updated molstar & packages

package-lock.json

@@ -97,12 +97,12 @@
             }
         },
         "@typescript-eslint/eslint-plugin": {
-            "version": "2.21.0",
-            "resolved": "https://registry.npmjs.org/@typescript-eslint/eslint-plugin/-/eslint-plugin-2.21.0.tgz",
-            "integrity": "sha512-b5jjjDMxzcjh/Sbjuo7WyhrQmVJg0WipTHQgXh5Xwx10uYm6nPWqN1WGOsaNq4HR3Zh4wUx4IRQdDkCHwyewyw==",
+            "version": "2.22.0",
+            "resolved": "https://registry.npmjs.org/@typescript-eslint/eslint-plugin/-/eslint-plugin-2.22.0.tgz",
+            "integrity": "sha512-BvxRLaTDVQ3N+Qq8BivLiE9akQLAOUfxNHIEhedOcg8B2+jY8Rc4/D+iVprvuMX1AdezFYautuGDwr9QxqSxBQ==",
             "dev": true,
             "requires": {
-                "@typescript-eslint/experimental-utils": "2.21.0",
+                "@typescript-eslint/experimental-utils": "2.22.0",
                 "eslint-utils": "^1.4.3",
                 "functional-red-black-tree": "^1.0.1",
                 "regexpp": "^3.0.0",
@@ -110,32 +110,32 @@
             }
         },
         "@typescript-eslint/experimental-utils": {
-            "version": "2.21.0",
-            "resolved": "https://registry.npmjs.org/@typescript-eslint/experimental-utils/-/experimental-utils-2.21.0.tgz",
-            "integrity": "sha512-olKw9JP/XUkav4lq0I7S1mhGgONJF9rHNhKFn9wJlpfRVjNo3PPjSvybxEldvCXnvD+WAshSzqH5cEjPp9CsBA==",
+            "version": "2.22.0",
+            "resolved": "https://registry.npmjs.org/@typescript-eslint/experimental-utils/-/experimental-utils-2.22.0.tgz",
+            "integrity": "sha512-sJt1GYBe6yC0dWOQzXlp+tiuGglNhJC9eXZeC8GBVH98Zv9jtatccuhz0OF5kC/DwChqsNfghHx7OlIDQjNYAQ==",
             "dev": true,
             "requires": {
                 "@types/json-schema": "^7.0.3",
-                "@typescript-eslint/typescript-estree": "2.21.0",
+                "@typescript-eslint/typescript-estree": "2.22.0",
                 "eslint-scope": "^5.0.0"
             }
         },
         "@typescript-eslint/parser": {
-            "version": "2.21.0",
-            "resolved": "https://registry.npmjs.org/@typescript-eslint/parser/-/parser-2.21.0.tgz",
-            "integrity": "sha512-VrmbdrrrvvI6cPPOG7uOgGUFXNYTiSbnRq8ZMyuGa4+qmXJXVLEEz78hKuqupvkpwJQNk1Ucz1TenrRP90gmBg==",
+            "version": "2.22.0",
+            "resolved": "https://registry.npmjs.org/@typescript-eslint/parser/-/parser-2.22.0.tgz",
+            "integrity": "sha512-FaZKC1X+nvD7qMPqKFUYHz3H0TAioSVFGvG29f796Nc5tBluoqfHgLbSFKsh7mKjRoeTm8J9WX2Wo9EyZWjG7w==",
             "dev": true,
             "requires": {
                 "@types/eslint-visitor-keys": "^1.0.0",
-                "@typescript-eslint/experimental-utils": "2.21.0",
-                "@typescript-eslint/typescript-estree": "2.21.0",
+                "@typescript-eslint/experimental-utils": "2.22.0",
+                "@typescript-eslint/typescript-estree": "2.22.0",
                 "eslint-visitor-keys": "^1.1.0"
             }
         },
         "@typescript-eslint/typescript-estree": {
-            "version": "2.21.0",
-            "resolved": "https://registry.npmjs.org/@typescript-eslint/typescript-estree/-/typescript-estree-2.21.0.tgz",
-            "integrity": "sha512-NC/nogZNb9IK2MEFQqyDBAciOT8Lp8O3KgAfvHx2Skx6WBo+KmDqlU3R9KxHONaijfTIKtojRe3SZQyMjr3wBw==",
+            "version": "2.22.0",
+            "resolved": "https://registry.npmjs.org/@typescript-eslint/typescript-estree/-/typescript-estree-2.22.0.tgz",
+            "integrity": "sha512-2HFZW2FQc4MhIBB8WhDm9lVFaBDy6h9jGrJ4V2Uzxe/ON29HCHBTj3GkgcsgMWfsl2U5as+pTOr30Nibaw7qRQ==",
             "dev": true,
             "requires": {
                 "debug": "^4.1.1",
@@ -4192,13 +4192,13 @@
             }
         },
         "molstar": {
-            "version": "0.5.5",
+            "version": "0.5.6",
             "dev": true,
             "requires": {
                 "@types/argparse": "^1.0.38",
                 "@types/benchmark": "^1.0.31",
                 "@types/compression": "1.7.0",
-                "@types/express": "^4.17.2",
+                "@types/express": "^4.17.3",
                 "@types/jest": "^25.1.3",
                 "@types/node": "^13.7.7",
