0.7.0-dev.3

.npmignore

@@ -0,0 +1 @@
+tsconfig.servers.buildinfo

package-lock.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "0.7.0-dev.1",
+  "version": "0.7.0-dev.3",
   "lockfileVersion": 1,
   "requires": true,
   "dependencies": {
@@ -3143,7 +3143,7 @@
     },
     "browserify-aes": {
       "version": "1.2.0",
-      "resolved": "http://registry.npmjs.org/browserify-aes/-/browserify-aes-1.2.0.tgz",
+      "resolved": "https://registry.npmjs.org/browserify-aes/-/browserify-aes-1.2.0.tgz",
       "integrity": "sha512-+7CHXqGuspUn/Sl5aO7Ea0xWGAtETPXNSAjHo48JfLdPWcMng33Xe4znFvQweqc/uzk5zSOI3H52CYnjCfb5hA==",
       "dev": true,
       "requires": {
@@ -3180,7 +3180,7 @@
     },
     "browserify-rsa": {
       "version": "4.0.1",
-      "resolved": "http://registry.npmjs.org/browserify-rsa/-/browserify-rsa-4.0.1.tgz",
+      "resolved": "https://registry.npmjs.org/browserify-rsa/-/browserify-rsa-4.0.1.tgz",
       "integrity": "sha1-IeCr+vbyApzy+vsTNWenAdQTVSQ=",
       "dev": true,
       "requires": {
@@ -3374,7 +3374,7 @@
     },
     "camelcase-keys": {
       "version": "2.1.0",
-      "resolved": "http://registry.npmjs.org/camelcase-keys/-/camelcase-keys-2.1.0.tgz",
+      "resolved": "https://registry.npmjs.org/camelcase-keys/-/camelcase-keys-2.1.0.tgz",
       "integrity": "sha1-MIvur/3ygRkFHvodkyITyRuPkuc=",
       "dev": true,
       "requires": {
@@ -3608,7 +3608,7 @@
         },
         "strip-ansi": {
           "version": "3.0.1",
-          "resolved": "http://registry.npmjs.org/strip-ansi/-/strip-ansi-3.0.1.tgz",
+          "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-3.0.1.tgz",
           "integrity": "sha1-ajhfuIU9lS1f8F0Oiq+UJ43GPc8=",
           "dev": true,
           "requires": {
@@ -4193,7 +4193,7 @@
     },
     "create-hash": {
       "version": "1.2.0",
-      "resolved": "http://registry.npmjs.org/create-hash/-/create-hash-1.2.0.tgz",
+      "resolved": "https://registry.npmjs.org/create-hash/-/create-hash-1.2.0.tgz",
       "integrity": "sha512-z00bCGNHDG8mHAkP7CtT1qVu+bFQUPjYq/4Iv3C3kWjTFV10zIjfSoeqXo9Asws8gwSHDGj/hl2u4OGIjapeCg==",
       "dev": true,
       "requires": {
@@ -4206,7 +4206,7 @@
     },
     "create-hmac": {
       "version": "1.1.7",
-      "resolved": "http://registry.npmjs.org/create-hmac/-/create-hmac-1.1.7.tgz",
+      "resolved": "https://registry.npmjs.org/create-hmac/-/create-hmac-1.1.7.tgz",
       "integrity": "sha512-MJG9liiZ+ogc4TzUwuvbER1JRdgvUFSB5+VR/g5h82fGaIRWMWddtKBHi7/sVhfjQZ6SehlyhvQYrcYkaUIpLg==",
       "dev": true,
       "requires": {
@@ -4580,7 +4580,7 @@
     },
     "diffie-hellman": {
       "version": "5.0.3",
-      "resolved": "http://registry.npmjs.org/diffie-hellman/-/diffie-hellman-5.0.3.tgz",
+      "resolved": "https://registry.npmjs.org/diffie-hellman/-/diffie-hellman-5.0.3.tgz",
       "integrity": "sha512-kqag/Nl+f3GwyK25fhUMYj81BUOrZ9IuJsjIcDE5icNM9FJHAVm3VcUDxdLPoQtTuUylWm6ZIknYJwwaPxsUzg==",
       "dev": true,
       "requires": {
@@ -4709,6 +4709,12 @@
       "resolved": "https://registry.npmjs.org/ee-first/-/ee-first-1.1.1.tgz",
       "integrity": "sha1-WQxhFWsK4vTwJVcyoViyZrxWsh0="
     },
+    "ejs": {
+      "version": "2.5.9",
+      "resolved": "https://registry.npmjs.org/ejs/-/ejs-2.5.9.tgz",
+      "integrity": "sha512-GJCAeDBKfREgkBtgrYSf9hQy9kTb3helv0zGdzqhM7iAkW8FA/ZF97VQDbwFiwIT8MQLLOe5VlPZOEvZAqtUAQ==",
+      "dev": true
+    },
     "elegant-spinner": {
       "version": "1.0.1",
       "resolved": "https://registry.npmjs.org/elegant-spinner/-/elegant-spinner-1.0.1.tgz",
@@ -5963,6 +5969,12 @@
         "readable-stream": "^2.0.0"
       }
     },
