diff --git a/data/rcsb-graphql/codegen.js b/data/rcsb-graphql/codegen.js
index 8982097ff6726ed4918d5547ac4b0cd40d9b34e8..1abc6b4f93e93c94235395dd748bd396c945a641 100644
--- a/data/rcsb-graphql/codegen.js
+++ b/data/rcsb-graphql/codegen.js
@@ -5,17 +5,16 @@ const basePath = path.join(__dirname, '..', '..', 'src', 'mol-model-props', 'rcs
generate({
schema: 'http://rest-dev.rcsb.org/graphql',
- documents: [
- path.join(basePath, 'symmetry.gql.ts')
- ],
+ documents: {
+ [path.join(basePath, 'symmetry.gql.ts')]: {
+ loader: path.join(__dirname, 'loader.js')
+ },
+ },
generates: {
[path.join(basePath, 'types.ts')]: {
plugins: ['time', 'typescript-common', 'typescript-client']
}
},
- // template: 'graphql-codegen-typescript-template',
- // out: path.join(basePath),
- // skipSchema: true,
overwrite: true,
config: path.join(__dirname, 'codegen.json')
}, true).then(
diff --git a/data/rcsb-graphql/loader.js b/data/rcsb-graphql/loader.js
new file mode 100644
index 0000000000000000000000000000000000000000..73e76e1c421b88367f334b95621e53710fe5d153
--- /dev/null
+++ b/data/rcsb-graphql/loader.js
@@ -0,0 +1,14 @@
+const { parse } = require('graphql');
+const { readFileSync } = require('fs');
+
+module.exports = function(docString, config) {
+ const str = readFileSync(docString, { encoding: 'utf-8' }).trim()
+ .replace(/^export default `/, '')
+ .replace(/`$/, '')
+ return [
+ {
+ filePath: docString,
+ content: parse(str)
+ }
+ ];
+};
\ No newline at end of file
diff --git a/package-lock.json b/package-lock.json
index 763951320022faa79a1de613aa74388c26a6ec04..4444de29a715c5abccb6351afde6e97dd2a96c96 100644
Binary files a/package-lock.json and b/package-lock.json differ
diff --git a/package.json b/package.json
index 2ba5f74e9f1abf9992be6e25283dc89d4aead432..5979a94a62bc4ef84e451c5d8914817c16a7ff89 100644
--- a/package.json
+++ b/package.json
@@ -75,16 +75,17 @@
"author": "",
"license": "MIT",
"devDependencies": {
- "@types/argparse": "^1.0.35",
+ "@types/argparse": "^1.0.36",
"@types/benchmark": "^1.0.31",
"@types/compression": "0.0.36",
"@types/express": "^4.16.1",
- "@types/jest": "^24.0.6",
- "@types/node": "^11.9.4",
+ "@types/jest": "^24.0.9",
+ "@types/node": "^11.9.6",
"@types/node-fetch": "^2.1.6",
- "@types/react": "^16.8.4",
+ "@types/react": "^16.8.6",
"@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",
@@ -95,9 +96,9 @@
"glslify": "^7.0.0",
"glslify-import": "^3.1.0",
"glslify-loader": "^2.0.0",
- "graphql-code-generator": "^0.16.1",
- "graphql-codegen-time": "^0.16.1",
- "graphql-codegen-typescript-template": "^0.16.1",
+ "graphql-code-generator": "^0.18.0",
+ "graphql-codegen-time": "^0.18.0",
+ "graphql-codegen-typescript-template": "^0.18.0",
"jest": "^24.1.0",
"jest-raw-loader": "^1.0.1",
"mini-css-extract-plugin": "^0.5.0",
@@ -107,11 +108,11 @@
"sass-loader": "^7.1.0",
"style-loader": "^0.23.1",
"ts-jest": "^24.0.0",
- "tslint": "^5.12.1",
+ "tslint": "^5.13.1",
"typescript": "^3.3.3",
"uglify-js": "^3.4.9",
"util.promisify": "^1.0.0",
- "webpack": "^4.29.5",
+ "webpack": "^4.29.6",
"webpack-cli": "^3.2.3"
},
"dependencies": {
@@ -121,8 +122,9 @@
"graphql": "^14.1.1",
"immutable": "^3.8.2",
"node-fetch": "^2.3.0",
- "react": "^16.8.2",
- "react-dom": "^16.8.2",
- "rxjs": "^6.4.0"
+ "react": "^16.8.3",
+ "react-dom": "^16.8.3",
+ "rxjs": "^6.4.0",
+ "swagger-ui-dist": "^3.20.9"
}
}
diff --git a/src/mol-io/reader/cif/schema/bird.ts b/src/mol-io/reader/cif/schema/bird.ts
index b525c0e6a49e20c5566a6e9a50fb64a93582f402..d8687247fa51c82a8d4ba95f85db40a5b92f7ca8 100644
--- a/src/mol-io/reader/cif/schema/bird.ts
+++ b/src/mol-io/reader/cif/schema/bird.ts
@@ -1,7 +1,7 @@
/**
* Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
- * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.304, IHM 0.139, CARB draft.
+ * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.305, IHM 0.139, CARB draft.
*
* @author mol-star package (src/apps/schema-generator/generate)
*/
diff --git a/src/mol-io/reader/cif/schema/ccd.ts b/src/mol-io/reader/cif/schema/ccd.ts
index e81dc33d1fb16e7128835722789802565748cfba..d053c6e1160b3034cd2c5328ccbea1fec2a2f27c 100644
--- a/src/mol-io/reader/cif/schema/ccd.ts
+++ b/src/mol-io/reader/cif/schema/ccd.ts
@@ -1,7 +1,7 @@
/**
* Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
- * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.304, IHM 0.139, CARB draft.
+ * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.305, IHM 0.139, CARB draft.
*
* @author mol-star package (src/apps/schema-generator/generate)
*/
diff --git a/src/mol-io/reader/cif/schema/mmcif.ts b/src/mol-io/reader/cif/schema/mmcif.ts
index 55e21efb5e009a557dddc44fccf0b7a250d01d5b..4da0f48ed23c3b4711710280254c10cf11117726 100644
--- a/src/mol-io/reader/cif/schema/mmcif.ts
+++ b/src/mol-io/reader/cif/schema/mmcif.ts
@@ -1,7 +1,7 @@
/**
* Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
- * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.304, IHM 0.139, CARB draft.
+ * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.305, IHM 0.139, CARB draft.
*
* @author mol-star package (src/apps/schema-generator/generate)
*/
@@ -850,7 +850,7 @@ export const mmCIF_Schema = {
* This data item is a pointer to _struct_conn_type.id in the
* STRUCT_CONN_TYPE category.
*/
- conn_type_id: Aliased<'covale' | 'disulf' | 'hydrog' | 'metalc' | 'mismat' | 'saltbr' | 'modres' | 'covale_base' | 'covale_sugar' | 'covale_phosphate'>(str),
+ conn_type_id: Aliased<'covale' | 'disulf' | 'metalc' | 'hydrog'>(str),
/**
* A description of special aspects of the connection.
*/
diff --git a/src/mol-model-formats/structure/mmcif/bonds/struct_conn.ts b/src/mol-model-formats/structure/mmcif/bonds/struct_conn.ts
index 21a5b9e57f6b076c6b7184738dee962ecd58164d..91c819e5a3b918e854029231df48cea4e3619fad 100644
--- a/src/mol-model-formats/structure/mmcif/bonds/struct_conn.ts
+++ b/src/mol-model-formats/structure/mmcif/bonds/struct_conn.ts
@@ -138,8 +138,6 @@ export namespace StructConn {
partners: { residueIndex: ResidueIndex, atomIndex: ElementIndex, symmetry: string }[]
}
- type StructConnType = typeof mmCIF_Schema.struct_conn.conn_type_id.T
-
export function attachFromMmCif(model: Model): boolean {
if (model.customProperties.has(Descriptor)) return true;
if (model.sourceData.kind !== 'mmCIF') return false;
@@ -213,7 +211,7 @@ export namespace StructConn {
const partners = _ps(i);
if (partners.length < 2) continue;
- const type = conn_type_id.value(i)! as StructConnType;
+ const type = conn_type_id.value(i) as typeof mmCIF_Schema.struct_conn_type.id.T; // TODO workaround for dictionary inconsistency
const orderType = (pdbx_value_order.value(i) || '').toLowerCase();
let flags = LinkType.Flag.None;
let order = 1;
@@ -234,7 +232,10 @@ export namespace StructConn {
flags = LinkType.Flag.Covalent;
break;
case 'disulf': flags = LinkType.Flag.Covalent | LinkType.Flag.Sulfide; break;
- case 'hydrog': flags = LinkType.Flag.Hydrogen; break;
+ case 'hydrog':
+ case 'mismat':
+ flags = LinkType.Flag.Hydrogen;
+ break;
case 'metalc': flags = LinkType.Flag.MetallicCoordination; break;
case 'saltbr': flags = LinkType.Flag.Ionic; break;
}
diff --git a/src/mol-model-props/rcsb/graphql/symmetry.gql.ts b/src/mol-model-props/rcsb/graphql/symmetry.gql.ts
index 1bdbbb60756bc1f470e55b2349a88ef544ebaa4c..87aec81b1deb5af462a61f845a57b474342a50f8 100644
--- a/src/mol-model-props/rcsb/graphql/symmetry.gql.ts
+++ b/src/mol-model-props/rcsb/graphql/symmetry.gql.ts
@@ -1,8 +1,4 @@
- // workaround so the query gets found by the codegen
-function gql (strs: TemplateStringsArray) { return strs.raw.join('') }
-
-export default
-gql`query AssemblySymmetry($pdbId: String!) {
+export default `query AssemblySymmetry($pdbId: String!) {
assemblies(pdbId: $pdbId) {
pdbx_struct_assembly {
id
diff --git a/src/mol-model-props/rcsb/graphql/types.ts b/src/mol-model-props/rcsb/graphql/types.ts
index cd4f277f4488f9383bbdc72f251907162371cf33..fc3e89fbf2463ac3c5746528728fa3b67614c76a 100644
--- a/src/mol-model-props/rcsb/graphql/types.ts
+++ b/src/mol-model-props/rcsb/graphql/types.ts
@@ -1,4 +1,4 @@
-// Generated in 2019-01-30T16:38:09-08:00
+// Generated in 2019-03-01T14:48:33-08:00
export type Maybe<T> = T | null;
/** Built-in scalar representing an instant in time */
diff --git a/src/mol-util/string.ts b/src/mol-util/string.ts
index 9e33986c6bf8f4c11fc773cb6e068df977b9dbaf..62ebf10cf0c16383d93237f2e008d1d1fb48bf5a 100644
--- a/src/mol-util/string.ts
+++ b/src/mol-util/string.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
@@ -46,4 +46,10 @@ export function substringStartsWith(str: string, start: number, end: number, tar
if (str.charCodeAt(start + i) !== target.charCodeAt(i)) return false;
}
return true;
+}
+
+export function interpolate(str: string, params: { [k: string]: any }) {
+ const names = Object.keys(params);
+ const values = Object.values(params);
+ return new Function(...names, `return \`${str}\`;`)(...values);
}
\ No newline at end of file
diff --git a/src/servers/common/swagger-ui/index.ts b/src/servers/common/swagger-ui/index.ts
new file mode 100644
index 0000000000000000000000000000000000000000..fadda6560e2a9977b850669dbe94a51f84978b0b
