updated rcsb assembly symmetry graphql schema

package-lock.json

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       "requires": {
-        "change-case": "3.0.2",
+        "change-case": "3.1.0",
         "common-tags": "1.8.0",
-        "graphql-codegen-core": "0.15.2",
-        "graphql-codegen-plugin-helpers": "0.15.2"
+        "graphql-codegen-core": "0.16.0",
+        "graphql-codegen-plugin-helpers": "0.16.0"
       }
     },
     "graphql-codegen-typescript-server": {
-      "version": "0.15.2",
-      "resolved": "https://registry.npmjs.org/graphql-codegen-typescript-server/-/graphql-codegen-typescript-server-0.15.2.tgz",
-      "integrity": "sha512-12rKf7+zAiPtDttb58uiq8WF0HmYCI6UN/+8UMdYSZbqHwVyY+D+aNRQLGq+wkw8oyN/mBtqEKuj89tQd/wt/w==",
+      "version": "0.16.0",
+      "resolved": "https://registry.npmjs.org/graphql-codegen-typescript-server/-/graphql-codegen-typescript-server-0.16.0.tgz",
+      "integrity": "sha512-sIhNi7LJM9F6FHPA6Zh4R8JhcGgda324ToIYX9gcU1dHBcHJRyVgzN7jsgOcDnpzIJwPnEa6LzX6MpSssygH5g==",
       "dev": true,
       "requires": {
-        "graphql-codegen-typescript-common": "0.15.2"
+        "graphql-codegen-typescript-common": "0.16.0"
       }
     },
     "graphql-codegen-typescript-template": {
-      "version": "0.15.2",
-      "resolved": "https://registry.npmjs.org/graphql-codegen-typescript-template/-/graphql-codegen-typescript-template-0.15.2.tgz",
-      "integrity": "sha512-4NF8vY9WDErlbdx3ATwxWTl3kII76tsx1azPWhBMULBcqyUcqs8ThUD91b8vKHOxMo9zvuj9NTq0OXLgmMgrng==",
+      "version": "0.16.0",
+      "resolved": "https://registry.npmjs.org/graphql-codegen-typescript-template/-/graphql-codegen-typescript-template-0.16.0.tgz",
+      "integrity": "sha512-AxkfCEWQ40FTkj4lkY/hUW/E37eRjUunRQZko9I5+kcZS9QPWmP/OLv0fTkHgQruhhD9fQIiBW69LqWqGWl+TA==",
       "dev": true,
       "requires": {
-        "graphql-codegen-typescript-client": "0.15.2",
-        "graphql-codegen-typescript-common": "0.15.2",
-        "graphql-codegen-typescript-server": "0.15.2"
+        "graphql-codegen-typescript-client": "0.16.0",
+        "graphql-codegen-typescript-common": "0.16.0",
+        "graphql-codegen-typescript-server": "0.16.0"
       }
     },
     "graphql-config": {
@@ -5919,15 +5957,15 @@
       }
     },
     "graphql-tag": {
-      "version": "2.10.0",
-      "resolved": "https://registry.npmjs.org/graphql-tag/-/graphql-tag-2.10.0.tgz",
-      "integrity": "sha512-9FD6cw976TLLf9WYIUPCaaTpniawIjHWZSwIRZSjrfufJamcXbVVYfN2TWvJYbw0Xf2JjYbl1/f2+wDnBVw3/w==",
+      "version": "2.10.1",
+      "resolved": "https://registry.npmjs.org/graphql-tag/-/graphql-tag-2.10.1.tgz",
+      "integrity": "sha512-jApXqWBzNXQ8jYa/HLkZJaVw9jgwNqZkywa2zfFn16Iv1Zb7ELNHkJaXHR7Quvd5SIGsy6Ny7SUKATgnu05uEg==",
       "dev": true
     },
     "graphql-tag-pluck": {
-      "version": "0.4.4",
-      "resolved": "https://registry.npmjs.org/graphql-tag-pluck/-/graphql-tag-pluck-0.4.4.tgz",
-      "integrity": "sha512-dvfRQ3aMxUYUYG+L+Z35npQ/OSNyitypYZ6wI908SqNQ6DQOWRX1WYcv590FOf2TrPOAY39dQEtq5u7mWMUGMw==",
+      "version": "0.5.0",
+      "resolved": "https://registry.npmjs.org/graphql-tag-pluck/-/graphql-tag-pluck-0.5.0.tgz",
+      "integrity": "sha512-SlsIpXKbrKIV2+QxYZ7bFPQ0DpIXFd0BEz3U+Krt8tuHYMFtElcctNDppW4EeQTrSX9H5zpStBZyfOYQjQOH1w==",
       "dev": true,
       "requires": {
         "@babel/parser": "^7.2.0",
@@ -7985,7 +8023,7 @@
     },
     "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=",
       "dev": true,
       "requires": {
@@ -8003,7 +8041,7 @@
       "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=",