+    "fs": {
+      "version": "0.0.1-security",
+      "resolved": "https://registry.npmjs.org/fs/-/fs-0.0.1-security.tgz",
+      "integrity": "sha1-invTcYa23d84E/I4WLV+yq9eQdQ=",
+      "dev": true
+    },
     "fs-extra": {
       "version": "9.0.0",
       "resolved": "https://registry.npmjs.org/fs-extra/-/fs-extra-9.0.0.tgz",
@@ -6096,7 +6108,7 @@
         },
         "strip-ansi": {
           "version": "3.0.1",
-          "resolved": "http://registry.npmjs.org/strip-ansi/-/strip-ansi-3.0.1.tgz",
+          "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-3.0.1.tgz",
           "integrity": "sha1-ajhfuIU9lS1f8F0Oiq+UJ43GPc8=",
           "dev": true,
           "requires": {
@@ -9133,7 +9145,7 @@
         },
         "chalk": {
           "version": "1.1.3",
-          "resolved": "http://registry.npmjs.org/chalk/-/chalk-1.1.3.tgz",
+          "resolved": "https://registry.npmjs.org/chalk/-/chalk-1.1.3.tgz",
           "integrity": "sha1-qBFcVeSnAv5NFQq9OHKCKn4J/Jg=",
           "dev": true,
           "requires": {
@@ -9171,7 +9183,7 @@
         },
         "strip-ansi": {
           "version": "3.0.1",
-          "resolved": "http://registry.npmjs.org/strip-ansi/-/strip-ansi-3.0.1.tgz",
+          "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-3.0.1.tgz",
           "integrity": "sha1-ajhfuIU9lS1f8F0Oiq+UJ43GPc8=",
           "dev": true,
           "requires": {
@@ -9668,7 +9680,7 @@
     },
     "meow": {
       "version": "3.7.0",
-      "resolved": "http://registry.npmjs.org/meow/-/meow-3.7.0.tgz",
+      "resolved": "https://registry.npmjs.org/meow/-/meow-3.7.0.tgz",
       "integrity": "sha1-cstmi0JSKCkKu/qFaJJYcwioAfs=",
       "dev": true,
       "requires": {
@@ -10022,7 +10034,7 @@
         },
         "semver": {
           "version": "5.3.0",
-          "resolved": "http://registry.npmjs.org/semver/-/semver-5.3.0.tgz",
+          "resolved": "https://registry.npmjs.org/semver/-/semver-5.3.0.tgz",
           "integrity": "sha1-myzl094C0XxgEq0yaqa00M9U+U8=",
           "dev": true
         }
@@ -10156,7 +10168,7 @@
         },
         "chalk": {
           "version": "1.1.3",
-          "resolved": "http://registry.npmjs.org/chalk/-/chalk-1.1.3.tgz",
+          "resolved": "https://registry.npmjs.org/chalk/-/chalk-1.1.3.tgz",
           "integrity": "sha1-qBFcVeSnAv5NFQq9OHKCKn4J/Jg=",
           "dev": true,
           "requires": {
@@ -10188,7 +10200,7 @@
         },
         "strip-ansi": {
           "version": "3.0.1",
-          "resolved": "http://registry.npmjs.org/strip-ansi/-/strip-ansi-3.0.1.tgz",
+          "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-3.0.1.tgz",
           "integrity": "sha1-ajhfuIU9lS1f8F0Oiq+UJ43GPc8=",
           "dev": true,
           "requires": {
@@ -12004,7 +12016,7 @@
       "dependencies": {
         "convert-source-map": {
           "version": "0.3.5",
-          "resolved": "http://registry.npmjs.org/convert-source-map/-/convert-source-map-0.3.5.tgz",
+          "resolved": "https://registry.npmjs.org/convert-source-map/-/convert-source-map-0.3.5.tgz",
           "integrity": "sha1-8dgClQr33SYxof6+BZZVDIarMZA=",
           "dev": true
         }
@@ -12294,7 +12306,7 @@
         },
         "strip-ansi": {
           "version": "3.0.1",
-          "resolved": "http://registry.npmjs.org/strip-ansi/-/strip-ansi-3.0.1.tgz",
+          "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-3.0.1.tgz",
           "integrity": "sha1-ajhfuIU9lS1f8F0Oiq+UJ43GPc8=",
           "dev": true,
           "requires": {
@@ -12442,7 +12454,7 @@
       "dependencies": {
         "source-map": {
