updated molstar and packages

package-lock.json

@@ -31,9 +31,9 @@
             }
         },
         "@jest/types": {
-            "version": "25.2.3",
-            "resolved": "https://registry.npmjs.org/@jest/types/-/types-25.2.3.tgz",
-            "integrity": "sha512-6oLQwO9mKif3Uph3RX5J1i3S7X7xtDHWBaaaoeKw8hOzV6YUd0qDcYcHZ6QXMHDIzSr7zzrEa51o2Ovlj6AtKQ==",
+            "version": "25.2.6",
+            "resolved": "https://registry.npmjs.org/@jest/types/-/types-25.2.6.tgz",
+            "integrity": "sha512-myJTTV37bxK7+3NgKc4Y/DlQ5q92/NOwZsZ+Uch7OXdElxOg61QYc72fPYNAjlvbnJ2YvbXLamIsa9tj48BmyQ==",
             "dev": true,
             "requires": {
                 "@types/istanbul-lib-coverage": "^2.0.0",
@@ -194,13 +194,13 @@
             }
         },
         "@types/jest": {
-            "version": "25.1.4",
-            "resolved": "https://registry.npmjs.org/@types/jest/-/jest-25.1.4.tgz",
-            "integrity": "sha512-QDDY2uNAhCV7TMCITrxz+MRk1EizcsevzfeS6LykIlq2V1E5oO4wXG8V2ZEd9w7Snxeeagk46YbMgZ8ESHx3sw==",
+            "version": "25.2.1",
+            "resolved": "https://registry.npmjs.org/@types/jest/-/jest-25.2.1.tgz",
+            "integrity": "sha512-msra1bCaAeEdkSyA0CZ6gW1ukMIvZ5YoJkdXw/qhQdsuuDlFTcEUrUw8CLCPt2rVRUfXlClVvK2gvPs9IokZaA==",
             "dev": true,
             "requires": {
-                "jest-diff": "^25.1.0",
-                "pretty-format": "^25.1.0"
+                "jest-diff": "^25.2.1",
+                "pretty-format": "^25.2.1"
             }
         },
         "@types/json-schema": {
@@ -216,9 +216,9 @@
             "dev": true
         },
         "@types/node": {
-            "version": "13.9.8",
-            "resolved": "https://registry.npmjs.org/@types/node/-/node-13.9.8.tgz",
-            "integrity": "sha512-1WgO8hsyHynlx7nhP1kr0OFzsgKz5XDQL+Lfc3b1Q3qIln/n8cKD4m09NJ0+P1Rq7Zgnc7N0+SsMnoD1rEb0kA==",
+            "version": "13.11.0",
+            "resolved": "https://registry.npmjs.org/@types/node/-/node-13.11.0.tgz",
+            "integrity": "sha512-uM4mnmsIIPK/yeO+42F2RQhGUIs39K2RFmugcJANppXe6J1nvH87PvzPZYpza7Xhhs8Yn9yIAVdLZ84z61+0xQ==",
             "dev": true
         },
         "@types/node-fetch": {
@@ -250,9 +250,9 @@
             "dev": true
         },
         "@types/react": {
-            "version": "16.9.31",
-            "resolved": "https://registry.npmjs.org/@types/react/-/react-16.9.31.tgz",
-            "integrity": "sha512-NpYJpNMWScFXtx3A2BJMeew2G3+9SEslVWMdxNJ6DLvxIuxWjY1bizK9q5Y1ujhln31vtjmhjOAYDr9Xx3k9FQ==",
+            "version": "16.9.32",
+            "resolved": "https://registry.npmjs.org/@types/react/-/react-16.9.32.tgz",
+            "integrity": "sha512-fmejdp0CTH00mOJmxUPPbWCEBWPvRIL4m8r0qD+BSDUqmutPyGQCHifzMpMzdvZwROdEdL78IuZItntFWgPXHQ==",
             "dev": true,
             "requires": {
                 "@types/prop-types": "*",
@@ -1968,9 +1968,9 @@
             "dev": true
         },
         "diff-sequences": {
-            "version": "25.2.1",
-            "resolved": "https://registry.npmjs.org/diff-sequences/-/diff-sequences-25.2.1.tgz",
-            "integrity": "sha512-foe7dXnGlSh3jR1ovJmdv+77VQj98eKCHHwJPbZ2eEf0fHwKbkZicpPxEch9smZ+n2dnF6QFwkOQdLq9hpeJUg==",
