Merge branch 'master' into feat/category-bar-chart

cBioPortal · Aug 19, 2024 · 66fcf9a · 66fcf9a
2 parents 1e659a4 + 50adab2
commit 66fcf9a
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diff --git a/OPEN-SOURCE-DOCUMENTATION b/OPEN-SOURCE-DOCUMENTATION
@@ -49,3 +49,20 @@ Available under license:
     5. Products derived from this software may not be called
     "ColorBrewer", nor may "ColorBrewer" appear in their name, without
     prior written permission of Cynthia Brewer.
+
+* JavaScript/CSS Font Detector
+
+JavaScript/CSS Font Detector
+----------------------------
+Available under license:
+
+    JavaScript code to detect available availability of a
+    particular font in a browser using JavaScript and CSS.
+
+    Author : Lalit Patel
+    Website: http://www.lalit.org/lab/javascript-css-font-detect/
+    License: Apache Software License 2.0
+             http://www.apache.org/licenses/LICENSE-2.0
+
+
+
diff --git a/my-index.ejs b/my-index.ejs
@@ -10,37 +10,36 @@
         window.frontendConfig = {
         }
 
+        /* REMOVED: This is an example of how to add custom tabs to the patient page. Enabling this will clobber localStorage.frontendConfig that is set through the browser console
         localStorage.frontendConfig = JSON.stringify(
-            {
-                serverConfig:{
-
-                       custom_tabs:[
- {
-            title: 'Sync Tab',
-            id: 'customTab1',
-            location: 'PATIENT_PAGE',
-            mountCallback: `(div)=>{
-                    $(div).html("tab for patient " + window.location.search.split("=").slice(-1))
-                }`,
-        },
         {
-            title: 'Async Tab',
-            id: 'customTab2',
-            location: 'PATIENT_PAGE',
-            hideAsync: `()=>{
-                           return new Promise((resolve)=>{
-                                setTimeout(()=>{
-                                    resolve(true);
-                                }, 2000);
-                           });
-                    }`,
-        },
-                                           ]
-
-                }
-
-           }
-        );
+            serverConfig:{
+
+                custom_tabs:[
+                    {
+                        title: 'Sync Tab',
+                        id: 'customTab1',
+                        location: 'PATIENT_PAGE',
+                        mountCallback: `(div)=>{
+                                $(div).html("tab for patient " + window.location.search.split("=").slice(-1))
+                            }`,
+                    },
+                    {
+                        title: 'Async Tab',
+                        id: 'customTab2',
+                        location: 'PATIENT_PAGE',
+                        hideAsync: `()=>{
+                                    return new Promise((resolve)=>{
+                                            setTimeout(()=>{
+                                                resolve(true);
+                                            }, 2000);
+                                    });
+                                }`,
+                    },
+                ]
+            }
+        });
+        */
 
     function renderCustomTab1(div, tab){
         $(div).append(`<div>this is the content for <strong>${tab.title}</strong></div>`);

diff --git a/notebook/README.md b/notebook/README.md
@@ -0,0 +1,5 @@
+
+## For using the notebook and its contents: 
+
+1. The code for the Jupyterlite extension and the environment can be accessed from [here](https://github.com/cBioPortal/cbio-jupyter).
+2. The instructions to use it present in this [file](https://github.com/cBioPortal/cbio-jupyter/blob/main/README.md)
diff --git a/package.json b/package.json
@@ -1,7 +1,7 @@
 {
   "name": "cbioportal-frontend",
   "private": true,
-  "version": "3.3.283",
+  "version": "3.3.284",
   "workspaces": {
     "packages": [
       ".",
@@ -159,10 +159,10 @@
     "bootstrap-sass": "3.4.1",
     "bowser": "^1.7.1",
     "bundle-loader": "^0.5.4",
-    "cbioportal-clinical-timeline": "^0.3.83",
-    "cbioportal-frontend-commons": "^0.5.67",
+    "cbioportal-clinical-timeline": "^0.3.84",
+    "cbioportal-frontend-commons": "^0.5.68",
     "cbioportal-ts-api-client": "^0.9.73",
-    "cbioportal-utils": "^0.3.41",
+    "cbioportal-utils": "^0.3.42",
     "chart.js": "^2.6.0",
     "classnames": "^2.2.5",
     "clinical-timeline": "0.0.30",
@@ -189,7 +189,7 @@
     "fmin": "^0.0.2",
     "font-awesome": "^4.7.0",
     "fork-ts-checker-webpack-plugin": "^6.3.3",
-    "genome-nexus-ts-api-client": "^1.1.32",
+    "genome-nexus-ts-api-client": "^1.1.33",
     "git-revision-webpack-plugin": "^5.0.0",
     "history": "4.10.1",
     "html-webpack-plugin": "^5.3.2",
@@ -227,7 +227,7 @@
     "mobx-utils": "6.0.1",
     "numeral": "^2.0.6",
     "object-sizeof": "^1.2.0",
-    "oncokb-frontend-commons": "^0.0.25",
+    "oncokb-frontend-commons": "^0.0.26",
     "oncokb-styles": "~1.4.2",
     "oncokb-ts-api-client": "^1.3.5",
     "oncoprintjs": "^6.0.5",
@@ -272,7 +272,7 @@
     "react-markdown": "^7.0.1",
     "react-mfb": "^0.6.0",
     "react-motion": "^0.4.7",
-    "react-mutation-mapper": "^0.8.111",
+    "react-mutation-mapper": "^0.8.112",
     "react-overlays": "0.7.4",
     "react-portal": "^4.2.0",
     "react-rangeslider": "^2.1.0",

