diff --git a/package-lock.json b/package-lock.json
index 763951320022faa79a1de613aa74388c26a6ec04..2d5ba0706c841759e5799a5ea660666943a15eda 100644
Binary files a/package-lock.json and b/package-lock.json differ
diff --git a/package.json b/package.json
index 2ba5f74e9f1abf9992be6e25283dc89d4aead432..b7d259bc66d9259e5ec1ca239f302d163a68bd69 100644
--- a/package.json
+++ b/package.json
@@ -85,6 +85,7 @@
"@types/react": "^16.8.4",
"@types/react-dom": "^16.8.2",
"@types/webgl2": "0.0.4",
+ "@types/swagger-ui-dist": "3.0.0",
"benchmark": "^2.1.4",
"circular-dependency-plugin": "^5.0.2",
"concurrently": "^4.1.0",
@@ -123,6 +124,7 @@
"node-fetch": "^2.3.0",
"react": "^16.8.2",
"react-dom": "^16.8.2",
- "rxjs": "^6.4.0"
+ "rxjs": "^6.4.0",
+ "swagger-ui-dist": "^3.20.9"
}
}
diff --git a/src/servers/common/swagger-ui/index.ts b/src/servers/common/swagger-ui/index.ts
new file mode 100644
index 0000000000000000000000000000000000000000..ae48a4b1c345f8858fb427f3be7a5eeee82417ac
--- /dev/null
+++ b/src/servers/common/swagger-ui/index.ts
@@ -0,0 +1,30 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import * as express from 'express'
+import * as fs from 'fs'
+import { getAbsoluteFSPath } from 'swagger-ui-dist'
+import { ServeStaticOptions } from 'serve-static';
+import { interpolate } from 'mol-util/string';
+
+export function swaggerUiAssetsHandler(options?: ServeStaticOptions) {
+ const opts = options || {}
+ opts.index = false
+ return express.static(getAbsoluteFSPath(), opts)
+}
+
+function createHTML(swaggerUrl: string, apiPrefix: string) {
+ const htmlTemplate = fs.readFileSync(`${__dirname}/indexTemplate.html`).toString()
+ return interpolate(htmlTemplate, { swaggerUrl, apiPrefix })
+}
+
+export function swaggerUiIndexHandler(swaggerUrl: string, apiPrefix: string): express.Handler {
+ const html = createHTML(swaggerUrl, apiPrefix)
+ return (req: express.Request, res: express.Response) => {
+ res.writeHead(200, { 'Content-Type': 'text/html; charset=utf-8' });
+ res.end(html);
+ }
+}
\ No newline at end of file
diff --git a/src/servers/common/swagger-ui/indexTemplate.html b/src/servers/common/swagger-ui/indexTemplate.html
new file mode 100644
index 0000000000000000000000000000000000000000..0f334da2c2270b1df2e2ab8b8ffda388609d444c
--- /dev/null
+++ b/src/servers/common/swagger-ui/indexTemplate.html
@@ -0,0 +1,64 @@
+<!DOCTYPE html>
+<html lang="en">
+ <head>
+ <meta charset="UTF-8">
+ <title>Swagger UI</title>
+ <link rel="stylesheet" type="text/css" href="${apiPrefix}/swagger-ui.css" >
+ <style>
+ html
+ {
+ box-sizing: border-box;
+ overflow: -moz-scrollbars-vertical;
+ overflow-y: scroll;
+ }
+ *,
+ *:before,
+ *:after
+ {
+ box-sizing: inherit;
+ }
+ body
+ {
+ margin:0;
+ background: #fafafa;
+ }
+ </style>
+ </head>
+
+ <body>
+ <div id="swagger-ui"></div>
+
+ <script src="${apiPrefix}/swagger-ui-bundle.js"> </script>
+ <script src="${apiPrefix}/swagger-ui-standalone-preset.js"> </script>
+ <script>
+ function HidePlugin() {
+ // this plugin overrides some components to return nothing
+ return {
+ components: {
+ Topbar: function () { return null },
+ Models: function () { return null },
+ }
+ }
+ }
+ window.onload = function () {
+ var ui = SwaggerUIBundle({
+ url: '${swaggerUrl}',
+ validatorUrl: null,
+ docExpansion: 'list',
+ dom_id: '#swagger-ui',
+ deepLinking: true,
+ presets: [
+ SwaggerUIBundle.presets.apis,
+ SwaggerUIStandalonePreset
+ ],
+ plugins: [
+ SwaggerUIBundle.plugins.DownloadUrl,
+ HidePlugin
+ ],
+ layout: 'StandaloneLayout'
+ })