--- /dev/null
+++ b/src/servers/common/swagger-ui/index.ts
@@ -0,0 +1,37 @@
+/**
+ * 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)
+}
+
+export interface SwaggerUIOptions {
+ openapiJsonUrl: string
+ apiPrefix: string
+ title: string
+ shortcutIconLink: string
+}
+
+function createHTML(options: SwaggerUIOptions) {
+ const htmlTemplate = fs.readFileSync(`${__dirname}/indexTemplate.html`).toString()
+ return interpolate(htmlTemplate, options)
+}
+
+export function swaggerUiIndexHandler(options: SwaggerUIOptions): express.Handler {
+ const html = createHTML(options)
+ return (req: express.Request, res: express.Response) => {
+ res.writeHead(200, { 'Content-Type': 'text/html; charset=utf-8' });
+ res.end(html);
+ }
+}
\ No newline at end of file
diff --git a/src/servers/common/swagger-ui/indexTemplate.html b/src/servers/common/swagger-ui/indexTemplate.html
new file mode 100644
index 0000000000000000000000000000000000000000..92869e8c5713a1f663fccefd9484562096cae5b1
--- /dev/null
+++ b/src/servers/common/swagger-ui/indexTemplate.html
@@ -0,0 +1,66 @@
+<!DOCTYPE html>
+<html lang="en">
+ <head>
+ <meta charset="UTF-8">
+ <title>${title}</title>
+ <link rel="stylesheet" type="text/css" href="${apiPrefix}/swagger-ui.css" >
+ ${shortcutIconLink}
+
+ <style>
+ html
+ {
+ box-sizing: border-box;
+ overflow: -moz-scrollbars-vertical;
+ overflow-y: scroll;
+ }
+ *,
+ *:before,
+ *:after
+ {
+ box-sizing: inherit;
+ }
+ body
+ {
+ margin:0;
+ background: #fafafa;
+ }
+ </style>
+ </head>
+
+ <body>
+ <div id="swagger-ui"></div>
+
+ <script src="${apiPrefix}/swagger-ui-bundle.js"> </script>
+ <script src="${apiPrefix}/swagger-ui-standalone-preset.js"> </script>
+ <script>
+ function HidePlugin() {
+ // this plugin overrides some components to return nothing
+ return {
+ components: {
+ Topbar: function () { return null },
+ Models: function () { return null },
+ }
+ }
+ }
+ window.onload = function () {
+ var ui = SwaggerUIBundle({
+ url: '${openapiJsonUrl}',
+ 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/config.ts b/src/servers/volume/config.ts
new file mode 100644
index 0000000000000000000000000000000000000000..236c1c7ba32beead71a5d9e7cf49e1eeb394fa42
--- /dev/null
+++ b/src/servers/volume/config.ts
@@ -0,0 +1,107 @@
+/**
+ * Copyright (c) 2019 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 * as argparse from 'argparse'
+
+export function addLimitsArgs(parser: argparse.ArgumentParser) {
+ parser.addArgument([ '--maxRequestBlockCount' ], {
+ defaultValue: DefaultLimitsConfig.maxRequestBlockCount,
+ metavar: 'COUNT',
+ help: `Maximum number of blocks that could be read in 1 query.
+This is somewhat tied to the maxOutputSizeInVoxelCountByPrecisionLevel
+in that the <maximum number of voxel> = maxRequestBlockCount * <block size>^3.
+The default block size is 96 which corresponds to 28,311,552 voxels with 32 max blocks.`
+ });
+ parser.addArgument([ '--maxFractionalBoxVolume' ], {
+ defaultValue: DefaultLimitsConfig.maxFractionalBoxVolume,
+ metavar: 'VOLUME',
+ help: `The maximum fractional volume of the query box (to prevent queries that are too big).`
+ });
+ parser.addArgument([ '--maxOutputSizeInVoxelCountByPrecisionLevel' ], {
+ nargs: '+',
+ defaultValue: DefaultLimitsConfig.maxOutputSizeInVoxelCountByPrecisionLevel,
+ metavar: 'LEVEL',
+ help: `What is the (approximate) maximum desired size in voxel count by precision level
+Rule of thumb: <response gzipped size> in [<voxel count> / 8, <voxel count> / 4].
+The maximum number of voxels is tied to maxRequestBlockCount.`
+ });
+}
+
+export function addServerArgs(parser: argparse.ArgumentParser) {
+ parser.addArgument([ '--apiPrefix' ], {
+ defaultValue: DefaultServerConfig.apiPrefix,
+ metavar: 'PREFIX',
+ help: `Specify the prefix of the API, i.e. <host>/<apiPrefix>/<API queries>`
+ });
+ parser.addArgument([ '--defaultPort' ], {
+ defaultValue: DefaultServerConfig.defaultPort,
+ metavar: 'PORT',
+ help: `Specify the prefix of the API, i.e. <host>/<apiPrefix>/<API queries>`
+ });
+
+ parser.addArgument([ '--shutdownTimeoutMinutes' ], {
+ defaultValue: DefaultServerConfig.shutdownTimeoutMinutes,
+ metavar: 'TIME',
+ help: `0 for off, server will shut down after this amount of minutes.`
+ });
+ parser.addArgument([ '--shutdownTimeoutVarianceMinutes' ], {
+ defaultValue: DefaultServerConfig.shutdownTimeoutVarianceMinutes,
+ metavar: 'VARIANCE',
+ help: `modifies the shutdown timer by +/- timeoutVarianceMinutes (to avoid multiple instances shutting at the same time)`
+ });
+ parser.addArgument([ '--idMap' ], {
+ nargs: 2,
+ action: 'append',
+ metavar: ['TYPE', 'PATH'] as any,
+ help: [
+ 'Map `id`s for a `type` to a file path.',
+ 'Example: x-ray \'../../data/mdb/xray/${id}-ccp4.mdb\'',
+ 'Note: Can be specified multiple times.'