           "version": "0.4.4",
-          "resolved": "http://registry.npmjs.org/source-map/-/source-map-0.4.4.tgz",
+          "resolved": "https://registry.npmjs.org/source-map/-/source-map-0.4.4.tgz",
           "integrity": "sha1-66T12pwNyZneaAMti092FzZSA2s=",
           "dev": true,
           "requires": {
@@ -12570,7 +12582,7 @@
     },
     "sha.js": {
       "version": "2.4.11",
-      "resolved": "http://registry.npmjs.org/sha.js/-/sha.js-2.4.11.tgz",
+      "resolved": "https://registry.npmjs.org/sha.js/-/sha.js-2.4.11.tgz",
       "integrity": "sha512-QMEp5B7cftE7APOjk5Y6xgrbWu+WkLVQwk8JNjZ8nKRciZaByEW6MubieAiToS7+dwvrjGhH8jRXz3MVd0AYqQ==",
       "dev": true,
       "requires": {
@@ -12650,7 +12662,7 @@
     },
     "slice-ansi": {
       "version": "0.0.4",
-      "resolved": "http://registry.npmjs.org/slice-ansi/-/slice-ansi-0.0.4.tgz",
+      "resolved": "https://registry.npmjs.org/slice-ansi/-/slice-ansi-0.0.4.tgz",
       "integrity": "sha1-7b+JA/ZvfOL46v1s7tZeJkyDGzU=",
       "dev": true
     },
@@ -13761,6 +13773,12 @@
       "integrity": "sha512-+O8/qh/Qj8CgC6eYBVBykMrNtp5Gebn4dlGD/kKXVkJNDwyrAwSIqwz8CDf+tsAIWVycKcku6gIXJ0qwx/ZXaQ==",
       "dev": true
     },
+    "underscore": {
+      "version": "1.6.0",
+      "resolved": "https://registry.npmjs.org/underscore/-/underscore-1.6.0.tgz",
+      "integrity": "sha1-izixDKze9jM3uLJOT/htRa6lKag=",
+      "dev": true
+    },
     "union": {
       "version": "0.5.0",
       "resolved": "https://registry.npmjs.org/union/-/union-0.5.0.tgz",
@@ -14429,6 +14447,7 @@
               "version": "2.9.0",
               "bundled": true,
               "dev": true,
+              "optional": true,
               "requires": {
                 "safe-buffer": "^5.1.2",
                 "yallist": "^3.0.0"
@@ -14447,6 +14466,7 @@
               "version": "0.5.3",
               "bundled": true,
               "dev": true,
+              "optional": true,
               "requires": {
                 "minimist": "^1.2.5"
               }
@@ -14550,6 +14570,7 @@
               "version": "1.4.0",
               "bundled": true,
               "dev": true,
+              "optional": true,
               "requires": {
                 "wrappy": "1"
               }
@@ -14627,7 +14648,8 @@
             "safe-buffer": {
               "version": "5.1.2",
               "bundled": true,
-              "dev": true
+              "dev": true,
+              "optional": true
             },
             "safer-buffer": {
               "version": "2.1.2",
@@ -14727,12 +14749,14 @@
             "wrappy": {
               "version": "1.0.2",
               "bundled": true,
-              "dev": true
+              "dev": true,
+              "optional": true
             },
             "yallist": {
               "version": "3.1.1",
               "bundled": true,
-              "dev": true
+              "dev": true,
+              "optional": true
             }
           }
         },
@@ -15278,6 +15302,17 @@
         }
       }
     },
+    "webpack-version-file-plugin": {
+      "version": "0.4.0",
+      "resolved": "https://registry.npmjs.org/webpack-version-file-plugin/-/webpack-version-file-plugin-0.4.0.tgz",
+      "integrity": "sha512-0+lgy3t04EAR3pIWDVKckytGlPKNmbGxPlB5DZ3vF3atC8DWtHwimUOuvdljEnGaTIpiTWitFJPaMLUvKCqO9g==",
+      "dev": true,
+      "requires": {
+        "ejs": "~> 2.5.5",
+        "fs": "^0.0.1-security",
+        "underscore": "~1.6.0"
+      }
+    },
     "whatwg-encoding": {
       "version": "1.0.5",
       "resolved": "https://registry.npmjs.org/whatwg-encoding/-/whatwg-encoding-1.0.5.tgz",

