diff --git a/src/servers/model/local.ts b/src/servers/model/local.ts
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..089706895d8ac9ea0b4e02b171ee9908f8b73882 100644
--- a/src/servers/model/local.ts
+++ b/src/servers/model/local.ts
@@ -0,0 +1,62 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import * as fs from 'fs'
+import Version from './version';
+import { LocalInput, runLocal } from './server/api-local';
+
+console.log(`Mol* ModelServer (${Version}), (c) 2018 Mol* authors`);
+console.log(``);
+
+let exampleWorkload: LocalInput = [{
+ input: 'c:/test/quick/1tqn.cif',
+ output: 'c:/test/quick/localapi/1tqn_full.cif',
+ query: 'full', // same as defined in Api/Queries
+ }, {
+ input: 'c:/test/quick/1tqn.cif',
+ output: 'c:/test/quick/localapi/1tqn_full.bcif',
+ query: 'full',
+ params: { binary: true }
+ }, {
+ input: 'c:/test/quick/1cbs_updated.cif',
+ output: 'c:/test/quick/localapi/1cbs_ligint.cif',
+ query: 'residueInteraction', // action is case sensitive
+ params: { label_comp_id: 'REA' }
+ }, {
+ input: 'c:/test/quick/1cbs_updated.cif', // multiple files that are repeated will only be parsed once
+ output: 'c:/test/quick/localapi/1cbs_ligint.bcif',
+ query: 'residueInteraction',
+ params: { label_comp_id: 'REA', binary: true } // parameters are just a JSON version of the query string
+ }
+];
+
+
+if (process.argv.length !== 3) {
+ let help = [
+ `Usage: `,
+ ``,
+ ` node local jobs.json`,
+ ``,
+ `jobs.json is a JSON version of the WebAPI. Query names are case sensitive.`,
+ `The jobs are automatically sorted by inputFilenama and the given file is only loaded once.`,
+ `All processing errors are sent to stderr.`,
+ ``,
+ `Jobs example:`,
+ ``,
+ JSON.stringify(exampleWorkload, null, 2)
+ ];
+
+ console.log(help.join('\n'));
+} else {
+ try {
+ const input = JSON.parse(fs.readFileSync(process.argv[2], 'utf8'));
+ runLocal(input);
+ } catch (e) {
+ console.error(e);
+ }
+}
+
+// TODO: write utility that splits jobs into multiple chunks?
diff --git a/src/servers/model/server.ts b/src/servers/model/server.ts
index b8f9f2cb85702c09d4c2a3792e9ffe8aaa7b1e90..22e5d8db9246b5121c7e286a009457a1eaecf019 100644
--- a/src/servers/model/server.ts
+++ b/src/servers/model/server.ts
@@ -9,7 +9,7 @@ import * as compression from 'compression'
import ServerConfig from './config'
import { ConsoleLogger } from 'mol-util/console-logger';
import { PerformanceMonitor } from 'mol-util/performance-monitor';
-import { initWebApi } from './server/web-api';
+import { initWebApi } from './server/api-web';
import Version from './version'
function setupShutdown() {
diff --git a/src/servers/model/server/api-local.ts b/src/servers/model/server/api-local.ts
new file mode 100644
index 0000000000000000000000000000000000000000..ec7ceec0389d4415bf0905bf7134718d11b744e8
--- /dev/null
+++ b/src/servers/model/server/api-local.ts
@@ -0,0 +1,107 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import * as fs from 'fs';
+import * as path from 'path';
+import { JobManager, Job } from './jobs';
+import { ConsoleLogger } from 'mol-util/console-logger';
+import { resolveJob } from './query';
+import { StructureCache } from './structure-wrapper';
+import { now } from 'mol-task';
+import { PerformanceMonitor } from 'mol-util/performance-monitor';
+
+export type LocalInput = {
+ input: string,
+ output: string,
+ query: string,
+ params?: any
+}[];
+
+export async function runLocal(input: LocalInput) {
+ if (!input.length) {
+ ConsoleLogger.error('Local', 'No input');
+ return;
+ }
+
+ for (const job of input) {