+ ].join('\n'),
+ });
+}
+
+const DefaultServerConfig = {
+ apiPrefix: '/VolumeServer',
+ defaultPort: 1337,
+ shutdownTimeoutMinutes: 24 * 60, /* a day */
+ shutdownTimeoutVarianceMinutes: 60,
+ idMap: [] as [string, string][]
+}
+export type ServerConfig = typeof DefaultServerConfig
+export const ServerConfig = { ...DefaultServerConfig }
+export function setServerConfig(config: ServerConfig) {
+ for (const name in DefaultServerConfig) {
+ ServerConfig[name as keyof ServerConfig] = config[name as keyof ServerConfig]
+ }
+}
+
+const DefaultLimitsConfig = {
+ maxRequestBlockCount: 32,
+ maxFractionalBoxVolume: 1024,
+ maxOutputSizeInVoxelCountByPrecisionLevel: [
+ 0.5 * 1024 * 1024, // ~ 80*80*80
+ 1 * 1024 * 1024,
+ 2 * 1024 * 1024,
+ 4 * 1024 * 1024,
+ 8 * 1024 * 1024,
+ 16 * 1024 * 1024, // ~ 256*256*256
+ 24 * 1024 * 1024
+ ]
+}
+export type LimitsConfig = typeof DefaultLimitsConfig
+export const LimitsConfig = { ...DefaultLimitsConfig }
+export function setLimitsConfig(config: LimitsConfig) {
+ for (const name in DefaultLimitsConfig) {
+ LimitsConfig[name as keyof LimitsConfig] = config[name as keyof LimitsConfig]
+ }
+}
+
+export function setConfig(config: ServerConfig & LimitsConfig) {
+ setServerConfig(config)
+ setLimitsConfig(config)
+}
\ No newline at end of file
diff --git a/src/servers/volume/local.ts b/src/servers/volume/local.ts
index 45e379769edf45f3c8d9c303b2d6847010f2d17d..99993cfbcfa10612463f83325ff959db7cd93f43 100644
--- a/src/servers/volume/local.ts
+++ b/src/servers/volume/local.ts
@@ -1,17 +1,19 @@
/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * 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 * as argparse from 'argparse'
import * as LocalApi from './server/local-api'
import VERSION from './server/version'
-
import * as fs from 'fs'
+import { LimitsConfig, addLimitsArgs, setLimitsConfig } from './config';
-console.log(`VolumeServer ${VERSION}, (c) 2016 - now, David Sehnal`);
+console.log(`VolumeServer Local ${VERSION}, (c) 2018-2019, Mol* contributors`);
console.log();
function help() {
@@ -48,21 +50,25 @@ function help() {
outputFolder: 'g:/test/local-test'
}];
- console.log('Usage: node local jobs.json');
- console.log();
- console.log('Example jobs.json:');
- console.log(JSON.stringify(exampleJobs, null, 2));
+ return `Usage: node local jobs.json\n\nExample jobs.json: ${JSON.stringify(exampleJobs, null, 2)}`
}
-async function run() {
- if (process.argv.length !== 3) {
- help();
- return;
- }
+const parser = new argparse.ArgumentParser({
+ addHelp: true,
+ description: help()
+});
+addLimitsArgs(parser)
+parser.addArgument(['jobs'], {
+ help: `Path to jobs JSON file.`
+})
+
+const config: LimitsConfig & { jobs: string } = parser.parseArgs()
+setLimitsConfig(config) // sets the config for global use
+async function run() {
let jobs: LocalApi.JobEntry[];
try {
- jobs = JSON.parse(fs.readFileSync(process.argv[2], 'utf-8'));
+ jobs = JSON.parse(fs.readFileSync(config.jobs, 'utf-8'));
} catch (e) {
console.log('Error:');
console.error(e);
diff --git a/src/servers/volume/pack.ts b/src/servers/volume/pack.ts
index ebf43fb45e103a4cfaceb59c0fb24271353f275b..b00d95c5e22b5eab39125e90eb1b1ba0796ea4a0 100644
--- a/src/servers/volume/pack.ts
+++ b/src/servers/volume/pack.ts
@@ -1,106 +1,92 @@
/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * 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 * as argparse from 'argparse'
import pack from './pack/main'
import VERSION from './pack/version'
+type FileFormat = 'ccp4' | 'dsn6'
+
interface Config {
input: { name: string, filename: string }[],
- format: 'ccp4' | 'dsn6',
+ format: FileFormat,
isPeriodic: boolean,
outputFilename: string,
blockSizeInMB: number
}
-let config: Config = {
- input: [],
- format: 'ccp4',
- isPeriodic: false,
- outputFilename: '',
- blockSizeInMB: 96
-};
-
-function getFormat(format: string): Config['format'] {
- switch (format.toLowerCase()) {
- case 'ccp4': return 'ccp4'
- case 'dsn6': return 'dsn6'
+function getConfig(args: Args) {
+ const config: Partial<Config> = {
+ blockSizeInMB: args.blockSizeInMB,
+ format: args.format,
+ outputFilename: args.output
+ }
+ switch (args.mode) {
+ case 'em':
+ config.input = [
+ { name: 'em', filename: args.inputEm }
+ ];
+ config.isPeriodic = false;
+ break
+ case 'xray':
+ config.input = [
+ { name: '2Fo-Fc', filename: args.input2fofc },
+ { name: 'Fo-Fc', filename: args.inputFofc }
+ ];
+ config.isPeriodic = true;
+ break
}
- throw new Error(`unsupported format '${format}'`)
+ return config as Config
}
-function printHelp() {
- let help = [
- `VolumeServer Packer ${VERSION}, (c) 2016 - now, David Sehnal`,
- ``,
- `The input data must be CCP4/MAP mode 2 (32-bit floats) files.`,