                 "@types/node-fetch": "^2.5.5",
@@ -4211,7 +4211,7 @@
                 "cors": "^2.8.5",
                 "express": "^4.17.1",
                 "graphql": "^14.6.0",
-                "immer": "^5.3.6",
+                "immer": "^6.0.0",
                 "immutable": "^3.8.2",
                 "node-fetch": "^2.6.0",
                 "react": "^16.13.0",
@@ -7385,7 +7385,7 @@
                 },
                 "@types/valid-url": {
                     "version": "1.0.2",
-                    "resolved": "https://registry.npmjs.org/@types/valid-url/-/valid-url-1.0.2.tgz",
+                    "resolved": "http://registry.npmjs.org/@types/valid-url/-/valid-url-1.0.2.tgz",
                     "integrity": "sha1-YPpDXOJL/VuhB7jSqAeWrq86j0U="
                 },
                 "@types/yargs": {
@@ -8749,7 +8749,7 @@
                 },
                 "camelcase-keys": {
                     "version": "2.1.0",
-                    "resolved": "https://registry.npmjs.org/camelcase-keys/-/camelcase-keys-2.1.0.tgz",
+                    "resolved": "http://registry.npmjs.org/camelcase-keys/-/camelcase-keys-2.1.0.tgz",
                     "integrity": "sha1-MIvur/3ygRkFHvodkyITyRuPkuc=",
                     "requires": {
                         "camelcase": "^2.0.0",
@@ -11725,7 +11725,7 @@
                         },
                         "strip-ansi": {
                             "version": "3.0.1",
-                            "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-3.0.1.tgz",
+                            "resolved": "http://registry.npmjs.org/strip-ansi/-/strip-ansi-3.0.1.tgz",
                             "integrity": "sha1-ajhfuIU9lS1f8F0Oiq+UJ43GPc8=",
                             "requires": {
                                 "ansi-regex": "^2.0.0"
@@ -16136,7 +16136,7 @@
                 },
                 "meow": {
                     "version": "3.7.0",
-                    "resolved": "https://registry.npmjs.org/meow/-/meow-3.7.0.tgz",
+                    "resolved": "http://registry.npmjs.org/meow/-/meow-3.7.0.tgz",
                     "integrity": "sha1-cstmi0JSKCkKu/qFaJJYcwioAfs=",
                     "requires": {
                         "camelcase-keys": "^2.0.0",
@@ -16153,7 +16153,7 @@
                     "dependencies": {
                         "minimist": {
                             "version": "1.2.0",
-                            "resolved": "https://registry.npmjs.org/minimist/-/minimist-1.2.0.tgz",
+                            "resolved": "http://registry.npmjs.org/minimist/-/minimist-1.2.0.tgz",
                             "integrity": "sha1-o1AIsg9BOD7sH7kU9M1d95omQoQ="
                         }
                     }
@@ -16440,7 +16440,7 @@
                     "dependencies": {
                         "semver": {
                             "version": "5.3.0",
-                            "resolved": "https://registry.npmjs.org/semver/-/semver-5.3.0.tgz",
+                            "resolved": "http://registry.npmjs.org/semver/-/semver-5.3.0.tgz",
                             "integrity": "sha1-myzl094C0XxgEq0yaqa00M9U+U8="
                         }
                     }
@@ -16563,7 +16563,7 @@
                         },
                         "chalk": {
                             "version": "1.1.3",
-                            "resolved": "https://registry.npmjs.org/chalk/-/chalk-1.1.3.tgz",
+                            "resolved": "http://registry.npmjs.org/chalk/-/chalk-1.1.3.tgz",
                             "integrity": "sha1-qBFcVeSnAv5NFQq9OHKCKn4J/Jg=",
                             "requires": {
                                 "ansi-styles": "^2.2.1",
@@ -16584,7 +16584,7 @@
                         },
                         "strip-ansi": {
                             "version": "3.0.1",
-                            "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-3.0.1.tgz",
+                            "resolved": "http://registry.npmjs.org/strip-ansi/-/strip-ansi-3.0.1.tgz",
                             "integrity": "sha1-ajhfuIU9lS1f8F0Oiq+UJ43GPc8=",
                             "requires": {