diff --git a/packages/cbioportal-clinical-timeline/package.json b/packages/cbioportal-clinical-timeline/package.json
@@ -1,7 +1,7 @@
 {
   "name": "cbioportal-clinical-timeline",
   "description": "cBioPortal Clinical Timeline",
-  "version": "0.3.83",
+  "version": "0.3.84",
   "main": "dist/index.js",
   "module": "dist/index.es.js",
   "jsnext:main": "dist/index.es.js",
@@ -39,7 +39,7 @@
   },
   "dependencies": {
     "autobind-decorator": "^2.1.0",
-    "cbioportal-frontend-commons": "^0.5.67",
+    "cbioportal-frontend-commons": "^0.5.68",
     "lodash": "^4.17.11",
     "react-bootstrap": "^0.31.5",
     "react-overlays": "0.7.4",

diff --git a/packages/cbioportal-frontend-commons/package.json b/packages/cbioportal-frontend-commons/package.json
@@ -1,7 +1,7 @@
 {
   "name": "cbioportal-frontend-commons",
   "description": "cBioPortal Frontend Modules",
-  "version": "0.5.67",
+  "version": "0.5.68",
   "main": "dist/index.js",
   "module": "dist/index.es.js",
   "jsnext:main": "dist/index.es.js",
@@ -38,7 +38,7 @@
   },
   "dependencies": {
     "autobind-decorator": "^2.1.0",
-    "cbioportal-utils": "^0.3.41",
+    "cbioportal-utils": "^0.3.42",
     "classnames": "^2.2.5",
     "jquery": "^3.2.1",
     "juice": "^10.0.0",

diff --git a/packages/cbioportal-utils/package.json b/packages/cbioportal-utils/package.json
@@ -1,7 +1,7 @@
 {
   "name": "cbioportal-utils",
   "description": "cBioPortal Utilities",
-  "version": "0.3.41",
+  "version": "0.3.42",
   "main": "dist/index.js",
   "module": "dist/index.es.js",
   "jsnext:main": "dist/index.es.js",
@@ -30,7 +30,7 @@
   },
   "dependencies": {
     "buffer": "^6.0.3",
-    "genome-nexus-ts-api-client": "^1.1.32",
+    "genome-nexus-ts-api-client": "^1.1.33",
     "lodash": "^4.17.15",
     "oncokb-ts-api-client": "^1.3.5",
     "superagent": "^3.8.3",

diff --git a/packages/genome-nexus-ts-api-client/package.json b/packages/genome-nexus-ts-api-client/package.json
@@ -1,7 +1,7 @@
 {
   "name": "genome-nexus-ts-api-client",
   "description": "Genome Nexus API Client for TypeScript",
-  "version": "1.1.32",
+  "version": "1.1.33",
   "main": "dist/index.js",
   "module": "dist/index.es.js",
   "jsnext:main": "dist/index.es.js",