- ``,
- `Usage: `,
- ``,
- ` node pack -v`,
- ` Print version.`,
- ``,
- ` node pack -xray main.ccp4 diff.ccp4 output.mdb [-blockSize 96]`,
- ` Pack main and diff density into a single block file.`,
- ` Optionally specify maximum block size.`,
- ``,
- ` node pack -em density.map output.mdb [-blockSize 96]`,
- ` Pack single density into a block file.`,
- ` Optionally specify maximum block size.`
- ];
- console.log(help.join('\n'));
+interface GeneralArgs {
+ blockSizeInMB: number
+ format: FileFormat
+ output: string
+}
+interface XrayArgs extends GeneralArgs {
+ mode: 'xray'
+ input2fofc: string
+ inputFofc: string
+}
+interface EmArgs extends GeneralArgs {
+ mode: 'em'
+ inputEm: string
}
+type Args = XrayArgs | EmArgs
-function parseInput() {
- let input = false;
+const parser = new argparse.ArgumentParser({
+ addHelp: true,
+ description: `VolumeServer Packer ${VERSION}, (c) 2018-2019, Mol* contributors`
+});
- if (process.argv.length <= 2) {
- printHelp();
- process.exit();
- return false;
- }
+const subparsers = parser.addSubparsers({
+ title: 'Packing modes',
+ dest: 'mode'
+});
- for (let i = 2; i < process.argv.length; i++) {
- switch (process.argv[i].toLowerCase()) {
- case '-blocksize':
- config.blockSizeInMB = +process.argv[++i];
- break;
- case '-format':
- config.format = getFormat(process.argv[++i]);
- break;
- case '-xray':
- input = true;
- config.input = [
- { name: '2Fo-Fc', filename: process.argv[++i] },
- { name: 'Fo-Fc', filename: process.argv[++i] }
- ];
- config.isPeriodic = true;
- config.outputFilename = process.argv[++i];
- break;
- case '-em':
- input = true;
- config.input = [
- { name: 'em', filename: process.argv[++i] }
- ];
- config.outputFilename = process.argv[++i];
- break;
- case '-v':
- console.log(VERSION);
- process.exit();
- return false;
- default:
- printHelp();
- process.exit();
- return false;
- }
- }
- return input;
+function addGeneralArgs(parser: argparse.ArgumentParser) {
+ parser.addArgument(['output'], { help: `Output path.` })
+ parser.addArgument(['--blockSizeInMB'], { defaultValue: 96, help: `Maximum block size.`, metavar: 'SIZE' })
+ parser.addArgument(['--format'], { defaultValue: 'ccp4', help: `Input file format.` })
}
-if (parseInput()) {
- pack(config.input, config.blockSizeInMB, config.isPeriodic, config.outputFilename, config.format);
-}
\ No newline at end of file
+const xrayParser = subparsers.addParser('xray', { addHelp: true })
+xrayParser.addArgument(['input2fofc'], { help: `Path to 2fofc file.`, metavar: '2FOFC' })
+xrayParser.addArgument(['inputFofc'], { help: `Path to fofc file.`, metavar: 'FOFC' })
+addGeneralArgs(xrayParser)
+
+const emParser = subparsers.addParser('em', { addHelp: true })
+emParser.addArgument(['inputEm'], { help: `Path to EM density file.`, metavar: 'EM' })
+addGeneralArgs(emParser)
+
+const args: Args = parser.parseArgs();
+const config = getConfig(args)
+
+pack(config.input, config.blockSizeInMB, config.isPeriodic, config.outputFilename, config.format);
diff --git a/src/servers/volume/server-config.ts b/src/servers/volume/server-config.ts
deleted file mode 100644
index 8a69aaed92aa4736214498e3a549556cba9c00c1..0000000000000000000000000000000000000000
--- a/src/servers/volume/server-config.ts
+++ /dev/null
@@ -1,77 +0,0 @@
-
-const Config = {
- limits: {
- /**
- * Maximum number of blocks that could be read in 1 query.
- * This is somewhat tied to the maxOutputSizeInVoxelCountByPrecisionLevel
- * in that the <maximum number of voxel> = maxRequestBlockCount * <block size>^3.
- * The default block size is 96 which corresponds to 28,311,552 voxels with 32 max blocks.
- */
- maxRequestBlockCount: 32,
-
- /**
- * The maximum fractional volume of the query box (to prevent queries that are too big).
- */
- maxFractionalBoxVolume: 1024,
-
- /**
- * What is the (approximate) maximum desired size in voxel count by precision level
- * Rule of thumb: <response gzipped size> \in [<voxel count> / 8, <voxel count> / 4];
- *
- * The maximum number of voxels is tied to maxRequestBlockCount.
- */
- maxOutputSizeInVoxelCountByPrecisionLevel: [
- 0.5 * 1024 * 1024, // ~ 80*80*80
- 1 * 1024 * 1024,
- 2 * 1024 * 1024,
- 4 * 1024 * 1024,
- 8 * 1024 * 1024,
- 16 * 1024 * 1024, // ~ 256*256*256
- 24 * 1024 * 1024
- ]
- },
-
- /**
- * Specify the prefix of the API, i.e.
- * <host>/<apiPrefix>/<API queries>
- */
- apiPrefix: '/VolumeServer',
-
- /**
- * If not specified otherwise by the 'port' environment variable, use this port.
- */
- defaultPort: 1337,
-
- /**
- * Node (V8) sometimes exhibits GC related issues that significantly slow down the execution
- * (https://github.com/nodejs/node/issues/8670).
