diff --git a/src/servers/model/CHANGELOG.md b/src/servers/model/CHANGELOG.md
index d522b8879c7e0b8c5a12c8e86b44139757e06d7a..1ed96c27f8f22368e875a638be715eb917d8d7c6 100644
--- a/src/servers/model/CHANGELOG.md
+++ b/src/servers/model/CHANGELOG.md
@@ -3,6 +3,7 @@
* Swagger UI support.
* Response schemas.
* Bug fixes.
+* Refactored config which can now be provided as a seprate JSON file.
# 0.8.0
* Let's call this an initial version.
\ No newline at end of file
diff --git a/src/servers/model/config.ts b/src/servers/model/config.ts
index 7a8c495b59fc609055c4e9e5c628e956e1ec0c1a..819880b3741e37077979cb431dbe93cfc5c22cda 100644
--- a/src/servers/model/config.ts
+++ b/src/servers/model/config.ts
@@ -1,10 +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.
*
* @author David Sehnal <david.sehnal@gmail.com>
*/
-const config = {
+const DefaultModelServerConfig = {
/**
* Determine if and how long to cache entries after a request.
*/
@@ -50,6 +50,7 @@ const config = {
/**
* Provide a property config or a path a JSON file with the config.
*/
+ // TODO: finish customProperty support
customProperties: <import('./property-provider').ModelPropertyProviderConfig | string>{
sources: [
// 'pdbe',
@@ -79,23 +80,37 @@ const config = {
}
},
+
+ /**
+ * Default source for fileMapping.
+ */
+ defaultSource: 'pdb-cif' as string,
+
/**
- * Maps a request identifier to a filename.
+ * Maps a request identifier to a filename given a 'source' and 'id' variables.
*
- * @param source
- * Source of the data.
- * @param id
- * Id provided in the request.
+ * /static query uses 'pdb-cif' and 'pdb-bcif' source names.
*/
- mapFile(source: string, id: string) {
- switch (source.toLowerCase()) {
- case 'pdb': return `e:/test/quick/${id}_updated.cif`;
- // case 'pdb': return `e:/test/mol-star/model/out/${id}_updated.bcif`;
- // case 'pdb-bcif': return `c:/test/mol-star/model/out/${id}_updated.bcif`;
- // case 'pdb-cif': return `c:/test/mol-star/model/out/${id}_updated.cif`;
- default: return void 0;
- }
- }
+ fileMapping: [
+ ['pdb-cif', 'e:/test/quick/${id}_updated.cif'],
+ // ['pdb-bcif', 'e:/test/quick/${id}.bcif'],
+ ] as [string, string][]
};
-export default config;
\ No newline at end of file
+export type ModelServerConfig = typeof DefaultModelServerConfig
+export const ModelServerConfig = DefaultModelServerConfig
+
+export let mapSourceAndIdToFilename: (source: string, id: string) => string = () => {
+ throw new Error('call setupConfig to initialize this function');
+}
+
+export function setupConfig(cfg?: ModelServerConfig) {
+ if (cfg) Object.assign(ModelServerConfig, cfg);
+ if (!ModelServerConfig.fileMapping) return;
+
+ mapSourceAndIdToFilename = new Function('source', 'id', [
+ 'switch (source.toLowerCase()) {',
+ ...ModelServerConfig.fileMapping.map(([source, path]) => `case '${source.toLowerCase()}': return \`${path}\`;`),
+ '}',
+ ].join('\n')) as any;
+}
\ No newline at end of file
diff --git a/src/servers/model/property-provider.ts b/src/servers/model/property-provider.ts
index d929c30c7320093b85d5b4677fe889fcb7c3b81f..20c1754105d04500f01c79daf11c2d11302f6686 100644
--- a/src/servers/model/property-provider.ts
+++ b/src/servers/model/property-provider.ts
@@ -6,7 +6,7 @@
import * as fs from 'fs'
import { Model } from '../../mol-model/structure';
-import Config from './config';
+import { ModelServerConfig as Config } from './config';
import { ConsoleLogger } from '../../mol-util/console-logger';
// TODO enable dynamic imports again
diff --git a/src/servers/model/server.ts b/src/servers/model/server.ts
index b227cedac82712a35acedd4774d2bd660bfcbced..f9b966a33d2848b52586f576d70359d260c0b83a 100644
--- a/src/servers/model/server.ts