+            "version": "25.2.6",
+            "resolved": "https://registry.npmjs.org/diff-sequences/-/diff-sequences-25.2.6.tgz",
+            "integrity": "sha512-Hq8o7+6GaZeoFjtpgvRBUknSXNeJiCx7V9Fr94ZMljNiCr9n9L8H8aJqgWOQiDDGdyn29fRNcDdRVJ5fdyihfg==",
             "dev": true
         },
         "diffie-hellman": {
@@ -2950,8 +2950,7 @@
                 "ansi-regex": {
                     "version": "2.1.1",
                     "bundled": true,
-                    "dev": true,
-                    "optional": true
+                    "dev": true
                 },
                 "aproba": {
                     "version": "1.2.0",
@@ -3368,8 +3367,7 @@
                 "safe-buffer": {
                     "version": "5.1.2",
                     "bundled": true,
-                    "dev": true,
-                    "optional": true
+                    "dev": true
                 },
                 "safer-buffer": {
                     "version": "2.1.2",
@@ -3425,7 +3423,6 @@
                     "version": "3.0.1",
                     "bundled": true,
                     "dev": true,
-                    "optional": true,
                     "requires": {
                         "ansi-regex": "^2.0.0"
                     }
@@ -3469,14 +3466,12 @@
                 "wrappy": {
                     "version": "1.0.2",
                     "bundled": true,
-                    "dev": true,
-                    "optional": true
+                    "dev": true
                 },
                 "yallist": {
                     "version": "3.1.1",
                     "bundled": true,
-                    "dev": true,
-                    "optional": true
+                    "dev": true
                 }
             }
         },
@@ -4377,15 +4372,15 @@
             "dev": true
         },
         "jest-diff": {
-            "version": "25.2.3",
-            "resolved": "https://registry.npmjs.org/jest-diff/-/jest-diff-25.2.3.tgz",
-            "integrity": "sha512-VtZ6LAQtaQpFsmEzps15dQc5ELbJxy4L2DOSo2Ev411TUEtnJPkAMD7JneVypeMJQ1y3hgxN9Ao13n15FAnavg==",
+            "version": "25.2.6",
+            "resolved": "https://registry.npmjs.org/jest-diff/-/jest-diff-25.2.6.tgz",
+            "integrity": "sha512-KuadXImtRghTFga+/adnNrv9s61HudRMR7gVSbP35UKZdn4IK2/0N0PpGZIqtmllK9aUyye54I3nu28OYSnqOg==",
             "dev": true,
             "requires": {
                 "chalk": "^3.0.0",
-                "diff-sequences": "^25.2.1",
-                "jest-get-type": "^25.2.1",
-                "pretty-format": "^25.2.3"
+                "diff-sequences": "^25.2.6",
+                "jest-get-type": "^25.2.6",
+                "pretty-format": "^25.2.6"
             },
             "dependencies": {
                 "ansi-styles": {
@@ -4441,9 +4436,9 @@
             }
         },
         "jest-get-type": {
-            "version": "25.2.1",
-            "resolved": "https://registry.npmjs.org/jest-get-type/-/jest-get-type-25.2.1.tgz",
-            "integrity": "sha512-EYjTiqcDTCRJDcSNKbLTwn/LcDPEE7ITk8yRMNAOjEsN6yp+Uu+V1gx4djwnuj/DvWg0YGmqaBqPVGsPxlvE7w==",
+            "version": "25.2.6",
+            "resolved": "https://registry.npmjs.org/jest-get-type/-/jest-get-type-25.2.6.tgz",