                                 "ansi-regex": "^2.0.0"
@@ -18192,7 +18192,7 @@
                     "dependencies": {
                         "convert-source-map": {
                             "version": "0.3.5",
-                            "resolved": "https://registry.npmjs.org/convert-source-map/-/convert-source-map-0.3.5.tgz",
+                            "resolved": "http://registry.npmjs.org/convert-source-map/-/convert-source-map-0.3.5.tgz",
                             "integrity": "sha1-8dgClQr33SYxof6+BZZVDIarMZA="
                         }
                     }
@@ -18610,7 +18610,7 @@
                         },
                         "os-locale": {
                             "version": "1.4.0",
-                            "resolved": "https://registry.npmjs.org/os-locale/-/os-locale-1.4.0.tgz",
+                            "resolved": "http://registry.npmjs.org/os-locale/-/os-locale-1.4.0.tgz",
                             "integrity": "sha1-IPnxeuKe00XoveWDsT0gCYA8FNk=",
                             "requires": {
                                 "lcid": "^1.0.0"
@@ -18633,7 +18633,7 @@
                         },
                         "strip-ansi": {
                             "version": "3.0.1",
-                            "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-3.0.1.tgz",
+                            "resolved": "http://registry.npmjs.org/strip-ansi/-/strip-ansi-3.0.1.tgz",
                             "integrity": "sha1-ajhfuIU9lS1f8F0Oiq+UJ43GPc8=",
                             "requires": {
                                 "ansi-regex": "^2.0.0"
@@ -18745,7 +18745,7 @@
                     "dependencies": {
                         "source-map": {
                             "version": "0.4.4",
-                            "resolved": "https://registry.npmjs.org/source-map/-/source-map-0.4.4.tgz",
+                            "resolved": "http://registry.npmjs.org/source-map/-/source-map-0.4.4.tgz",
                             "integrity": "sha1-66T12pwNyZneaAMti092FzZSA2s=",
                             "requires": {
                                 "amdefine": ">=0.0.4"
@@ -22974,9 +22974,9 @@
             }
         },
         "terser": {
-            "version": "4.6.3",
-            "resolved": "https://registry.npmjs.org/terser/-/terser-4.6.3.tgz",
-            "integrity": "sha512-Lw+ieAXmY69d09IIc/yqeBqXpEQIpDGZqT34ui1QWXIUpR2RjbqEkT8X7Lgex19hslSqcWM5iMN2kM11eMsESQ==",
+            "version": "4.6.6",
+            "resolved": "https://registry.npmjs.org/terser/-/terser-4.6.6.tgz",
+            "integrity": "sha512-4lYPyeNmstjIIESr/ysHg2vUPRGf2tzF9z2yYwnowXVuVzLEamPN1Gfrz7f8I9uEPuHcbFlW4PLIAsJoxXyJ1g==",
             "dev": true,
             "requires": {
                 "commander": "^2.20.0",
@@ -23395,9 +23395,9 @@
             }
         },
         "webpack": {
-            "version": "4.41.6",
-            "resolved": "https://registry.npmjs.org/webpack/-/webpack-4.41.6.tgz",
-            "integrity": "sha512-yxXfV0Zv9WMGRD+QexkZzmGIh54bsvEs+9aRWxnN8erLWEOehAKUTeNBoUbA6HPEZPlRo7KDi2ZcNveoZgK9MA==",
+            "version": "4.42.0",
+            "resolved": "https://registry.npmjs.org/webpack/-/webpack-4.42.0.tgz",
+            "integrity": "sha512-EzJRHvwQyBiYrYqhyjW9AqM90dE4+s1/XtCfn7uWg6cS72zH+2VPFAlsnW0+W0cDi0XRjNKUMoJtpSi50+Ph6w==",
             "dev": true,
             "requires": {
                 "@webassemblyjs/ast": "1.8.5",
@@ -23432,9 +23432,9 @@
                     "dev": true
                 },
                 "ajv": {
-                    "version": "6.11.0",
-                    "resolved": "https://registry.npmjs.org/ajv/-/ajv-6.11.0.tgz",
-                    "integrity": "sha512-nCprB/0syFYy9fVYU1ox1l2KN8S9I+tziH8D4zdZuLT3N6RMlGSGt5FSTpAiHB/Whv8Qs1cWHma1aMKZyaHRKA==",
+                    "version": "6.12.0",
+                    "resolved": "https://registry.npmjs.org/ajv/-/ajv-6.12.0.tgz",
+                    "integrity": "sha512-D6gFiFA0RRLyUbvijN74DWAjXSFxWKaWP7mldxkVhyhAV3+SWA9HEJPHQ2c9soIeTFJqcSdFDGFgdqs1iUU2Hw==",
                     "dev": true,
                     "requires": {
                         "fast-deep-equal": "^3.1.1",