           "dev": true
         }
@@ -8380,7 +8418,7 @@
       "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=",
           "dev": true
         }
@@ -8511,7 +8549,7 @@
         },
         "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=",
           "dev": true,
           "requires": {
@@ -8623,7 +8661,7 @@
         },
         "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=",
           "dev": true,
           "requires": {
@@ -9329,9 +9367,9 @@
       "dev": true
     },
     "prettier": {
-      "version": "1.15.3",
-      "resolved": "https://registry.npmjs.org/prettier/-/prettier-1.15.3.tgz",
-      "integrity": "sha512-gAU9AGAPMaKb3NNSUUuhhFAS7SCO4ALTN4nRIn6PJ075Qd28Yn2Ig2ahEJWdJwJmlEBTUfC7mMUSFy8MwsOCfg==",
+      "version": "1.16.0",
+      "resolved": "https://registry.npmjs.org/prettier/-/prettier-1.16.0.tgz",
+      "integrity": "sha512-MCBCYeAuZfejUPdEpkleLWvpRBwLii/Sp5jQs0eb8Ul/drGIDjkL6tAU24tk6yCGf0KPV5rhPPPlczfBmN2pWQ==",
       "dev": true
     },
     "pretty-format": {
@@ -10465,7 +10503,7 @@
         },
         "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=",
           "dev": true,
           "requires": {
@@ -10485,7 +10523,7 @@
         },
         "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=",
           "dev": true,
           "requires": {
@@ -10609,7 +10647,7 @@
       "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=",
           "dev": true,
           "requires": {
@@ -10719,7 +10757,7 @@
     },
     "sha.js": {
       "version": "2.4.11",
-      "resolved": "https://registry.npmjs.org/sha.js/-/sha.js-2.4.11.tgz",
+      "resolved": "http://registry.npmjs.org/sha.js/-/sha.js-2.4.11.tgz",
       "integrity": "sha512-QMEp5B7cftE7APOjk5Y6xgrbWu+WkLVQwk8JNjZ8nKRciZaByEW6MubieAiToS7+dwvrjGhH8jRXz3MVd0AYqQ==",
       "dev": true,
       "requires": {
@@ -11124,7 +11162,7 @@
     },
     "stream-browserify": {
       "version": "2.0.1",
-      "resolved": "https://registry.npmjs.org/stream-browserify/-/stream-browserify-2.0.1.tgz",
+      "resolved": "http://registry.npmjs.org/stream-browserify/-/stream-browserify-2.0.1.tgz",
       "integrity": "sha1-ZiZu5fm9uZQKTkUUyvtDu3Hlyds=",
       "dev": true,
       "requires": {
@@ -11163,7 +11201,7 @@
         },
         "readable-stream": {
           "version": "2.3.6",
-          "resolved": "https://registry.npmjs.org/readable-stream/-/readable-stream-2.3.6.tgz",
+          "resolved": "http://registry.npmjs.org/readable-stream/-/readable-stream-2.3.6.tgz",
           "integrity": "sha512-tQtKA9WIAhBF3+VLAseyMqZeBjW0AHJoxOtYqSUZNJxauErmLbVm2FW1y+J/YA9dUrAC39ITejlZWhVIwawkKw==",
           "dev": true,
           "requires": {
@@ -11375,7 +11413,7 @@
     },
     "tar": {
       "version": "2.2.1",
-      "resolved": "https://registry.npmjs.org/tar/-/tar-2.2.1.tgz",
+      "resolved": "http://registry.npmjs.org/tar/-/tar-2.2.1.tgz",
       "integrity": "sha1-jk0qJWwOIYXGsYrWlK7JaLg8sdE=",
       "dev": true,
       "requires": {
@@ -13405,9 +13443,9 @@
       }
     },
     "zen-observable": {
-      "version": "0.8.11",
-      "resolved": "https://registry.npmjs.org/zen-observable/-/zen-observable-0.8.11.tgz",
-      "integrity": "sha512-N3xXQVr4L61rZvGMpWe8XoCGX8vhU35dPyQ4fm5CY/KDlG0F75un14hjbckPXTDuKUY6V0dqR2giT6xN8Y4GEQ==",
+      "version": "0.8.13",
+      "resolved": "https://registry.npmjs.org/zen-observable/-/zen-observable-0.8.13.tgz",
+      "integrity": "sha512-fa+6aDUVvavYsefZw0zaZ/v3ckEtMgCFi30sn91SEZea4y/6jQp05E3omjkX91zV6RVdn15fqnFZ6RKjRGbp2g==",
       "dev": true
     },
     "zen-observable-ts": {