+            "integrity": "sha512-DxjtyzOHjObRM+sM1knti6or+eOgcGU4xVSb2HNP1TqO4ahsT+rqZg+nyqHWJSvWgKC5cG3QjGFBqxLghiF/Ig==",
             "dev": true
         },
         "js-base64": {
@@ -4938,19 +4933,19 @@
             }
         },
         "molstar": {
-            "version": "0.6.0-dev.11",
-            "resolved": "https://registry.npmjs.org/molstar/-/molstar-0.6.0-dev.11.tgz",
-            "integrity": "sha512-TPlhEnx+WRqQ0dMSXtvG53/lkKWyzAafjazXjSpDDAmeXXwe6bp5FNiWwD0tNXCbn3dSQX57xU9Q+b6rDRPAFg==",
+            "version": "0.6.1",
+            "resolved": "https://registry.npmjs.org/molstar/-/molstar-0.6.1.tgz",
+            "integrity": "sha512-KnHfw8xnn2f9wcFoWuqXW5Ejuie721zivRfV2SS559JxINoZRi0kBjdc3iInhSOAmrUdKKBVo7F/099puGQTUw==",
             "dev": true,
             "requires": {
                 "@types/argparse": "^1.0.38",
                 "@types/benchmark": "^1.0.31",
                 "@types/compression": "1.7.0",
                 "@types/express": "^4.17.4",
-                "@types/jest": "^25.1.4",
-                "@types/node": "^13.9.8",
+                "@types/jest": "^25.2.1",
+                "@types/node": "^13.11.0",
                 "@types/node-fetch": "^2.5.5",
-                "@types/react": "^16.9.31",
+                "@types/react": "^16.9.32",
                 "@types/react-dom": "^16.9.6",
                 "@types/swagger-ui-dist": "3.0.5",
                 "argparse": "^1.0.10",
@@ -4964,11 +4959,22 @@
                 "node-fetch": "^2.6.0",
                 "react": "^16.13.1",
                 "react-dom": "^16.13.1",
-                "rxjs": "^6.5.4",
+                "rxjs": "^6.5.5",
                 "swagger-ui-dist": "^3.25.0",
                 "tslib": "^1.11.1",
                 "util.promisify": "^1.0.1",
                 "xhr2": "^0.2.0"
+            },
+            "dependencies": {
+                "rxjs": {
+                    "version": "6.5.5",
+                    "resolved": "https://registry.npmjs.org/rxjs/-/rxjs-6.5.5.tgz",
+                    "integrity": "sha512-WfQI+1gohdf0Dai/Bbmk5L5ItH5tYqm3ki2c5GdWhKjalzjg93N3avFjVStyZZz+A2Em+ZxKH5bNghw9UeylGQ==",
+                    "dev": true,
+                    "requires": {
+                        "tslib": "^1.9.0"
+                    }
+                }
             }
         },
         "move-concurrently": {
@@ -5784,12 +5790,12 @@
             "dev": true
         },
         "pretty-format": {
-            "version": "25.2.3",
-            "resolved": "https://registry.npmjs.org/pretty-format/-/pretty-format-25.2.3.tgz",
-            "integrity": "sha512-IP4+5UOAVGoyqC/DiomOeHBUKN6q00gfyT2qpAsRH64tgOKB2yF7FHJXC18OCiU0/YFierACup/zdCOWw0F/0w==",
+            "version": "25.2.6",
+            "resolved": "https://registry.npmjs.org/pretty-format/-/pretty-format-25.2.6.tgz",
+            "integrity": "sha512-DEiWxLBaCHneffrIT4B+TpMvkV9RNvvJrd3lY9ew1CEQobDzEXmYT1mg0hJhljZty7kCc10z13ohOFAE8jrUDg==",
             "dev": true,
             "requires": {
-                "@jest/types": "^25.2.3",
+                "@jest/types": "^25.2.6",
                 "ansi-regex": "^5.0.0",
                 "ansi-styles": "^4.0.0",
                 "react-is": "^16.12.0"

