From d7ebb30e05da107025d3e77f246f09ded77da686 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Sat, 8 Feb 2020 16:26:29 +0100
Subject: [PATCH] servers/plugin-state
---
README.md | 1 +
package-lock.json | Bin 764447 -> 765664 bytes
package.json | 3 +
src/servers/model/server/api-local.ts | 15 +-
src/servers/plugin-state/index.ts | 242 ++++++++++++++++++++++++++
5 files changed, 247 insertions(+), 14 deletions(-)
create mode 100644 src/servers/plugin-state/index.ts
diff --git a/README.md b/README.md
index d5dd8c109..91d48e5e5 100644
--- a/README.md
+++ b/README.md
@@ -38,6 +38,7 @@ Moreover, the project contains the imlementation of `servers`, including
- `servers/model` A tool for accessing coordinate and annotation data of molecular structures.
- `servers/volume` A tool for accessing volumetric experimental data related to molecular structures.
+- `servers/plugin-state` A basic server to store Mol* Plugin states.
The project also contains performance tests (`perf-tests`), `examples`, and basic proof of concept `apps` (CIF to BinaryCIF converter and JSON domain annotation to CIF converter).
diff --git a/package-lock.json b/package-lock.json
index 3cc465afa6de76dc269c4ad9dab41dd3bfd21d0c..9c313aac8c467562d01a37da6bac6b63406507e1 100644
GIT binary patch
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diff --git a/package.json b/package.json
index f6d8ef285..9f4a69ce9 100644
--- a/package.json
+++ b/package.json
@@ -25,6 +25,7 @@
"model-server": "node lib/servers/model/server.js",
"model-server-watch": "nodemon --watch lib lib/servers/model/server.js",
"volume-server": "node lib/servers/volume/server.js --idMap em 'test/${id}.mdb' --defaultPort 1336",
+ "plugin-state": "node lib/servers/plugin-state/index.js",
"preversion": "npm run test",
"postversion": "git push && git push --tags",
"prepublishOnly": "npm run test && npm run build"
@@ -70,6 +71,7 @@
"@graphql-codegen/typescript-graphql-files-modules": "^1.11.2",
"@graphql-codegen/typescript-graphql-request": "^1.11.2",
"@graphql-codegen/typescript-operations": "^1.11.2",
+ "@types/cors": "^2.8.6",
"@typescript-eslint/eslint-plugin": "^2.17.0",
"@typescript-eslint/eslint-plugin-tslint": "^2.17.0",
"@typescript-eslint/parser": "^2.17.0",
@@ -112,6 +114,7 @@
"argparse": "^1.0.10",
"body-parser": "^1.19.0",
"compression": "^1.7.4",
+ "cors": "^2.8.5",
"express": "^4.17.1",
"graphql": "^14.5.8",
"immutable": "^3.8.2",
diff --git a/src/servers/model/server/api-local.ts b/src/servers/model/server/api-local.ts
index 5b27b9859..31aca674e 100644
--- a/src/servers/model/server/api-local.ts
+++ b/src/servers/model/server/api-local.ts
@@ -13,6 +13,7 @@ import { StructureCache } from './structure-wrapper';
import { now } from '../../../mol-util/now';
import { PerformanceMonitor } from '../../../mol-util/performance-monitor';
import { QueryName } from './api';
+import { makeDir } from '../../../mol-util/make-dir';
export type LocalInput = {
input: string,
@@ -103,18 +104,4 @@ export function wrapFileToWriter(fn: string) {
};
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/plugin-state/index.ts b/src/servers/plugin-state/index.ts
new file mode 100644
index 000000000..0c37c4959
--- /dev/null
+++ b/src/servers/plugin-state/index.ts
@@ -0,0 +1,242 @@
+/**
+ * Copyright (c) 2019-2020 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 * as cors from 'cors'
+import * as bodyParser from 'body-parser'
+import * as argparse from 'argparse'
+import * as fs from 'fs'
+import * as path from 'path'
+import { makeDir } from '../../mol-util/make-dir'
+
+interface Config {
+ working_folder: string,
+ port?: string | number,
+ app_prefix: string,
+ max_states: number
+}
+
+const cmdParser = new argparse.ArgumentParser({
+ addHelp: true
+});
+cmdParser.addArgument(['--working-folder'], { help: 'Working forlder path.', required: true });
+cmdParser.addArgument(['--port'], { help: 'Server port. Altenatively use ENV variable PORT.', type: 'int', required: false });
+cmdParser.addArgument(['--app-prefix'], { help: 'Server app prefix.', defaultValue: '', required: false });
+cmdParser.addArgument(['--max-states'], { help: 'Maxinum number of states that could be saved.', defaultValue: 40, type: 'int', required: false });
+
+const Config = cmdParser.parseArgs() as Config;
+
+if (!Config.port) Config.port = process.env.port || 1339;
+
+const app = express();
+app.use(compression(<any>{ level: 6, memLevel: 9, chunkSize: 16 * 16384, filter: () => true }));
+app.use(cors({ methods: ['GET', 'PUT'] }));
+app.use(bodyParser.json({ limit: '20mb' }));
+
+type Index = { timestamp: number, id: string, name: string, description: string, isSticky?: boolean }[]
+
+function createIndex() {
+ const fn = path.join(Config.working_folder, 'index.json');
+ if (fs.existsSync(fn)) return;