- *
- * Therefore an option is provided that automatically shuts down the server.
- * For this to work, the server must be run using a deamon (i.e. forever.js on Linux
- * or IISnode on Windows) so that the server is automatically restarted when the shutdown happens.
- */
- shutdownParams: {
- // 0 for off, server will shut down after this amount of minutes.
- timeoutMinutes: 24 * 60 /* a day */,
- // modifies the shutdown timer by +/- timeoutVarianceMinutes (to avoid multiple instances shutting at the same time)
- timeoutVarianceMinutes: 60
- },
-
- /**
- * Maps a request identifier to a filename.
- *
- * @param source
- * Source of the data.
- * @param id
- * Id provided in the request. For xray, PDB id, for emd, EMDB id number.
- */
- mapFile(source: string, id: string) {
- switch (source.toLowerCase()) {
- case 'x-ray': return `g:/test/mdb/xray-${id.toLowerCase()}.mdb`;
- case 'emd': return `g:/test/mdb/${id.toLowerCase()}.mdb`;
- default: return void 0;
- }
- }
-}
-
-export default Config;
\ No newline at end of file
diff --git a/src/servers/volume/server.ts b/src/servers/volume/server.ts
index 5d796f6287477133a8aef1894836214b94eeb40a..d8b6149a265082eca4cccc66e3b03dd8621e930e 100644
--- a/src/servers/volume/server.ts
+++ b/src/servers/volume/server.ts
@@ -1,9 +1,10 @@
/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * 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 * as express from 'express'
@@ -11,19 +12,20 @@ import * as compression from 'compression'
import init from './server/web-api'
import VERSION from './server/version'
-import ServerConfig from './server-config'
import { ConsoleLogger } from 'mol-util/console-logger'
import { State } from './server/state'
+import { addServerArgs, addLimitsArgs, LimitsConfig, setConfig, ServerConfig } from './config';
+import * as argparse from 'argparse'
function setupShutdown() {
- if (ServerConfig.shutdownParams.timeoutVarianceMinutes > ServerConfig.shutdownParams.timeoutMinutes) {
+ if (ServerConfig.shutdownTimeoutVarianceMinutes > ServerConfig.shutdownTimeoutMinutes) {
ConsoleLogger.log('Server', 'Shutdown timeout variance is greater than the timer itself, ignoring.');
} else {
let tVar = 0;
- if (ServerConfig.shutdownParams.timeoutVarianceMinutes > 0) {
- tVar = 2 * (Math.random() - 0.5) * ServerConfig.shutdownParams.timeoutVarianceMinutes;
+ if (ServerConfig.shutdownTimeoutVarianceMinutes > 0) {
+ tVar = 2 * (Math.random() - 0.5) * ServerConfig.shutdownTimeoutVarianceMinutes;
}
- let tMs = (ServerConfig.shutdownParams.timeoutMinutes + tVar) * 60 * 1000;
+ let tMs = (ServerConfig.shutdownTimeoutMinutes + tVar) * 60 * 1000;
console.log(`----------------------------------------------------------------------------`);
console.log(` The server will shut down in ${ConsoleLogger.formatTime(tMs)} to prevent slow performance.`);
@@ -42,20 +44,29 @@ function setupShutdown() {
}
}
+const parser = new argparse.ArgumentParser({
+ addHelp: true,
+ description: `VolumeServer ${VERSION}, (c) 2018-2019, Mol* contributors`
+});
+addServerArgs(parser)
+addLimitsArgs(parser)
-let port = process.env.port || ServerConfig.defaultPort;
+const config: ServerConfig & LimitsConfig = parser.parseArgs()
+setConfig(config) // sets the config for global use
-let app = express();
+const port = process.env.port || ServerConfig.defaultPort;
+
+const app = express();
app.use(compression({ level: 6, memLevel: 9, chunkSize: 16 * 16384, filter: () => true }));
init(app);
app.listen(port);
-console.log(`VolumeServer ${VERSION}, (c) 2016 - now, David Sehnal`);
+console.log(`VolumeServer ${VERSION}, (c) 2018-2019, Mol* contributors`);
console.log(``);
console.log(`The server is running on port ${port}.`);
console.log(``);
-if (ServerConfig.shutdownParams && ServerConfig.shutdownParams.timeoutMinutes > 0) {
+if (config.shutdownTimeoutMinutes > 0) {
setupShutdown();
}
\ No newline at end of file
diff --git a/src/servers/volume/server/api.ts b/src/servers/volume/server/api.ts
index 42f028cf0f6890cc38cc70d5626e33c7955eab38..e3a9c247ab5808dc5a10e5e0a88b7302f0777154 100644
--- a/src/servers/volume/server/api.ts
+++ b/src/servers/volume/server/api.ts
@@ -11,41 +11,46 @@ import execute from './query/execute'
import * as Data from './query/data-model'
import { ConsoleLogger } from 'mol-util/console-logger'
import * as DataFormat from '../common/data-format'
-import ServerConfig from '../server-config'
import { FileHandle } from 'mol-io/common/file-handle';
+import { LimitsConfig } from '../config';
export function getOutputFilename(source: string, id: string, { asBinary, box, detail, forcedSamplingLevel }: Data.QueryParams) {
function n(s: string) { return (s || '').replace(/[ \n\t]/g, '').toLowerCase() }
function r(v: number) { return Math.round(10 * v) / 10; }
const det = forcedSamplingLevel !== void 0
? `l${forcedSamplingLevel}`
- : `d${Math.min(Math.max(0, detail | 0), ServerConfig.limits.maxOutputSizeInVoxelCountByPrecisionLevel.length - 1)}`;