+ window.ui = ui
+ }
+ </script>
+ </body>
+</html>
\ No newline at end of file
diff --git a/src/servers/volume/common/data-format.ts b/src/servers/volume/common/data-format.ts
index 2f0525475388dd923732969a3f110181ba32d926..e3a51fe8cc89353ca46d4801c975378f64330d91 100644
--- a/src/servers/volume/common/data-format.ts
+++ b/src/servers/volume/common/data-format.ts
@@ -32,7 +32,7 @@ export interface Sampling {
rate: number,
valuesInfo: ValuesInfo[],
- /** Number of samples along each axis, in axisOrder */
+ /** Number of samples along each axis, in axisOrder */
sampleCount: number[]
}
diff --git a/src/servers/volume/server/api.ts b/src/servers/volume/server/api.ts
index 6fa227adf6ded744658c075b3eb43e008d925a54..e3a9c247ab5808dc5a10e5e0a88b7302f0777154 100644
--- a/src/servers/volume/server/api.ts
+++ b/src/servers/volume/server/api.ts
@@ -26,16 +26,21 @@ export function getOutputFilename(source: string, id: string, { asBinary, box, d
return `${n(source)}_${n(id)}-${boxInfo}_${det}.${asBinary ? 'bcif' : 'cif'}`;
}
+export interface ExtendedHeader extends DataFormat.Header {
+ availablePrecisions: { precision: number, maxVoxels: number }[]
+ isAvailable: boolean
+}
+
/** Reads the header and includes information about available detail levels */
-export async function getHeaderJson(filename: string | undefined, sourceId: string) {
+export async function getExtendedHeaderJson(filename: string | undefined, sourceId: string) {
ConsoleLogger.log('Header', sourceId);
try {
if (!filename || !File.exists(filename)) {
ConsoleLogger.error(`Header ${sourceId}`, 'File not found.');
return void 0;
}
- const header = { ...await readHeader(filename, sourceId) } as DataFormat.Header;
- const { sampleCount } = header!.sampling[0];
+ const header: Partial<ExtendedHeader> = { ...await readHeader(filename, sourceId) };
+ const { sampleCount } = header.sampling![0];
const maxVoxelCount = sampleCount[0] * sampleCount[1] * sampleCount[2];
const precisions = LimitsConfig.maxOutputSizeInVoxelCountByPrecisionLevel
.map((maxVoxels, precision) => ({ precision, maxVoxels }));
@@ -44,8 +49,8 @@ export async function getHeaderJson(filename: string | undefined, sourceId: stri
availablePrecisions.push(p);
if (p.maxVoxels > maxVoxelCount) break;
}
- (header as any).availablePrecisions = availablePrecisions;
- (header as any).isAvailable = true;
+ header.availablePrecisions = availablePrecisions;
+ header.isAvailable = true;
return JSON.stringify(header, null, 2);
} catch (e) {
ConsoleLogger.error(`Header ${sourceId}`, e);
diff --git a/src/servers/volume/server/documentation.ts b/src/servers/volume/server/documentation.ts
deleted file mode 100644
index 4713359d9342b46c7ca4cc67e2b6433719422ca2..0000000000000000000000000000000000000000
--- a/src/servers/volume/server/documentation.ts
+++ /dev/null
@@ -1,177 +0,0 @@
-/**
- * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * Taken/adapted from DensityServer (https://github.com/dsehnal/DensityServer)
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-import VERSION from './version'
-import { LimitsConfig } from '../config';
-
-export function getDocumentation() {
- function detail(i: number) {
- return `<span class='id'>${i}</span><small> (${Math.round(100 * LimitsConfig.maxOutputSizeInVoxelCountByPrecisionLevel[i] / 1000 / 1000) / 100 }M voxels)</small>`;
- }
- const detailMax = LimitsConfig.maxOutputSizeInVoxelCountByPrecisionLevel.length - 1;
-
- // TODO get from config