package.json

@@ -41,8 +41,8 @@
         "@types/node-fetch": "^2.5.5",
         "@types/react": "^16.9.23",
         "@types/react-dom": "^16.9.5",
-        "@typescript-eslint/eslint-plugin": "^2.21.0",
-        "@typescript-eslint/parser": "^2.21.0",
+        "@typescript-eslint/eslint-plugin": "^2.22.0",
+        "@typescript-eslint/parser": "^2.22.0",
         "concurrently": "^5.1.0",
         "cpx2": "^2.0.0",
         "css-loader": "^3.4.2",
@@ -50,7 +50,7 @@
         "extra-watch-webpack-plugin": "^1.0.3",
         "file-loader": "^5.1.0",
         "mini-css-extract-plugin": "^0.9.0",
-        "molstar": "0.5.5",
+        "molstar": "^0.5.6",
         "node-fetch": "^2.6.0",
         "node-sass": "^4.13.1",
         "raw-loader": "^4.0.0",
@@ -61,7 +61,7 @@
         "sass-loader": "^8.0.2",
         "style-loader": "^1.1.3",
         "typescript": "3.8.3",
-        "webpack": "^4.41.6",
+        "webpack": "^4.42.0",
         "webpack-cli": "^3.3.11"
     },
     "dependencies": {}

src/structure-viewer/helpers/model.ts

@@ -5,11 +5,11 @@
  */
 
 import { StateElements, StructureViewerState, LoadParams } from '../types';
-import { PluginCommands } from 'molstar/lib/mol-plugin/command';
+import { PluginCommands } from 'molstar/lib/mol-plugin/commands';
 import { StateBuilder } from 'molstar/lib/mol-state';
-import { StateTransforms } from 'molstar/lib/mol-plugin/state/transforms';
+import { StateTransforms } from 'molstar/lib/mol-plugin-state/transforms';
 import { PluginContext } from 'molstar/lib/mol-plugin/context';
-import { PluginStateObject as PSO } from 'molstar/lib/mol-plugin/state/objects';
+import { PluginStateObject as PSO } from 'molstar/lib/mol-plugin-state/objects';
 