+ if (!fs.existsSync(Config.working_folder)) makeDir(Config.working_folder);
+ fs.writeFileSync(fn, '[]', 'utf-8');
+}
+
+function writeIndex(index: Index) {
+ const fn = path.join(Config.working_folder, 'index.json');
+ if (!fs.existsSync(Config.working_folder)) makeDir(Config.working_folder);
+ fs.writeFileSync(fn, JSON.stringify(index, null, 2), 'utf-8');
+}
+
+function readIndex() {
+ const fn = path.join(Config.working_folder, 'index.json');
+ if (!fs.existsSync(fn)) return [];
+ return JSON.parse(fs.readFileSync(fn, 'utf-8')) as Index;
+}
+
+function validateIndex(index: Index) {
+ if (index.length > Config.max_states) {
+ const deletes: Index = [], newIndex: Index = [];
+ const toDelete = index.length - Config.max_states;
+
+ for (const e of index) {
+ if (!e.isSticky && deletes.length < toDelete) {
+ deletes.push(e);
+ } else {
+ newIndex.push(e);
+ }
+ }
+ // index.slice(0, index.length - 30);
+ for (const d of deletes) {
+ try {
+ fs.unlinkSync(path.join(Config.working_folder, d.id + '.json'))
+ } catch { }
+ }
+ return newIndex;
+ }
+ return index;
+}
+
+function remove(id: string) {
+ let index = readIndex();
+ let i = 0;
+ for (const e of index) {
+ if (e.id !== id) {
+ i++;
+ continue;
+ }
+ try {
+ for (let j = i + 1; j < index.length; j++) {
+ index[j - 1] = index[j];
+ }
+ index.pop();
+ writeIndex(index);
+ } catch { }
+ try {
+ fs.unlinkSync(path.join(Config.working_folder, e.id + '.json'))
+ } catch { }
+ return;
+ }
+}
+
+function clear() {
+ let index = readIndex();
+ for (const e of index) {
+ try {
+ fs.unlinkSync(path.join(Config.working_folder, e.id + '.json'))
+ } catch { }
+ }
+ writeIndex([]);
+}
+
+export function createv4() {
+ let d = (+new Date());
+ const uuid = 'xxxxxxxx-xxxx-4xxx-yxxx-xxxxxxxxxxxx'.replace(/[xy]/g, function(c) {
+ const r = (d + Math.random()*16)%16 | 0;
+ d = Math.floor(d/16);
+ return (c==='x' ? r : (r&0x3|0x8)).toString(16);
+ });
+ return uuid.toLowerCase();
+}
+
+function mapPath(path: string) {
+ if (!Config.app_prefix) return path;
+ return `/${Config.app_prefix}/${path}`;
+}
+
+app.get(mapPath(`/get/:id`), (req, res) => {
+ const id: string = req.params.id || '';
+ console.log('Reading', id);
+ if (id.length === 0 || id.indexOf('.') >= 0 || id.indexOf('/') >= 0 || id.indexOf('\\') >= 0) {
+ res.status(404);
+ res.end();
+ return;
+ }
+
+ fs.readFile(path.join(Config.working_folder, id + '.json'), 'utf-8', (err, data) => {
+ if (err) {
+ res.status(404);
+ res.end();
+ return;
+ }
+
+ res.writeHead(200, {
+ 'Content-Type': 'application/json; charset=utf-8',
+ });
+ res.write(data);
+ res.end();
+ });
+});
+
+app.get(mapPath(`/clear`), (req, res) => {
+ clear();
+ res.status(200);
+ res.end();
+});
+
+app.get(mapPath(`/remove/:id`), (req, res) => {
+ remove((req.params.id as string || '').toLowerCase());
+ res.status(200);
+ res.end();
+});
+
+app.get(mapPath(`/latest`), (req, res) => {
+ const index = readIndex();
+ const id: string = index.length > 0 ? index[index.length - 1].id : '';
+ console.log('Reading', id);
+ if (id.length === 0 || id.indexOf('.') >= 0 || id.indexOf('/') >= 0 || id.indexOf('\\') >= 0) {
+ res.status(404);
+ res.end();
+ return;
+ }
+
+ fs.readFile(path.join(Config.working_folder, id + '.json'), 'utf-8', (err, data) => {
+ if (err) {
+ res.status(404);
+ res.end();
+ return;
+ }
+
+ res.writeHead(200, {
+ 'Content-Type': 'application/json; charset=utf-8',
+ });
+ res.write(data);
+ res.end();
+ });
+});
+
+app.get(mapPath(`/list`), (req, res) => {
+ const index = readIndex();
+ res.writeHead(200, {
+ 'Content-Type': 'application/json; charset=utf-8',
+ });
+ res.write(JSON.stringify(index, null, 2));
+ res.end();
+});
+
+app.post(mapPath(`/set`), (req, res) => {
+ console.log('SET', req.query.name, req.query.description);
+ const index = readIndex();
+ validateIndex(index);
+
+ const name = (req.query.name as string || new Date().toUTCString()).substr(0, 50);
+ const description = (req.query.description as string || '').substr(0, 100);
+
+ index.push({ timestamp: +new Date(), id: createv4(), name, description });
+ const entry = index[index.length - 1];
+
+ const data = JSON.stringify({
+ id: entry.id,
+ name,
+ description,
+ data: req.body
+ });
+
+ fs.writeFile(path.join(Config.working_folder, entry.id + '.json'), data, { encoding: 'utf8' }, () => res.end());
+ writeIndex(index);
+});
+
+app.get(`*`, (req, res) => {
+ res.writeHead(200, {
+ 'Content-Type': 'text/plain; charset=utf-8'
+ });
+ res.write(`
+GET /list
+GET /get/:id
+GET /remove/:id
+GET /latest
+POST /set?name=...&description=... [JSON data]
+`);
+ res.end();
+})
+
+createIndex();
+app.listen(Config.port);
+
+console.log(`Mol* PluginState Server`);
+console.log('');
+console.log(JSON.stringify(Config, null, 2));
\ No newline at end of file
--
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