- const dataSource = `Specifies the data source (determined by the experiment method). Currently, <span class='id'>x-ray</span> and <span class='id'>em</span> sources are supported.`;
- const entryId = `Id of the entry. For <span class='id'>x-ray</span>, use PDB ID (i.e. <span class='id'>1cbs</span>) and for <span class='id'>em</span> use EMDB id (i.e. <span class='id'>emd-8116</span>).`;
-
- return `<!DOCTYPE html>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<meta charset="utf-8" />
-<link rel='shortcut icon' href='data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAACAAAAAgCAMAAABEpIrGAAAABGdBTUEAALGPC/xhBQAAAAFzUkdCAK7OHOkAAAAnUExURQAAAMIrHrspHr0oH7soILonHrwqH7onILsoHrsoH7soH7woILwpIKgVokoAAAAMdFJOUwAQHzNxWmBHS5XO6jdtAmoAAACZSURBVDjLxZNRCsQgDAVNXmwb9f7nXZEaLRgXloXOhwQdjMYYwpOLw55fBT46KhbOKhmRR2zLcFJQj8UR+HxFgArIF5BKJbEncC6NDEdI5SatBRSDJwGAoiFDONrEJXWYhGMIcRJGCrb1TOtDahfUuQXd10jkFYq0ViIrbUpNcVT6redeC1+b9tH2WLR93Sx2VCzkv/7NjfABxjQHksGB7lAAAAAASUVORK5CYII=' />
-<title>VolumeServer (${VERSION})</title>
-<style>
-html { -ms-text-size-adjust: 100%; -webkit-text-size-adjust: 100%; }
-body { margin: 0; font-family: "Helvetica Neue",Helvetica,Arial,sans-serif; font-weight: 300; color: #333; line-height: 1.42857143; font-size: 14px }
-.container { padding: 0 15px; max-width: 970px; margin: 0 auto; }
-small { font-size: 80% }
-h2, h4 { font-weight: 500; line-height: 1.1; }
-h2 { color: black; font-size: 24px; }
-h4 { font-size: 18px; margin: 20px 0 10px 0 }
-h2 small { color: #777; font-weight: 300 }
-hr { box-sizing: content-box; height: 0; overflow: visible; }
-a { background-color: transparent; -webkit-text-decoration-skip: objects; text-decoration: none }
-a:active, a:hover { outline-width: 0; }
-a:focus, a:hover { text-decoration: underline; color: #23527c }
-.list-unstyled { padding: 0; list-style: none; margin: 0 0 10px 0 }
-.cs-docs-query-wrap { padding: 24px 0; border-bottom: 1px solid #eee }
-.cs-docs-query-wrap > h2 { margin: 0; color: black; }
-.cs-docs-query-wrap > h2 > span { color: #DE4D4E; font-family: Menlo,Monaco,Consolas,"Courier New",monospace; font-size: 90% }
-.cs-docs-param-name, .cs-docs-template-link { color: #DE4D4E; font-family: Menlo,Monaco,Consolas,"Courier New",monospace }
-table {margin: 0; padding: 0; }
-table th { font-weight: bold; border-bottom: none; text-align: left; padding: 6px 12px }
-td { padding: 6px 12px }
-td:not(:last-child), th:not(:last-child) { border-right: 1px dotted #ccc }
-tr:nth-child(even) { background: #f9f9f9 }
-span.id { color: #DE4D4E; font-family: Menlo,Monaco,Consolas,"Courier New",monospace; }
-</style>
-</head>
-<body>
-<div class="container">
-<div style='text-align: center; margin-top: 24px;'><span style='font-weight: bold; font-size: 16pt'>VolumeServer</span> <span>${VERSION}</span></div>
-
-<div style='text-align: justify; padding: 24px 0; border-bottom: 1px solid #eee'>
- <p>
- <b>VolumeServer</b> is a service for accessing subsets of volumetric density data. It automatically downsamples the data
- depending on the volume of the requested region to reduce the bandwidth requirements and provide near-instant access to even the
- largest data sets.
- </p>
- <p>
- It uses the text based <a href='https://en.wikipedia.org/wiki/Crystallographic_Information_File'>CIF</a> and binary
- <a href='https://github.com/dsehnal/BinaryCIF' style='font-weight: bold'>BinaryCIF</a>
- formats to deliver the data to the client.
- The server support is integrated into the <a href='https://github.com/dsehnal/LiteMol' style='font-weight: bold'>LiteMol Viewer</a>.