+++ b/src/servers/model/server.ts
@@ -1,12 +1,14 @@
/**
- * 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 David Sehnal <david.sehnal@gmail.com>
*/
import * as express from 'express'
import * as compression from 'compression'
-import ServerConfig from './config'
+import * as fs from 'fs'
+import * as argparse from 'argparse'
+import { ModelServerConfig as ServerConfig, setupConfig } from './config'
import { ConsoleLogger } from '../../mol-util/console-logger';
import { PerformanceMonitor } from '../../mol-util/performance-monitor';
import { initWebApi } from './server/api-web';
@@ -39,34 +41,37 @@ function setupShutdown() {
}
}
-const port = process.env.port || ServerConfig.defaultPort;
+const cmdParser = new argparse.ArgumentParser({
+ addHelp: true
+});
+
+cmdParser.addArgument(['--cfg'], { help: 'Config file path.', required: false });
+
+interface CmdArgs {
+ cfg?: string
+}
+
+const cmdArgs = cmdParser.parseArgs() as CmdArgs;
function startServer() {
let app = express();
app.use(compression(<any>{ level: 6, memLevel: 9, chunkSize: 16 * 16384, filter: () => true }));
- // app.get(ServerConfig.appPrefix + '/documentation', (req, res) => {
- // res.writeHead(200, { 'Content-Type': 'text/html' });
- // res.write(Documentation.getHTMLDocs(ServerConfig.appPrefix));
- // res.end();
- // });
+ const cfg = cmdArgs.cfg ? JSON.parse(fs.readFileSync(cmdArgs.cfg, 'utf8')) : void 0;
+ setupConfig(cfg);
initWebApi(app);
- // app.get('*', (req, res) => {
- // res.writeHead(200, { 'Content-Type': 'text/html' });
- // res.write(Documentation.getHTMLDocs(ServerConfig.appPrefix));
- // res.end();
- // });
-
+ const port = process.env.port || ServerConfig.defaultPort;
app.listen(port);
+
+ console.log(`Mol* ModelServer ${Version}`);
+ console.log(``);
+ console.log(`The server is running on port ${port}.`);
+ console.log(``);
}
startServer();
-console.log(`Mol* ModelServer ${Version}`);
-console.log(``);
-console.log(`The server is running on port ${port}.`);
-console.log(``);
if (ServerConfig.shutdownParams && ServerConfig.shutdownParams.timeoutMinutes > 0) {
setupShutdown();
diff --git a/src/servers/model/server/api-schema.ts b/src/servers/model/server/api-schema.ts
index f22f874f1b7725b2b0338be8898e464986cd0c29..c52df819262feffcb32a507b74e2cc7d606a40d1 100644
--- a/src/servers/model/server/api-schema.ts
+++ b/src/servers/model/server/api-schema.ts
@@ -6,7 +6,7 @@
import VERSION from '../version'
import { QueryParamInfo, QueryParamType, QueryDefinition, CommonQueryParamsInfo, QueryList } from './api';
-import ServerConfig from '../config';
+import { ModelServerConfig as ServerConfig } from '../config';
export const shortcutIconLink = `<link rel='shortcut icon' href='data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAACAAAAAgCAMAAABEpIrGAAAABGdBTUEAALGPC/xhBQAAAAFzUkdCAK7OHOkAAAAnUExURQAAAMIrHrspHr0oH7soILonHrwqH7onILsoHrsoH7soH7woILwpIKgVokoAAAAMdFJOUwAQHzNxWmBHS5XO6jdtAmoAAACZSURBVDjLxZNRCsQgDAVNXmwb9f7nXZEaLRgXloXOhwQdjMYYwpOLw55fBT46KhbOKhmRR2zLcFJQj8UR+HxFgArIF5BKJbEncC6NDEdI5SatBRSDJwGAoiFDONrEJXWYhGMIcRJGCrb1TOtDahfUuQXd10jkFYq0ViIrbUpNcVT6redeC1+b9tH2WLR93Sx2VCzkv/7NjfABxjQHksGB7lAAAAAASUVORK5CYII=' />`
diff --git a/src/servers/model/server/api-web.ts b/src/servers/model/server/api-web.ts
index daf1c760bfdd0a6143dbbca45dd7b95305dcb11e..9dd4bb8f096d180c82125dc22b3ff8688479d6b3 100644
--- a/src/servers/model/server/api-web.ts
+++ b/src/servers/model/server/api-web.ts
@@ -7,7 +7,7 @@
import * as fs from 'fs';
import * as path from 'path';
import * as express from 'express';
-import Config from '../config';
+import { ModelServerConfig as Config, ModelServerConfig, mapSourceAndIdToFilename } from '../config';