 export class ModelLoader {
     get customState() {
@@ -35,7 +35,7 @@ export class ModelLoader {
         if (!fileOrUrl) return
 
         const state = this.plugin.state.dataState;
-        await PluginCommands.State.RemoveObject.dispatch(this.plugin, { state, ref: state.tree.root.ref })
+        await PluginCommands.State.RemoveObject(this.plugin, { state, ref: state.tree.root.ref })
 
         const isBinary = format === 'bcif'
         const data = fileOrUrl instanceof File
@@ -46,7 +46,7 @@ export class ModelLoader {
     }
 
     async applyState(tree: StateBuilder) {
-        await PluginCommands.State.Update.dispatch(this.plugin, { state: this.plugin.state.dataState, tree })
+        await PluginCommands.State.Update(this.plugin, { state: this.plugin.state.dataState, tree }).catch(e => console.log(e))
     }
 
     constructor(private plugin: PluginContext) {

src/structure-viewer/helpers/structure.ts

@@ -5,12 +5,12 @@
  */
 
 import { StateElements, AssemblyNames, StructureViewerState, ModelNames } from '../types';
-import { PluginCommands } from 'molstar/lib/mol-plugin/command';
+import { PluginCommands } from 'molstar/lib/mol-plugin/commands';
 import { StateBuilder, State, StateSelection } from 'molstar/lib/mol-state';
-import { StateTransforms } from 'molstar/lib/mol-plugin/state/transforms';
+import { StateTransforms } from 'molstar/lib/mol-plugin-state/transforms';
 import { Vec3 } from 'molstar/lib/mol-math/linear-algebra';
 import { PluginContext } from 'molstar/lib/mol-plugin/context';
-import { PluginStateObject as PSO } from 'molstar/lib/mol-plugin/state/objects';
+import { PluginStateObject as PSO } from 'molstar/lib/mol-plugin-state/objects';
 import { AssemblySymmetryProvider } from 'molstar/lib/mol-model-props/rcsb/assembly-symmetry';
 import { Task } from 'molstar/lib/mol-task';
 import { AssemblySymmetry3D } from 'molstar/lib/mol-plugin/behavior/dynamic/custom-props/rcsb/assembly-symmetry';
@@ -23,7 +23,7 @@ export class StructureView {
     }
 
     async applyState(tree: StateBuilder) {
-        await PluginCommands.State.Update.dispatch(this.plugin, { state: this.plugin.state.dataState, tree });
+        await PluginCommands.State.Update(this.plugin, { state: this.plugin.state.dataState, tree });
     }
 
     get experimentalData () {

src/structure-viewer/helpers/volume.ts

@@ -5,7 +5,7 @@
  */
 
 import { StateElements, StructureViewerState } from '../types';
-import { PluginCommands } from 'molstar/lib/mol-plugin/command';
+import { PluginCommands } from 'molstar/lib/mol-plugin/commands';
 import { StateSelection, StateBuilder } from 'molstar/lib/mol-state';
 import { PluginContext } from 'molstar/lib/mol-plugin/context';
 import { InitVolumeStreaming, CreateVolumeStreamingInfo, CreateVolumeStreamingBehavior } from 'molstar/lib/mol-plugin/behavior/dynamic/volume-streaming/transformers';
@@ -24,7 +24,7 @@ export class VolumeData {
     }
 
     async applyState(tree: StateBuilder) {
-        await PluginCommands.State.Update.dispatch(this.plugin, { state: this.state, tree });
+        await PluginCommands.State.Update(this.plugin, { state: this.state, tree });
     }
 
     async init() {
@@ -80,7 +80,7 @@ export class VolumeData {
     async remove() {
         const r = this.state.select(StateSelection.Generators.ofTransformer(CreateVolumeStreamingInfo))[0]
         if (!r) return
-        await PluginCommands.State.RemoveObject.dispatch(this.plugin, { state: this.state, ref: r.transform.ref })
+        await PluginCommands.State.RemoveObject(this.plugin, { state: this.state, ref: r.transform.ref })
     }
 
