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Alexander Rose authoredAlexander Rose authored
web-schema.ts 12.20 KiB
/**
* Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
* @author David Sehnal <david.sehnal@gmail.com>
*/
import VERSION from './version'
import { LimitsConfig, ServerConfig } from '../config';
export function getSchema() {
function detail(i: number) {
return `${i} (${Math.round(100 * LimitsConfig.maxOutputSizeInVoxelCountByPrecisionLevel[i] / 1000 / 1000) / 100 }M voxels)`;
}
const detailMax = LimitsConfig.maxOutputSizeInVoxelCountByPrecisionLevel.length - 1;
const sources = ServerConfig.idMap.map(m => m[0])
return {
openapi: '3.0.0',
info: {
version: VERSION,
title: 'Volume Server',
description: 'The VolumeServer is a service for accessing subsets of volumetric data. It automatically downsamples the data depending on the volume of the requested region to reduce the bandwidth requirements and provide near-instant access to even the largest data sets.',
},
tags: [
{
name: 'General',
}
],
paths: {
[`${ServerConfig.apiPrefix}/{source}/{id}/`]: {
get: {
tags: ['General'],
summary: 'Returns a JSON response specifying if data is available and the maximum region that can be queried.',
operationId: 'getInfo',
parameters: [
{ $ref: '#/components/parameters/source' },
{ $ref: '#/components/parameters/id' },
],
responses: {
200: {
description: 'Volume availability and info',
content: {
'application/json': {
schema: { $ref: '#/components/schemas/info' }
}
}
},
},
}
},
[`${ServerConfig.apiPrefix}/{source}/{id}/box/{a1,a2,a3}/{b1,b2,b3}/`]: {
get: {
tags: ['General'],
summary: 'Returns density data inside the specified box for the given entry. For X-ray data, returns 2Fo-Fc and Fo-Fc volumes in a single response.',
operationId: 'getBox',
parameters: [
{ $ref: '#/components/parameters/source' },
{ $ref: '#/components/parameters/id' },
{
name: 'bottomLeftCorner',
in: 'path',
description: 'Bottom left corner of the query region in Cartesian or fractional coordinates (determined by the `space` query parameter).',
required: true,
schema: {
type: 'list',
items: {
type: 'float',
}
}, style: 'simple'
},
{
name: 'topRightCorner',
in: 'path',
description: 'Top right corner of the query region in Cartesian or fractional coordinates (determined by the `space` query parameter).',
required: true,
schema: {
type: 'list',
items: {
type: 'float',
}
},
style: 'simple'
},
{ $ref: '#/components/parameters/encoding' },
{ $ref: '#/components/parameters/detail' },
{
name: 'space',
in: 'query',
description: 'Determines the coordinate space the query is in. Can be cartesian or fractional. An optional argument, default values is cartesian.',
schema: {
type: 'string',
enum: ['cartesian', 'fractional']
},
style: 'form'
}
],
responses: {
200: {
description: 'Volume box',
content: {
'text/plain': {},
'application/octet-stream': {},
}
},
},
}
},
[`${ServerConfig.apiPrefix}/{source}/{id}/cell/`]: {
get: {
tags: ['General'],
summary: 'Returns (downsampled) volume data for the entire "data cell". For X-ray data, returns unit cell of 2Fo-Fc and Fo-Fc volumes, for EM data returns everything.',
operationId: 'getCell',
parameters: [
{ $ref: '#/components/parameters/source' },
{ $ref: '#/components/parameters/id' },
{ $ref: '#/components/parameters/encoding' },
{ $ref: '#/components/parameters/detail' },
],
responses: {
200: {
description: 'Volume cell',
content: {
'text/plain': {},
'application/octet-stream': {},
}
},
},
}
}
},
components: {
schemas: {
// TODO how to keep in sync with (or derive from) `api.ts/ExtendedHeader`
info: {
properties: {
formatVersion: {
type: 'string',
description: 'Format version number' },
axisOrder: {
type: 'array',
items: { type: 'number' },
description: 'Axis order from the slowest to fastest moving, same as in CCP4'
},
origin: {
type: 'array',
items: { type: 'number' },
description: 'Origin in fractional coordinates, in axisOrder'
},
dimensions: {
type: 'array',
items: { type: 'number' },
description: 'Dimensions in fractional coordinates, in axisOrder'
},
spacegroup: {
properties: {
number: { type: 'number' },
size: {
type: 'array',
items: { type: 'number' }
},
angles: {
type: 'array',
items: { type: 'number' }
},
isPeriodic: {
type: 'boolean',
description: 'Determine if the data should be treated as periodic or not. (e.g. X-ray = periodic, EM = not periodic)'
},
}
},
channels: {
type: 'array',
items: { type: 'string' }
},
valueType: {
type: 'string',
enum: ['float32', 'int16', 'int8'],
description: 'Determines the data type of the values'
},
blockSize: {
type: 'number',
description: 'The value are stored in blockSize^3 cubes'
},
sampling: {
type: 'array',
items: {
properties: {
byteOffset: { type: 'number' },
rate: {
type: 'number',
description: 'How many values along each axis were collapsed into 1'
},
valuesInfo: {
properties: {
mean: { type: 'number' },
sigma: { type: 'number' },
min: { type: 'number' },
max: { type: 'number' },
}
},
sampleCount: {
type: 'array',
items: { type: 'number' },
description: 'Number of samples along each axis, in axisOrder'
},
}
} }
}
}
},
parameters: {
source: {
name: 'source',
in: 'path',
description: `Specifies the data source (determined by the experiment method). Currently supported sources are: ${sources.join(', ')}.`,
required: true,
schema: {
type: 'string',
enum: sources
},
style: 'simple'
},
id: {
name: 'id',
in: 'path',
description: 'Id of the entry. For x-ray, use PDB ID (i.e. 1cbs) and for em use EMDB id (i.e. emd-8116).',
required: true,
schema: {
type: 'string',
},
style: 'simple'
},
encoding: {
name: 'encoding',
in: 'query',
description: 'Determines if text based CIF or binary BinaryCIF encoding is used. An optional argument, default is BinaryCIF encoding.',
schema: {
type: 'string',
enum: ['cif', 'bcif']
},
style: 'form'
},
detail: {
name: 'detail',
in: 'query',
description: `Determines the maximum number of voxels the query can return. Possible values are in the range from ${detail(0)} to ${detail(detailMax)}. Default value is 0. Note: different detail levels might lead to the same result.`,
schema: {
type: 'integer',
},
style: 'form'
}
}
}
}
}
export const shortcutIconLink = `<link rel='shortcut icon' href='data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAACAAAAAgCAMAAABEpIrGAAAABGdBTUEAALGPC/xhBQAAAAFzUkdCAK7OHOkAAAAnUExURQAAAMIrHrspHr0oH7soILonHrwqH7onILsoHrsoH7soH7woILwpIKgVokoAAAAMdFJOUwAQHzNxWmBHS5XO6jdtAmoAAACZSURBVDjLxZNRCsQgDAVNXmwb9f7nXZEaLRgXloXOhwQdjMYYwpOLw55fBT46KhbOKhmRR2zLcFJQj8UR+HxFgArIF5BKJbEncC6NDEdI5SatBRSDJwGAoiFDONrEJXWYhGMIcRJGCrb1TOtDahfUuQXd10jkFYq0ViIrbUpNcVT6redeC1+b9tH2WLR93Sx2VCzkv/7NjfABxjQHksGB7lAAAAAASUVORK5CYII=' />`