package.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "0.7.0-dev.1",
+  "version": "0.7.0-dev.3",
   "description": "A comprehensive macromolecular library.",
   "homepage": "https://github.com/molstar/molstar#readme",
   "repository": {
@@ -45,7 +45,7 @@
     "cif2bcif": "lib/apps/cif2bcif/index.js",
     "cifschema": "lib/apps/cifschema/index.js",
     "model-server": "lib/servers/servers/model/server.js",
-    "model-server-query": "lib/servers/servers/model/local.js",
+    "model-server-query": "lib/servers/servers/model/query.js",
     "model-server-preprocess": "lib/servers/servers/model/preprocess.js",
     "volume-server": "lib/servers/servers/volume/server.js",
     "volume-server-query": "lib/servers/servers/volume/query.js",
@@ -115,7 +115,8 @@
     "ts-jest": "^25.4.0",
     "typescript": "^3.8.3",
     "webpack": "^4.42.1",
-    "webpack-cli": "^3.3.11"
+    "webpack-cli": "^3.3.11",
+    "webpack-version-file-plugin": "^0.4.0"
   },
   "dependencies": {
     "@material-ui/core": "^4.9.10",

src/extensions/rcsb/validation-report/behavior.ts

@@ -71,8 +71,7 @@ export const RCSBValidationReport = PluginBehavior.create<{ autoAttach: boolean,
         }
 
         unregister() {
-            // TODO
-            // DefaultQueryRuntimeTable.removeCustomProp(this.provider.descriptor);
+            DefaultQueryRuntimeTable.removeCustomProp(this.provider.descriptor);
 
             this.ctx.customStructureProperties.unregister(this.provider.descriptor.name);
 

src/mol-plugin/behavior/dynamic/custom-props/computed/accessible-surface-area.ts

@@ -51,8 +51,7 @@ export const AccessibleSurfaceArea = PluginBehavior.create<{ autoAttach: boolean
         }
 
         unregister() {
-            // TODO
-            // DefaultQueryRuntimeTable.removeCustomProp(this.provider.descriptor);
+            DefaultQueryRuntimeTable.removeCustomProp(this.provider.descriptor);
 
             this.ctx.customStructureProperties.unregister(this.provider.descriptor.name);
             this.ctx.representation.structure.themes.colorThemeRegistry.remove(AccessibleSurfaceAreaColorThemeProvider);

src/mol-plugin/version.ts

@@ -5,11 +5,8 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-/** version from package.json, to be filled in at bundle build time */
-declare const __VERSION__: string;
-export const PLUGIN_VERSION = __VERSION__;
+/** version from package.json, to be filled in at build time */
+export const PLUGIN_VERSION = '';
 