package.json

@@ -37,9 +37,9 @@
     "license": "MIT",
     "devDependencies": {
         "@types/argparse": "^1.0.38",
-        "@types/node": "^13.9.8",
+        "@types/node": "^13.11.0",
         "@types/node-fetch": "^2.5.5",
-        "@types/react": "^16.9.31",
+        "@types/react": "^16.9.32",
         "@types/react-dom": "^16.9.6",
         "@typescript-eslint/eslint-plugin": "^2.26.0",
         "@typescript-eslint/parser": "^2.26.0",
@@ -50,14 +50,13 @@
         "extra-watch-webpack-plugin": "^1.0.3",
         "file-loader": "^6.0.0",
         "mini-css-extract-plugin": "^0.9.0",
-        "molstar": "^0.6.0-dev.11",
+        "molstar": "^0.6.1",
         "node-fetch": "^2.6.0",
         "node-sass": "^4.13.1",
         "raw-loader": "^4.0.0",
         "react": "^16.13.1",
         "react-dom": "^16.13.1",
         "resolve-url-loader": "^3.1.1",
-        "rxjs": "^6.5.4",
         "sass-loader": "^8.0.2",
         "style-loader": "^1.1.3",
         "tslib": "^1.11.1",

src/structure-viewer/helpers/preset.ts

@@ -9,7 +9,7 @@ import { MolScriptBuilder as MS } from 'molstar/lib/mol-script/language/builder'
 import Expression from 'molstar/lib/mol-script/language/expression';
 import { ParamDefinition as PD } from 'molstar/lib/mol-util/param-definition';
 import { TrajectoryHierarchyPresetProvider } from 'molstar/lib/mol-plugin-state/builder/structure/hierarchy-preset';
-import { ValidationReportPreset } from 'molstar/lib/mol-plugin/behavior/dynamic/custom-props/rcsb/validation-report';
+import { ValidationReportGeometryQualityPreset } from 'molstar/lib/mol-plugin/behavior/dynamic/custom-props/rcsb/validation-report';
 import { AssemblySymmetryPreset } from 'molstar/lib/mol-plugin/behavior/dynamic/custom-props/rcsb/assembly-symmetry';
 import { PluginStateObject } from 'molstar/lib/mol-plugin-state/objects';
 import { RootStructureDefinition } from 'molstar/lib/mol-plugin-state/helpers/root-structure';
@@ -130,7 +130,7 @@ export const RcsbPreset = TrajectoryHierarchyPresetProvider({
         let representation: StructureRepresentationPresetProvider.Result | undefined = undefined
 
         if (p.kind === 'validation') {
-            representation = await plugin.builders.structure.representation.applyPreset(structureProperties, ValidationReportPreset);
+            representation = await plugin.builders.structure.representation.applyPreset(structureProperties, ValidationReportGeometryQualityPreset);
         } else if (p.kind === 'symmetry') {
             representation = await plugin.builders.structure.representation.applyPreset<any>(structureProperties, AssemblySymmetryPreset, { symmetryIndex: p.symmetryIndex });
         } else {

webpack.config.js

@@ -31,11 +31,9 @@ const sharedConfig = {
             ],
         }),
         new webpack.DefinePlugin({
-            __PLUGIN_VERSION_TIMESTAMP__: webpack.DefinePlugin.runtimeValue(() => `${new Date().valueOf()}`, true),
-            __RCSB_MOLSTAR_VERSION__: webpack.DefinePlugin.runtimeValue(() => {
-                const version = JSON.parse(fs.readFileSync('./package.json')).version;
-                return `'${version}'`;
-            }, true),
+            __VERSION__: webpack.DefinePlugin.runtimeValue(() => JSON.stringify(require('./node_modules/molstar/package.json').version), true),
+            __VERSION_TIMESTAMP__: webpack.DefinePlugin.runtimeValue(() => `${new Date().valueOf()}`, true),
+            __RCSB_MOLSTAR_VERSION__: webpack.DefinePlugin.runtimeValue(() => JSON.stringify(require('./package.json').version), true),
             'process.env.DEBUG': JSON.stringify(process.env.DEBUG)
         }),
         new MiniCssExtractPlugin({ filename: 'app.css' })