }) {
return Task.create('Raw Data', async () => {
if (typeof p.data !== 'string' && isTypedArray(p.data)) { throw new Error('Supplied binary data must be a plain array.');
}
return typeof p.data === 'string'
? new SO.Data.String(p.data as string, { label: p.label ? p.label : 'String' })
: new SO.Data.Binary(new Uint8Array(p.data), { label: p.label ? p.label : 'Binary' });
});
},
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;
}
});
type ReadFile = typeof ReadFile
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: PluginContext) {
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 as any).asset = asset;
const o = p.isBinary
? new SO.Data.Binary(asset.data as Uint8Array, { label: p.label ? p.label : p.file.name })
: new SO.Data.String(asset.data as string, { label: p.label ? p.label : p.file.name });
return o;
});
},
dispose({ cache }) {
((cache as any)?.asset as Asset.Wrapper | undefined)?.dispose();
},
update({ oldParams, newParams, b }) {
if (oldParams.label !== newParams.label) {
(b.label as string) = newParams.label || oldParams.file?.name || '';
return StateTransformer.UpdateResult.Updated;
}
return StateTransformer.UpdateResult.Unchanged;
},
isSerializable: () => ({ isSerializable: false, reason: 'Cannot serialize user loaded files.' })
});
type ParseBlob = typeof ParseBlob
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', 'cif']])
}, e => `${e.id}: ${e.format}`)
}})({
apply({ a, params }, plugin: PluginContext) {
return Task.create('Parse Blob', async ctx => {
const map = new Map<string, string>();
for (const f of params.formats) map.set(f.id, f.format);
const entries: SO.Format.BlobEntry[] = [];
for (const e of a.data) {
if (!map.has(e.id)) continue;
const parsed = await (e.kind === 'string' ? CIF.parse(e.data) : CIF.parseBinary(e.data)).runInContext(ctx);
if (parsed.isError) throw new Error(`${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;
// }
});
type ParseCif = typeof ParseCif
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 (SO.Data.String.is(a) ? CIF.parse(a.data) : CIF.parseBinary(a.data)).runInContext(ctx);
if (parsed.isError) throw new Error(parsed.message);
return new SO.Format.Cif(parsed.result);
});
}
});
type ParsePsf = typeof ParsePsf
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);
});
}
});
type ParsePly = typeof ParsePly
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.parse(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' });
});
}
});
type ParseCcp4 = typeof ParseCcp4
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).runInContext(ctx);
if (parsed.isError) throw new Error(parsed.message);
return new SO.Format.Ccp4(parsed.result);
});
}
});
type ParseDsn6 = typeof ParseDsn6
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).runInContext(ctx);
if (parsed.isError) throw new Error(parsed.message);
return new SO.Format.Dsn6(parsed.result);
});
}
});
type ImportString = typeof ImportString
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.' })
});
type ImportJson = typeof ImportJson
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<any>({}),
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.' })
});
type ParseJson = typeof ParseJson
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(a.data)).json(); // async JSON parsing via fetch API
return new SO.Format.Json(json);
});
}
});