import { ConsoleLogger } from '../../../mol-util/console-logger';
import { resolveJob } from './query';
import { JobManager } from './jobs';
@@ -92,7 +92,7 @@ function mapQuery(app: express.Express, queryName: string, queryDefinition: Quer
const queryParams = normalizeRestQueryParams(queryDefinition, req.query);
const commonParams = normalizeRestCommonParams(req.query);
const jobId = JobManager.add({
- sourceId: commonParams.data_source || 'pdb',
+ sourceId: commonParams.data_source || ModelServerConfig.defaultSource,
entryId,
queryName: queryName as any,
queryParams,
@@ -107,7 +107,7 @@ export function initWebApi(app: express.Express) {
app.get(makePath('static/:format/:id'), async (req, res) => {
const binary = req.params.format === 'bcif';
const id = req.params.id;
- const fn = Config.mapFile(binary ? 'pdb-bcif' : 'pdb-cif', id);
+ const fn = mapSourceAndIdToFilename(binary ? 'pdb-bcif' : 'pdb-cif', id);
if (!fn || !fs.existsSync(fn)) {
res.status(404);
res.end();
diff --git a/src/servers/model/server/cache.ts b/src/servers/model/server/cache.ts
index 24cafe58fe172c885ead26fb25a20d398c1a956d..b2978044db48d6ccfecf9a8e441b68c6188ff9c9 100644
--- a/src/servers/model/server/cache.ts
+++ b/src/servers/model/server/cache.ts
@@ -6,7 +6,7 @@
import { ConsoleLogger } from '../../../mol-util/console-logger'
import { LinkedList } from '../../../mol-data/generic';
-import ServerConfig from '../config';
+import { ModelServerConfig as ServerConfig } from '../config';
interface CacheEntry<T> {
key: string,
diff --git a/src/servers/model/server/query.ts b/src/servers/model/server/query.ts
index 7cf76311a85d5ca82ff24496e7bd2a8feb865e02..9bbcf807c932e4ba80520f9f3dc1ec065a77e57c 100644
--- a/src/servers/model/server/query.ts
+++ b/src/servers/model/server/query.ts
@@ -12,7 +12,7 @@ import { Progress } from '../../../mol-task';
import { now } from '../../../mol-util/now';
import { ConsoleLogger } from '../../../mol-util/console-logger';
import { PerformanceMonitor } from '../../../mol-util/performance-monitor';
-import Config from '../config';
+import { ModelServerConfig as Config } from '../config';
import Version from '../version';
import { Job } from './jobs';
import { createStructureWrapperFromJob, StructureWrapper, resolveStructures } from './structure-wrapper';
diff --git a/src/servers/model/server/structure-wrapper.ts b/src/servers/model/server/structure-wrapper.ts
index 596ccd3e31bf4da7c763dff4c2df058d6b4a4f5b..148f3e35aff67a18608c9145de65c5c95b83650a 100644
--- a/src/servers/model/server/structure-wrapper.ts
+++ b/src/servers/model/server/structure-wrapper.ts
@@ -7,7 +7,7 @@
import { Structure, Model } from '../../../mol-model/structure';
import { PerformanceMonitor } from '../../../mol-util/performance-monitor';
import { Cache } from './cache';
-import Config from '../config';
+import { ModelServerConfig as Config, mapSourceAndIdToFilename } from '../config';
import { CIF, CifFrame, CifBlock } from '../../../mol-io/reader/cif'
import * as util from 'util'
import * as fs from 'fs'
@@ -109,7 +109,7 @@ export async function readDataAndFrame(filename: string, key?: string): Promise<
}
export async function readStructureWrapper(key: string, sourceId: string | '_local_', entryId: string, propertyProvider: ModelPropertiesProvider | undefined) {
- const filename = sourceId === '_local_' ? entryId : Config.mapFile(sourceId, entryId);
+ const filename = sourceId === '_local_' ? entryId : mapSourceAndIdToFilename(sourceId, entryId);
if (!filename) throw new Error(`Cound not map '${key}' to a valid filename.`);
if (!fs.existsSync(filename)) throw new Error(`Could not find source file for '${key}'.`);