-/** unix time stamp, to be filled in at bundle build time */
-declare const __VERSION_TIMESTAMP__: number;
-export const PLUGIN_VERSION_TIMESTAMP = __VERSION_TIMESTAMP__;
-export const PLUGIN_VERSION_DATE = new Date(PLUGIN_VERSION_TIMESTAMP);
+/** to be filled in at build time */
+export const PLUGIN_VERSION_DATE = +new Date();

src/mol-script/runtime/query/base.ts

@@ -11,9 +11,13 @@ import { MSymbol } from '../../language/symbol';
 export class QueryRuntimeTable {
     private map = new Map<string, QuerySymbolRuntime>();
 
+    removeSymbol(runtime: QuerySymbolRuntime) {
+        this.map.delete(runtime.symbol.id);
+    }
+
     addSymbol(runtime: QuerySymbolRuntime) {
         if (this.map.has(runtime.symbol.id)) {
-            throw new Error(`Symbol '${runtime.symbol.id}' already added.`);
+            console.warn(`Symbol '${runtime.symbol.id}' already added. Call removeSymbol/removeCustomProps re-adding the symbol.`);
         }
         this.map.set(runtime.symbol.id, runtime);
     }
@@ -26,6 +30,14 @@ export class QueryRuntimeTable {
         }
     }
 
+    removeCustomProp(desc: CustomPropertyDescriptor<any>) {
+        if (!desc.symbols) return;
+
+        for (const k of Object.keys(desc.symbols)) {
+            this.removeSymbol((desc.symbols as any)[k]);
+        }
+    }
+
     getRuntime(id: string) {
         return this.map.get(id);
     }

webpack.config.common.js

@@ -2,6 +2,7 @@ const path = require('path');
 const webpack = require('webpack');
 const ExtraWatchWebpackPlugin = require('extra-watch-webpack-plugin');
 const MiniCssExtractPlugin = require('mini-css-extract-plugin');
+const VersionFile = require('webpack-version-file-plugin');
 // const CircularDependencyPlugin = require('circular-dependency-plugin');
 
 const sharedConfig = {
@@ -38,11 +39,17 @@ const sharedConfig = {
             ],
         }),
         new webpack.DefinePlugin({
-            __VERSION__: webpack.DefinePlugin.runtimeValue(() => JSON.stringify(require('./package.json').version), true),
-            __VERSION_TIMESTAMP__: webpack.DefinePlugin.runtimeValue(() => `${new Date().valueOf()}`, true),
+            // __VERSION__: webpack.DefinePlugin.runtimeValue(() => JSON.stringify(require('./package.json').version), true),
+            // __VERSION_TIMESTAMP__: webpack.DefinePlugin.runtimeValue(() => `${new Date().valueOf()}`, true),
             'process.env.DEBUG': JSON.stringify(process.env.DEBUG)
         }),
-        new MiniCssExtractPlugin({ filename: 'app.css' })
+        new MiniCssExtractPlugin({ filename: 'app.css' }),
+        new VersionFile({
+            extras: { timestamp: `${new Date().valueOf()}` },
+            packageFile: path.resolve(__dirname, 'package.json'),
+            templateString: `export const PLUGIN_VERSION = '<%= package.version %>';\nexport const PLUGIN_VERSION_DATE = new Date(<%= extras.timestamp %>);`,
+            outputFile: path.resolve(__dirname, 'lib/mol-plugin/version.js')
+        })
     ],
     resolve: {
         modules: [