package.json

@@ -94,8 +94,9 @@
     "glslify": "^7.0.0",
     "glslify-import": "^3.1.0",
     "glslify-loader": "^2.0.0",
-    "graphql-code-generator": "^0.15.2",
-    "graphql-codegen-typescript-template": "^0.15.2",
+    "graphql-code-generator": "^0.16.0",
+    "graphql-codegen-time": "^0.16.0",
+    "graphql-codegen-typescript-template": "^0.16.0",
     "jest": "^23.6.0",
     "jest-raw-loader": "^1.0.1",
     "mini-css-extract-plugin": "^0.5.0",

src/mol-model-props/rcsb/assembly-symmetry.ts

@@ -44,18 +44,17 @@ function createDatabaseFromJson(assemblies: ReadonlyArray<AssemblySymmetryGraphQ
     let id = 1 // start feature ids at 1
     let clusterCount = 0
     for (let i = 0, il = assemblies.length; i < il; ++i) {
-        const { pdbx_struct_assembly, rcsb_struct_symmetry, rcsb_struct_symmetry_provenance } = assemblies[i]
-        if (!pdbx_struct_assembly || !rcsb_struct_symmetry ||!rcsb_struct_symmetry_provenance) continue
+        const { pdbx_struct_assembly, rcsb_struct_symmetry } = assemblies[i]
+        if (!pdbx_struct_assembly || !rcsb_struct_symmetry) continue
         const assembly_id = pdbx_struct_assembly.id
         for (let j = 0, jl = rcsb_struct_symmetry.length; j < jl; ++j) {
             const rss = rcsb_struct_symmetry[j]! // TODO upstream, array members should not be nullable
             featureRows.push({
                 id,
                 assembly_id,
-                provenance: rcsb_struct_symmetry_provenance,
-                type: rss.type,
+                type: rss.type as SymmetryType,
                 stoichiometry: rss.stoichiometry as string[],  // TODO upstream, array members should not be nullable
-                kind: rss.kind,
+                kind: rss.kind as SymmetryKind,
                 symbol: rss.symbol,
                 oligomeric_state: rss.oligomeric_state
             })
@@ -181,6 +180,9 @@ export function AssemblySymmetry(db: AssemblySymmetry.Database): AssemblySymmetr
     }
 }
 
+type SymmetryKind = 'GLOBAL' | 'LOCAL' | 'PSEUDO'
+type SymmetryType = 'ASYMMETRIC' | 'CYCLIC' | 'DIHEDRAL' | 'HELICAL' | 'ICOSAHEDRAL' | 'OCTAHEDRAL' | 'TETRAHEDRAL'
+
 const Client = new GraphQLClient(AssemblySymmetry.GraphQLEndpointURL, (url: string, type: 'string' | 'binary', body?: string) => ajaxGet({ url, type, body }) )
 
 export namespace AssemblySymmetry {
@@ -200,10 +202,8 @@ export namespace AssemblySymmetry {
              * The value 'deposited' refers to the coordinates as given in the file.
              * */
             assembly_id: str,
-            /** Name and version of software used to calculate assembly symmetry */
-            provenance: str,
             /** Type of protein symmetry */
-            kind: Aliased<'GLOBAL' | 'LOCAL' | 'PSEUDO'>(str),
+            kind: Aliased<SymmetryKind>(str),
             /** Quantitative description of every individual subunit in a given protein */
             stoichiometry: List(',', x => x),
             /**
@@ -212,7 +212,7 @@ export namespace AssemblySymmetry {
              */
             symbol: str,
             /** Point group or helical symmetry */
-            type: Aliased<'ASYMMETRIC' | 'CYCLIC' | 'DIHEDRAL' | 'HELICAL' | 'ICOSAHEDRAL' | 'OCTAHEDRAL' | 'TETRAHEDRAL'>(str),
+            type: Aliased<SymmetryType>(str),
             /**
              * Oligomeric state refers to a composition of subunits in quaternary structure.
              * Quaternary structure may be composed either exclusively of several copies of identical

src/mol-model-props/rcsb/graphql/symmetry.gql.ts

@@ -26,6 +26,5 @@ gql`query AssemblySymmetry($pdbId: String!) {
             symbol
             type
         }
-        rcsb_struct_symmetry_provenance
     }
 }`