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/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 ${port}.`);
console.log(``);
-if (ServerConfig.shutdownParams && ServerConfig.shutdownParams.timeoutMinutes > 0) {
+if (config.shutdownTimeoutMinutes > 0) {
setupShutdown();
}
\ No newline at end of file
diff --git a/src/servers/volume/server/api.ts b/src/servers/volume/server/api.ts
index 42f028cf0f6890cc38cc70d5626e33c7955eab38..6fa227adf6ded744658c075b3eb43e008d925a54 100644
--- a/src/servers/volume/server/api.ts
+++ b/src/servers/volume/server/api.ts
@@ -11,15 +11,15 @@ import execute from './query/execute'
import * as Data from './query/data-model'
import { ConsoleLogger } from 'mol-util/console-logger'
import * as DataFormat from '../common/data-format'
-import ServerConfig from '../server-config'
import { FileHandle } from 'mol-io/common/file-handle';
+import { LimitsConfig } from '../config';
export function getOutputFilename(source: string, id: string, { asBinary, box, detail, forcedSamplingLevel }: Data.QueryParams) {
function n(s: string) { return (s || '').replace(/[ \n\t]/g, '').toLowerCase() }
function r(v: number) { return Math.round(10 * v) / 10; }
const det = forcedSamplingLevel !== void 0
? `l${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])}_${r(box.b[2])}`;
@@ -37,7 +37,7 @@ export async function getHeaderJson(filename: string | undefined, sourceId: stri
const header = { ...await readHeader(filename, sourceId) } as DataFormat.Header;
const { sampleCount } = header!.sampling[0];
const maxVoxelCount = sampleCount[0] * sampleCount[1] * sampleCount[2];
- const precisions = ServerConfig.limits.maxOutputSizeInVoxelCountByPrecisionLevel
+ const precisions = LimitsConfig.maxOutputSizeInVoxelCountByPrecisionLevel
.map((maxVoxels, precision) => ({ precision, maxVoxels }));
const availablePrecisions = [];
for (const p of precisions) {
diff --git a/src/servers/volume/server/documentation.ts b/src/servers/volume/server/documentation.ts
index 8fa43ad817af85f12cbb1c7aa44b28f4a8c034b3..4713359d9342b46c7ca4cc67e2b6433719422ca2 100644
--- a/src/servers/volume/server/documentation.ts
+++ b/src/servers/volume/server/documentation.ts
@@ -1,23 +1,26 @@
/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* Taken/adapted from DensityServer (https://github.com/dsehnal/DensityServer)
*
* @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import VERSION from './version'
-import ServerConfig from '../server-config'
+import { LimitsConfig } from '../config';
-function detail(i: number) {
- return `<span class='id'>${i}</span><small> (${Math.round(100 * ServerConfig.limits.maxOutputSizeInVoxelCountByPrecisionLevel[i] / 1000 / 1000) / 100 }M voxels)</small>`;
-}
-const detailMax = ServerConfig.limits.maxOutputSizeInVoxelCountByPrecisionLevel.length - 1;
-const dataSource = `Specifies the data source (determined by the experiment method). Currently, <span class='id'>x-ray</span> and <span class='id'>em</span> sources are supported.`;
-const entryId = `Id of the entry. For <span class='id'>x-ray</span>, use PDB ID (i.e. <span class='id'>1cbs</span>) and for <span class='id'>em</span> use EMDB id (i.e. <span class='id'>emd-8116</span>).`;
+export function getDocumentation() {
+ function detail(i: number) {
+ return `<span class='id'>${i}</span><small> (${Math.round(100 * LimitsConfig.maxOutputSizeInVoxelCountByPrecisionLevel[i] / 1000 / 1000) / 100 }M voxels)</small>`;
+ }
+ const detailMax = LimitsConfig.maxOutputSizeInVoxelCountByPrecisionLevel.length - 1;
-export default `
-<!DOCTYPE html>
+ // 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" />
@@ -170,5 +173,5 @@ span.id { color: #DE4D4E; font-family: Menlo,Monaco,Consolas,"Courier New",mono
<div style="color: #999;font-size:smaller;margin: 20px 0; text-align: right">© 2016 – now, David Sehnal | Node ${process.version}</div>
</body>
-</html>
-`;
\ No newline at end of file
+</html>`;
+}
\ No newline at end of file
diff --git a/src/servers/volume/server/query/execute.ts b/src/servers/volume/server/query/execute.ts
index 0e76f5afdbbb25d4a5c4fbce3296894644a731f1..9314cb5217c2aec09ba3bbd0f81f03bec912f5a4 100644
--- a/src/servers/volume/server/query/execute.ts
+++ b/src/servers/volume/server/query/execute.ts
@@ -13,7 +13,6 @@ import * as Coords from '../algebra/coordinate'
import * as Box from '../algebra/box'
import { ConsoleLogger } from 'mol-util/console-logger'
import { State } from '../state'
-import ServerConfig from '../../server-config'
import identify from './identify'
import compose from './compose'
@@ -23,13 +22,14 @@ import { Vec3 } from 'mol-math/linear-algebra';
import { UUID } from 'mol-util';
import { FileHandle } from 'mol-io/common/file-handle';
import { createTypedArray, TypedArrayValueType } from 'mol-io/common/typed-array';
+import { LimitsConfig } from 'servers/volume/config';
export default async function execute(params: Data.QueryParams, outputProvider: () => Data.QueryOutputStream) {
const start = getTime();
State.pendingQueries++;
const guid = UUID.create22() as any as string;
- params.detail = Math.min(Math.max(0, params.detail | 0), ServerConfig.limits.maxOutputSizeInVoxelCountByPrecisionLevel.length - 1);
+ params.detail = Math.min(Math.max(0, params.detail | 0), LimitsConfig.maxOutputSizeInVoxelCountByPrecisionLevel.length - 1);
ConsoleLogger.logId(guid, 'Info', `id=${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..0b9dbc1d0f93c7a5cf3ac572f269123725e07b6f 100644
--- a/src/servers/volume/server/web-api.ts
+++ b/src/servers/volume/server/web-api.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'
@@ -12,12 +13,14 @@ 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 { 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';
export default function init(app: express.Express) {
+ app.locals.mapFile = getMapFileFn()
function makePath(p: string) {
return ServerConfig.apiPrefix + '/' + p;
}
@@ -31,16 +34,26 @@ export default function init(app: express.Express) {
app.get('*', (req, res) => {
res.writeHead(200, { 'Content-Type': 'text/html; charset=utf-8' });
- res.end(Docs);
+ res.end(getDocumentation());
});
}
-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('${path}', { id });`
+ }),
+ ' default: return void 0;',
+ '}'
+ ].join('\n'))
+ return (type: string, id: string) => map(type, id, interpolate)
}
function wrapResponse(fn: string, res: express.Response) {
- const w = {
+ return {
do404(this: any) {
if (!this.headerWritten) {
res.writeHead(404);
@@ -74,13 +87,11 @@ function wrapResponse(fn: string, res: express.Response) {
ended: false,
headerWritten: false
};
-
- return w;
}
function getSourceInfo(req: express.Request) {
return {
- filename: mapFile(req.params.source, req.params.id),
+ filename: req.app.locals.mapFile(req.params.source, req.params.id),
id: `${req.params.source}/${req.params.id}`
};
}
@@ -130,7 +141,7 @@ 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 +151,7 @@ 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,