+ : `d${Math.min(Math.max(0, detail | 0), LimitsConfig.maxOutputSizeInVoxelCountByPrecisionLevel.length - 1)}`;
const boxInfo = box.kind === 'Cell'
? 'cell'
: `${box.kind === 'Cartesian' ? 'cartn' : 'frac'}_${r(box.a[0])}_${r(box.a[1])}_${r(box.a[2])}_${r(box.b[0])}_${r(box.b[1])}_${r(box.b[2])}`;
return `${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 = ServerConfig.limits.maxOutputSizeInVoxelCountByPrecisionLevel
+ const precisions = LimitsConfig.maxOutputSizeInVoxelCountByPrecisionLevel
.map((maxVoxels, precision) => ({ precision, maxVoxels }));
const availablePrecisions = [];
for (const p of precisions) {
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 ${sourceId}`, e);
diff --git a/src/servers/volume/server/documentation.ts b/src/servers/volume/server/documentation.ts
deleted file mode 100644
index 8fa43ad817af85f12cbb1c7aa44b28f4a8c034b3..0000000000000000000000000000000000000000
--- a/src/servers/volume/server/documentation.ts
+++ /dev/null
@@ -1,174 +0,0 @@
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * Taken/adapted from DensityServer (https://github.com/dsehnal/DensityServer)
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-import VERSION from './version'
-import ServerConfig from '../server-config'
-
-function detail(i: number) {
- return `<span class='id'>${i}</span><small> (${Math.round(100 * ServerConfig.limits.maxOutputSizeInVoxelCountByPrecisionLevel[i] / 1000 / 1000) / 100 }M voxels)</small>`;
-}
-const detailMax = ServerConfig.limits.maxOutputSizeInVoxelCountByPrecisionLevel.length - 1;
-const dataSource = `Specifies the data source (determined by the experiment method). Currently, <span class='id'>x-ray</span> and <span class='id'>em</span> sources are supported.`;
-const entryId = `Id of the entry. For <span class='id'>x-ray</span>, use PDB ID (i.e. <span class='id'>1cbs</span>) and for <span class='id'>em</span> use EMDB id (i.e. <span class='id'>emd-8116</span>).`;
-
-export default `
-<!DOCTYPE html>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<meta charset="utf-8" />
-<link rel='shortcut icon' href='data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAACAAAAAgCAMAAABEpIrGAAAABGdBTUEAALGPC/xhBQAAAAFzUkdCAK7OHOkAAAAnUExURQAAAMIrHrspHr0oH7soILonHrwqH7onILsoHrsoH7soH7woILwpIKgVokoAAAAMdFJOUwAQHzNxWmBHS5XO6jdtAmoAAACZSURBVDjLxZNRCsQgDAVNXmwb9f7nXZEaLRgXloXOhwQdjMYYwpOLw55fBT46KhbOKhmRR2zLcFJQj8UR+HxFgArIF5BKJbEncC6NDEdI5SatBRSDJwGAoiFDONrEJXWYhGMIcRJGCrb1TOtDahfUuQXd10jkFYq0ViIrbUpNcVT6redeC1+b9tH2WLR93Sx2VCzkv/7NjfABxjQHksGB7lAAAAAASUVORK5CYII=' />
-<title>VolumeServer (${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 ${process.version}</div>
-
-</body>
-</html>
-`;
\ No newline at end of file
diff --git a/src/servers/volume/server/query/execute.ts b/src/servers/volume/server/query/execute.ts
index 0e76f5afdbbb25d4a5c4fbce3296894644a731f1..9314cb5217c2aec09ba3bbd0f81f03bec912f5a4 100644
--- a/src/servers/volume/server/query/execute.ts
+++ b/src/servers/volume/server/query/execute.ts
@@ -13,7 +13,6 @@ import * as Coords from '../algebra/coordinate'
import * as Box from '../algebra/box'
import { ConsoleLogger } from 'mol-util/console-logger'
import { State } from '../state'
-import ServerConfig from '../../server-config'
import identify from './identify'
import compose from './compose'
@@ -23,13 +22,14 @@ import { Vec3 } from 'mol-math/linear-algebra';
import { UUID } from 'mol-util';
import { FileHandle } from 'mol-io/common/file-handle';
import { createTypedArray, TypedArrayValueType } from 'mol-io/common/typed-array';
+import { LimitsConfig } from 'servers/volume/config';
export default async function execute(params: Data.QueryParams, outputProvider: () => Data.QueryOutputStream) {
const start = getTime();
State.pendingQueries++;
const guid = UUID.create22() as any as string;
- params.detail = Math.min(Math.max(0, params.detail | 0), ServerConfig.limits.maxOutputSizeInVoxelCountByPrecisionLevel.length - 1);
+ params.detail = Math.min(Math.max(0, params.detail | 0), LimitsConfig.maxOutputSizeInVoxelCountByPrecisionLevel.length - 1);
ConsoleLogger.logId(guid, 'Info', `id=${params.sourceId},encoding=${params.asBinary ? 'binary' : 'text'},detail=${params.detail},${queryBoxToString(params.box)}`);
let sourceFile: FileHandle | undefined;
@@ -114,7 +114,7 @@ function pickSampling(data: Data.DataContext, queryBox: Box.Fractional, forcedLe
return createQuerySampling(data, data.sampling[Math.min(data.sampling.length, forcedLevel) - 1], queryBox);
}
- const sizeLimit = ServerConfig.limits.maxOutputSizeInVoxelCountByPrecisionLevel[precision] || (2 * 1024 * 1024);
+ const sizeLimit = LimitsConfig.maxOutputSizeInVoxelCountByPrecisionLevel[precision] || (2 * 1024 * 1024);
for (const s of data.sampling) {
const gridBox = Box.fractionalToGrid(queryBox, s.dataDomain);
@@ -122,7 +122,7 @@ function pickSampling(data: Data.DataContext, queryBox: Box.Fractional, forcedLe
if (approxSize <= sizeLimit) {