- </p>
-</div>
-
-<div class="cs-docs-query-wrap">
- <h2>Data Header / Check Availability <span>/<source>/<id></span><br>
- <small>Returns a JSON response specifying if data is available and the maximum region that can be queried.</small></h2>
- <div id="coordserver-documentation-ambientResidues-body" style="margin: 24px 24px 0 24px">
- <h4>Examples</h4>
- <a href="/VolumeServer/x-ray/1cbs" class="cs-docs-template-link" target="_blank" rel="nofollow">/x-ray/1cbs</a><br>
- <a href="/VolumeServer/em/emd-8116" class="cs-docs-template-link" target="_blank" rel="nofollow">/em/emd-8116</a>
- <h4>Parameters</h4>
- <table cellpadding="0" cellspacing="0" style='width: 100%'>
- <tbody><tr><th style='width: 80px'>Name</th><th>Description</th></tr>
- <tr>
- <td class="cs-docs-param-name">source</td>
- <td>${dataSource}</td>
- </tr>
- <tr>
- <td class="cs-docs-param-name">id</td>
- <td>${entryId}</td>
- </tr>
- </tbody></table>
- </div>
-</div>
-
-<div class="cs-docs-query-wrap">
- <h2>Box <span>/<source>/<id>/box/<a,b,c>/<u,v,w>?<optional parameters></span><br>
- <small>Returns density data inside the specified box for the given entry. For X-ray data, returns 2Fo-Fc and Fo-Fc volumes in a single response.</small></h2>
- <div style="margin: 24px 24px 0 24px">
- <h4>Examples</h4>
- <a href="/VolumeServer/em/emd-8003/box/-2,7,10/4,10,15.5?encoding=cif&space=cartesian" class="cs-docs-template-link" target="_blank" rel="nofollow">/em/emd-8003/box/-2,7,10/4,10,15.5?excoding=cif&space=cartesian</a><br>
- <a href="/VolumeServer/x-ray/1cbs/box/0.1,0.1,0.1/0.23,0.31,0.18?space=fractional" class="cs-docs-template-link" target="_blank" rel="nofollow">/x-ray/1cbs/box/0.1,0.1,0.1/0.23,0.31,0.18?space=fractional</a>
- <h4>Parameters</h4>
- <table cellpadding="0" cellspacing="0" style='width: 100%'>
- <tbody><tr><th style='width: 80px'>Name</th><th>Description</th></tr>
- <tr>
- <td class="cs-docs-param-name">source</td>
- <td>${dataSource}</td>
- </tr>
- <tr>
- <td class="cs-docs-param-name">id</td>
- <td>${entryId}</td>
- </tr>
- <tr>
- <td class="cs-docs-param-name">a,b,c</td>
- <td>Bottom left corner of the query region in Cartesian or fractional coordinates (determined by the <span class='id'>&space</span> query parameter).</td>
- </tr>
- <tr>
- <td class="cs-docs-param-name">u,v,w</td>
- <td>Top right corner of the query region in Cartesian or fractional coordinates (determined by the <span class='id'>&space</span> query parameter).</td>
- </tr>
- <tr>
- <td class="cs-docs-param-name">encoding</td>
- <td>Determines if text based <span class='id'>CIF</span> or binary <span class='id'>BinaryCIF</span> encoding is used. An optional argument, default is <span class='id'>BinaryCIF</span> encoding.</td>
- </tr>
- <tr>
- <td class="cs-docs-param-name">space</td>
- <td>Determines the coordinate space the query is in. Can be <span class='id'>cartesian</span> or <span class='id'>fractional</span>. An optional argument, default values is <span class='id'>cartesian</span>.</td>
- </tr>
- <tr>
- <td class="cs-docs-param-name">detail</td>
- <td>
- Determines the maximum number of voxels the query can return. Possible values are in the range from ${detail(0)} to ${detail(detailMax)}.
- Default value is <span class='id'>0</span>. Note: different detail levels might lead to the same result.