diff --git a/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPI-docs.json b/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPI-docs.json
@@ -1348,6 +1348,18 @@
         }
       }
     },
+    "AlphaMissense": {
+      "type": "object",
+      "properties": {
+        "pathogenicity": {
+          "type": "string"
+        },
+        "score": {
+          "type": "number",
+          "format": "double"
+        }
+      }
+    },
     "ArticleAbstract": {
       "type": "object",
       "properties": {
@@ -3309,6 +3321,9 @@
         "transcript_id"
       ],
       "properties": {
+        "alphaMissense": {
+          "$ref": "#/definitions/AlphaMissense"
+        },
         "amino_acids": {
           "type": "string",
           "description": "Amino acids"
@@ -3413,6 +3428,9 @@
         "transcriptId"
       ],
       "properties": {
+        "alphaMissense": {
+          "$ref": "#/definitions/AlphaMissense"
+        },
         "aminoAcidAlt": {
           "type": "string",
           "description": "Alt Amino Acid"
@@ -3725,6 +3743,9 @@
         "variant"
       ],
       "properties": {
+        "alphaMissense": {
+          "$ref": "#/definitions/AlphaMissense"
+        },
         "assemblyName": {
           "type": "string",
           "description": "Assembly name"

diff --git a/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPI.ts b/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPI.ts
@@ -72,6 +72,12 @@ export type AlleleNumber = {
 export type Alleles = {
     'allele': string
 
+};
+export type AlphaMissense = {
+    'pathogenicity': string
+
+        'score': number
+
 };
 export type ArticleAbstract = {
     'abstract': string
@@ -840,7 +846,9 @@ export type StatsByTumorType = {
 
 };
 export type TranscriptConsequence = {
-    'amino_acids': string
+    'alphaMissense': AlphaMissense
+
+        'amino_acids': string
 
         'canonical': string
 
@@ -886,7 +894,9 @@ export type TranscriptConsequence = {
 
 };
 export type TranscriptConsequenceSummary = {
-    'aminoAcidAlt': string
+    'alphaMissense': AlphaMissense
+
+        'aminoAcidAlt': string
 
         'aminoAcidRef': string
 
@@ -1026,7 +1036,9 @@ export type VariantAnnotation = {
 
 };
 export type VariantAnnotationSummary = {
-    'assemblyName': string
+    'alphaMissense': AlphaMissense
+
+        'assemblyName': string
 
         'canonicalTranscriptId': string
 

diff --git a/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPIInternal-docs.json b/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPIInternal-docs.json
@@ -1104,6 +1104,18 @@
         }
       }
     },
+    "AlphaMissense": {
+      "type": "object",
+      "properties": {
+        "pathogenicity": {
+          "type": "string"
+        },
+        "score": {
+          "type": "number",
+          "format": "double"
+        }
+      }
+    },
     "Cosmic": {
       "type": "object",
       "properties": {
@@ -2211,6 +2223,9 @@
         "transcriptId"
       ],
       "properties": {
+        "alphaMissense": {
+          "$ref": "#/definitions/AlphaMissense"
+        },
         "aminoAcidAlt": {
           "type": "string",
           "description": "Alt Amino Acid"
@@ -2306,6 +2321,9 @@
         "variant"
       ],
       "properties": {
+        "alphaMissense": {
+          "$ref": "#/definitions/AlphaMissense"
+        },
         "assemblyName": {
           "type": "string",
           "description": "Assembly name"

diff --git a/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPIInternal.ts b/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPIInternal.ts
@@ -76,6 +76,12 @@ export type AlleleNumber = {
 export type Alleles = {
     'allele': string
 
+};
+export type AlphaMissense = {
+    'pathogenicity': string
+
+        'score': number
+
 };
 export type Cosmic = {
     'alt': string
@@ -542,7 +548,9 @@ export type StatsByTumorType = {
 
 };
 export type TranscriptConsequenceSummary = {
-    'aminoAcidAlt': string
+    'alphaMissense': AlphaMissense
+
+        'aminoAcidAlt': string
 
         'aminoAcidRef': string
 
@@ -586,7 +594,9 @@ export type TranscriptConsequenceSummary = {
 
 };
 export type VariantAnnotationSummary = {
-    'assemblyName': string
+    'alphaMissense': AlphaMissense
+
+        'assemblyName': string
 
         'canonicalTranscriptId': string
 

diff --git a/packages/oncokb-frontend-commons/package.json b/packages/oncokb-frontend-commons/package.json
@@ -1,6 +1,6 @@
 {
   "name": "oncokb-frontend-commons",
-  "version": "0.0.25",
+  "version": "0.0.26",
   "description": "OncoKB Frontend Modules",
   "main": "dist/index.js",
   "module": "dist/index.es.js",
@@ -35,7 +35,7 @@
     "react-dom": "^15.0.0 || ^16.0.0"
   },
   "dependencies": {
-    "cbioportal-utils": "^0.3.41",
+    "cbioportal-utils": "^0.3.42",
     "classnames": "^2.2.5",
     "lodash": "^4.17.15",
     "oncokb-styles": "~1.4.2",