const sampling = createQuerySampling(data, s, queryBox);
- if (sampling.blocks.length <= ServerConfig.limits.maxRequestBlockCount) {
+ if (sampling.blocks.length <= LimitsConfig.maxRequestBlockCount) {
return sampling;
}
}
@@ -168,7 +168,7 @@ function createQueryContext(data: Data.DataContext, params: Data.QueryParams, gu
throw `The query box is not defined.`;
}
- if (dimensions[0] * dimensions[1] * dimensions[2] > ServerConfig.limits.maxFractionalBoxVolume) {
+ if (dimensions[0] * dimensions[1] * dimensions[2] > LimitsConfig.maxFractionalBoxVolume) {
throw `The query box volume is too big.`;
}
diff --git a/src/servers/volume/server/web-api.ts b/src/servers/volume/server/web-api.ts
index 28a0b33845f65f6d833217651d0498d8f0624da7..9630f314b9f63a0e51293ef0b40b01a879a7dda8 100644
--- a/src/servers/volume/server/web-api.ts
+++ b/src/servers/volume/server/web-api.ts
@@ -1,25 +1,28 @@
/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * 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 * as express from 'express'
import * as Api from './api'
-
import * as Data from './query/data-model'
import * as Coords from './algebra/coordinate'
-import Docs from './documentation'
-import ServerConfig from '../server-config'
import { ConsoleLogger } from 'mol-util/console-logger'
import { State } from './state'
+import { LimitsConfig, ServerConfig } from '../config';
+import { interpolate } from 'mol-util/string';
+import { getSchema, shortcutIconLink } 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}/${p}`;
}
// Header
@@ -29,18 +32,40 @@ export default function init(app: express.Express) {
// Cell /:src/:id/cell/?text=0|1&space=cartesian|fractional
app.get(makePath(':source/:id/cell/?'), (req, res) => queryBox(req, res, getQueryParams(req, true)));
- app.get('*', (req, res) => {
- res.writeHead(200, { 'Content-Type': 'text/html; charset=utf-8' });
- res.end(Docs);
+ app.get(makePath('openapi.json'), (req, res) => {
+ res.writeHead(200, {
+ 'Content-Type': 'application/json; charset=utf-8',
+ 'Access-Control-Allow-Origin': '*',
+ 'Access-Control-Allow-Headers': 'X-Requested-With'
+ });
+ res.end(JSON.stringify(getSchema()));
});
+
+ app.use(makePath(''), swaggerUiAssetsHandler());
+ app.get(makePath(''), swaggerUiIndexHandler({
+ openapiJsonUrl: makePath('openapi.json'),
+ apiPrefix: ServerConfig.apiPrefix,
+ title: 'VolumeServer API',
+ shortcutIconLink
+ }));
}
-function mapFile(type: string, id: string) {
- return ServerConfig.mapFile(type || '', id || '');
+function getMapFileFn() {
+ const map = new Function('type', 'id', 'interpolate', [
+ 'id = id.toLowerCase()',
+ 'switch (type.toLowerCase()) {',
+ ...ServerConfig.idMap.map(mapping => {
+ const [type, path] = mapping
+ return ` case '${type}': return interpolate('${path}', { id });`
+ }),
+ ' default: return void 0;',
+ '}'
+ ].join('\n'))
+ return (type: string, id: string) => map(type, id, interpolate)
}
function wrapResponse(fn: string, res: express.Response) {
- const w = {
+ return {
do404(this: any) {
if (!this.headerWritten) {
res.writeHead(404);
@@ -74,13 +99,11 @@ function wrapResponse(fn: string, res: express.Response) {
ended: false,
headerWritten: false
};
-
- return w;
}
function getSourceInfo(req: express.Request) {
return {
- filename: mapFile(req.params.source, req.params.id),
+ filename: req.app.locals.mapFile(req.params.source, req.params.id),
id: `${req.params.source}/${req.params.id}`
};
}
@@ -104,7 +127,7 @@ 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;
@@ -130,7 +153,7 @@ function getQueryParams(req: express.Request, isCell: boolean): Data.QueryParams
const a = [+req.params.a1, +req.params.a2, +req.params.a3];
const b = [+req.params.b1, +req.params.b2, +req.params.b3];
- const detail = Math.min(Math.max(0, (+req.query.detail) | 0), ServerConfig.limits.maxOutputSizeInVoxelCountByPrecisionLevel.length - 1)
+ const detail = Math.min(Math.max(0, (+req.query.detail) | 0), LimitsConfig.maxOutputSizeInVoxelCountByPrecisionLevel.length - 1)
const isCartesian = (req.query.space || '').toLowerCase() !== 'fractional';
const box: Data.QueryParamsBox = isCell
@@ -140,7 +163,7 @@ function getQueryParams(req: express.Request, isCell: boolean): Data.QueryParams
: { kind: 'Fractional', a: Coords.fractional(a[0], a[1], a[2]), b: Coords.fractional(b[0], b[1], b[2]) });
const asBinary = (req.query.encoding || '').toLowerCase() !== 'cif';
- const sourceFilename = mapFile(req.params.source, req.params.id)!;
+ const sourceFilename = req.app.locals.mapFile(req.params.source, req.params.id)!;
return {
sourceFilename,
diff --git a/src/servers/volume/server/web-schema.ts b/src/servers/volume/server/web-schema.ts
new file mode 100644
index 0000000000000000000000000000000000000000..05c743af26cb9dde7e9bd9c197e0c70c284f916d
--- /dev/null
+++ b/src/servers/volume/server/web-schema.ts
@@ -0,0 +1,261 @@
+/**
+ * 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=' />`
\ No newline at end of file