- </td>
- </tr>
- </tbody></table>
- </div>
-</div>
-
-<div class="cs-docs-query-wrap">
- <h2>Cell <span>/<source>/<id>/cell?<optional parameters></span><br>
- <small>Returns (downsampled) volume data for the entire "data cell". For X-ray data, returns unit cell of 2Fo-Fc and Fo-Fc volumes, for EM data returns everything.</small></h2>
- <div style="margin: 24px 24px 0 24px">
- <h4>Example</h4>
- <a href="/VolumeServer/em/emd-8116/cell?detail=1" class="cs-docs-template-link" target="_blank" rel="nofollow">/em/emd-8116/cell?detail=1</a><br>
- <h4>Parameters</h4>
- <table cellpadding="0" cellspacing="0" style='width: 100%'>
- <tbody><tr><th style='width: 80px'>Name</th><th>Description</th></tr>
- <tr>
- <td class="cs-docs-param-name">source</td>
- <td>${dataSource}</td>
- </tr>
- <tr>
- <td class="cs-docs-param-name">id</td>
- <td>${entryId}</td>
- </tr>
- <tr>
- <td class="cs-docs-param-name">encoding</td>
- <td>Determines if text based <span class='id'>CIF</span> or binary <span class='id'>BinaryCIF</span> encoding is used. An optional argument, default is <span class='id'>BinaryCIF</span> encoding.</td>
- </tr>
- <tr>
- <td class="cs-docs-param-name">detail</td>
- <td>
- 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 <span class='id'>0</span>. Note: different detail levels might lead to the same result.
- </td>
- </tr>
- </tbody></table>
- </div>
-</div>
-
-
-<div style="color: #999;font-size:smaller;margin: 20px 0; text-align: right">© 2016 – now, David Sehnal | Node ${process.version}</div>
-
-</body>
-</html>`;
-}
\ No newline at end of file
diff --git a/src/servers/volume/server/web-api.ts b/src/servers/volume/server/web-api.ts
index 0b9dbc1d0f93c7a5cf3ac572f269123725e07b6f..4ac65fcf96ca40ad9b12eb5f8209e692acbebb6b 100644
--- a/src/servers/volume/server/web-api.ts
+++ b/src/servers/volume/server/web-api.ts
@@ -10,19 +10,19 @@
import * as express from 'express'
import * as Api from './api'
-
import * as Data from './query/data-model'
import * as Coords from './algebra/coordinate'
-import { getDocumentation } from './documentation'
import { ConsoleLogger } from 'mol-util/console-logger'
import { State } from './state'
import { LimitsConfig, ServerConfig } from '../config';
import { interpolate } from 'mol-util/string';
+import { getSchema } from './web-schema';
+import { swaggerUiIndexHandler, swaggerUiAssetsHandler } from 'servers/common/swagger-ui';
export default function init(app: express.Express) {
app.locals.mapFile = getMapFileFn()
function makePath(p: string) {
- return ServerConfig.apiPrefix + '/' + p;
+ return `${ServerConfig.apiPrefix}/${p}`;
}
// Header
@@ -32,10 +32,17 @@ export default function init(app: express.Express) {
// Cell /:src/:id/cell/?text=0|1&space=cartesian|fractional
app.get(makePath(':source/:id/cell/?'), (req, res) => queryBox(req, res, getQueryParams(req, true)));
- app.get('*', (req, res) => {
- res.writeHead(200, { 'Content-Type': 'text/html; charset=utf-8' });
- res.end(getDocumentation());
+ app.get(makePath('openapi.json'), (req, res) => {
+ res.writeHead(200, {
+ 'Content-Type': 'application/json; charset=utf-8',
+ 'Access-Control-Allow-Origin': '*',
+ 'Access-Control-Allow-Headers': 'X-Requested-With'
+ });
+ res.end(JSON.stringify(getSchema()));
});
+
+ app.use(makePath(''), swaggerUiAssetsHandler());
+ app.get(makePath(''), swaggerUiIndexHandler(makePath('openapi.json'), ServerConfig.apiPrefix));
}
function getMapFileFn() {
@@ -115,7 +122,7 @@ async function getHeader(req: express.Request, res: express.Response) {
try {
const { filename, id } = getSourceInfo(req);
- const header = await Api.getHeaderJson(filename, id);
+ const header = await Api.getExtendedHeaderJson(filename, id);
if (!header) {
res.writeHead(404);
return;
diff --git a/src/servers/volume/server/web-schema.ts b/src/servers/volume/server/web-schema.ts
new file mode 100644
index 0000000000000000000000000000000000000000..e24eb39a4ce8252aa6995ca4f0b6da4b532a0a46
--- /dev/null
+++ b/src/servers/volume/server/web-schema.ts
@@ -0,0 +1,259 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import VERSION from './version'
+import { LimitsConfig, ServerConfig } from '../config';
+
+export function getSchema() {
+ function detail(i: number) {
+ return `${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'
+ }
+ }
+ }
+ }
+}