+ JobManager.add('_local_', job.input, job.query, job.params || { }, job.output);
+ }
+ JobManager.sort();
+
+ const started = now();
+
+ let job: Job | undefined = JobManager.getNext();
+ let key = job.key;
+ let progress = 0;
+ while (job) {
+ try {
+ const encoder = await resolveJob(job);
+ const writer = wrapFile(job.outputFilename!);
+ encoder.writeTo(writer);
+ writer.end();
+ ConsoleLogger.logId(job.id, 'Query', 'Written.');
+
+ if (JobManager.hasNext()) {
+ job = JobManager.getNext();
+ if (key !== job.key) StructureCache.expire(key);
+ key = job.key;
+ } else {
+ break;
+ }
+ } catch (e) {
+ ConsoleLogger.errorId(job.id, e);
+ }
+ ConsoleLogger.log('Progress', `[${++progress}/${input.length}] after ${PerformanceMonitor.format(now() - started)}.`);
+ }
+
+ ConsoleLogger.log('Progress', `Done in ${PerformanceMonitor.format(now() - started)}.`);
+ StructureCache.expireAll();
+}
+
+function wrapFile(fn: string) {
+ const w = {
+ open(this: any) {
+ if (this.opened) return;
+ makeDir(path.dirname(fn));
+ this.file = fs.openSync(fn, 'w');
+ this.opened = true;
+ },
+ writeBinary(this: any, data: Uint8Array) {
+ this.open();
+ fs.writeSync(this.file, new Buffer(data));
+ return true;
+ },
+ writeString(this: any, data: string) {
+ this.open();
+ fs.writeSync(this.file, data);
+ return true;
+ },
+ end(this: any) {
+ if (!this.opened || this.ended) return;
+ fs.close(this.file, function () { });
+ this.ended = true;
+ },
+ file: 0,
+ ended: false,
+ opened: false
+ };
+
+ return w;
+}
+
+function makeDir(path: string, root?: string): boolean {
+ let dirs = path.split(/\/|\\/g),
+ dir = dirs.shift();
+
+ root = (root || '') + dir + '/';
+
+ try { fs.mkdirSync(root); }
+ catch (e) {
+ if (!fs.statSync(root).isDirectory()) throw new Error(e);
+ }
+
+ return !dirs.length || makeDir(dirs.join('/'), root);
+}
\ No newline at end of file
diff --git a/src/servers/model/server/web-api.ts b/src/servers/model/server/api-web.ts
similarity index 100%
rename from src/servers/model/server/web-api.ts
rename to src/servers/model/server/api-web.ts
diff --git a/src/servers/model/server/jobs.ts b/src/servers/model/server/jobs.ts
index 3282838633900c6ceadad5b040192747347785d8..8791d26b101074bf32ded4a5e837eff91e954af1 100644
--- a/src/servers/model/server/jobs.ts
+++ b/src/servers/model/server/jobs.ts
@@ -22,10 +22,12 @@ export interface Job {
queryDefinition: QueryDefinition,
normalizedParams: any,
- responseFormat: ResponseFormat
+ responseFormat: ResponseFormat,
+
+ outputFilename?: string
}
-export function createJob(sourceId: '_local_' | string, entryId: string, queryName: string, params: any): Job {
+export function createJob(sourceId: '_local_' | string, entryId: string, queryName: string, params: any, outputFilename?: string): Job {
const queryDefinition = getQueryByName(queryName);
if (!queryDefinition) throw new Error(`Query '${queryName}' is not supported.`);
@@ -39,7 +41,8 @@ export function createJob(sourceId: '_local_' | string, entryId: string, queryNa
entryId,
queryDefinition,
normalizedParams,
- responseFormat: { isBinary: !!params.binary }
+ responseFormat: { isBinary: !!params.binary },
+ outputFilename
};
}
@@ -50,8 +53,8 @@ class _JobQueue {
return this.list.count;
}
- add(sourceId: '_local_' | string, entryId: string, queryName: string, params: any) {
- const job = createJob(sourceId, entryId, queryName, params);
+ add(sourceId: '_local_' | string, entryId: string, queryName: string, params: any, outputFilename?: string) {
+ const job = createJob(sourceId, entryId, queryName, params, outputFilename);
this.list.addLast(job);
return job.id;
}