     constructor(private plugin: PluginContext) {

src/structure-viewer/index.ts

@@ -9,9 +9,9 @@ import { Plugin } from 'molstar/lib/mol-plugin-ui/plugin'
 import './index.html'
 import './favicon.ico'
 import { PluginContext } from 'molstar/lib/mol-plugin/context';
-import { PluginCommands } from 'molstar/lib/mol-plugin/command';
+import { PluginCommands } from 'molstar/lib/mol-plugin/commands';
 import { PluginBehaviors } from 'molstar/lib/mol-plugin/behavior';
-import { AnimateModelIndex } from 'molstar/lib/mol-plugin/state/animation/built-in';
+import { AnimateModelIndex } from 'molstar/lib/mol-plugin-state/animation/built-in';
 import { SupportedFormats, StructureViewerState, StructureViewerProps, LoadParams } from './types';
 import { ControlsWrapper, ViewportWrapper } from './ui/controls';
 import { PluginSpec } from 'molstar/lib/mol-plugin/spec';
@@ -103,9 +103,9 @@ export class StructureViewer {
         ReactDOM.render(React.createElement(Plugin, { plugin: this.plugin }), target)
 
         const renderer = this.plugin.canvas3d!.props.renderer;
-        PluginCommands.Canvas3D.SetSettings.dispatch(this.plugin, { settings: { renderer: { ...renderer, backgroundColor: ColorNames.white } } })
+        PluginCommands.Canvas3D.SetSettings(this.plugin, { settings: { renderer: { ...renderer, backgroundColor: ColorNames.white } } })
 
-        PluginCommands.Toast.Show.dispatch(this.plugin, {
+        PluginCommands.Toast.Show(this.plugin, {
             title: 'Welcome',
             message: `RCSB PDB Mol* Viewer ${RCSB_MOLSTAR_VERSION}`,
             key: 'toast-welcome',
@@ -120,10 +120,10 @@ export class StructureViewer {
 
     async loadPdbId(pdbId: string, props?: PresetProps) {
         const p = this.props.modelUrlProvider(pdbId)
-        this.load({ fileOrUrl: p.url, format: p.format }, props)
+        await this.load({ fileOrUrl: p.url, format: p.format }, props)
     }
 
     async loadUrl(url: string, props?: PresetProps) {
-        this.load({ fileOrUrl: url, format: 'cif', }, props)
+        await this.load({ fileOrUrl: url, format: 'cif', }, props)
     }
 }

src/structure-viewer/ui/open.tsx

@@ -7,7 +7,7 @@
 import * as React from 'react';
 import { ParamDefinition as PD } from 'molstar/lib/mol-util/param-definition';
 import { StateAction, StateTransform } from 'molstar/lib/mol-state';
-import { PluginStateObject } from 'molstar/lib/mol-plugin/state/objects';
+import { PluginStateObject } from 'molstar/lib/mol-plugin-state/objects';
 import { PluginContext } from 'molstar/lib/mol-plugin/context';
 import { Task } from 'molstar/lib/mol-task';
 import { ApplyActionControl } from 'molstar/lib/mol-plugin-ui/state/apply-action';

src/structure-viewer/ui/structure.tsx

@@ -10,8 +10,8 @@ import { StateElements, AssemblyNames, StructureViewerState } from '../types';
 import { ParameterControls } from 'molstar/lib/mol-plugin-ui/controls/parameters';
 import { ParamDefinition as PD } from 'molstar/lib/mol-util/param-definition';
 import { StateObject, StateTree, StateSelection } from 'molstar/lib/mol-state';
-import { PluginStateObject as PSO } from 'molstar/lib/mol-plugin/state/objects';
-import { StateTransforms } from 'molstar/lib/mol-plugin/state/transforms';
+import { PluginStateObject as PSO } from 'molstar/lib/mol-plugin-state/objects';
+import { StateTransforms } from 'molstar/lib/mol-plugin-state/transforms';
 import { stringToWords } from 'molstar/lib/mol-util/string';
 import { ModelSymmetry } from 'molstar/lib/mol-model-formats/structure/property/symmetry';
 import { AssemblySymmetryProvider } from 'molstar/lib/mol-model-props/rcsb/assembly-symmetry'