Release6.0.17

.github/workflows/maven.yml

@@ -0,0 +1,21 @@
+# This workflow will build a Java project with Maven
+# For more information see: https://help.github.com/actions/language-and-framework-guides/building-and-testing-java-with-maven
+
+name: Maven build
+
+on:
+  push:
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up JDK 1.8
+      uses: actions/setup-java@v1
+      with:
+        java-version: 1.8
+    - name: Build with Maven
+      run: mvn -B package --file pom.xml

.gitignore

@@ -66,3 +66,4 @@ junit.xml
 .nvim.lua
 .luarc.json
 .vs/
+env/custom.sh

attributes.json

@@ -0,0 +1,6 @@
+{
+    "PATIENT_DISPLAY_NAME": {
+        "primary": true,
+        "order": 0
+    }
+}

env/custom.sh

@@ -0,0 +1,7 @@
+# set e.g.
+export CBIOPORTAL_URL="http://localhost:8080"
+export GENOME_NEXUS_URL="https://www.genomenexus.org"
+# export FHIRSPARK_HOST=localhost
+export FHIRSPARK_PORT=3001
+export CANCERDRUGS_URL="https://componc.github.io/cancerdrugs"
+export CANCERDRUGSJSON_URL="https://componc.github.io/cancerdrugs/data/drugs/"

package.json

@@ -192,6 +192,7 @@
     "genome-nexus-ts-api-client": "^1.1.33",
     "git-revision-webpack-plugin": "^5.0.0",
     "history": "4.10.1",
+    "html-react-parser": "^1.4.8",
     "html-webpack-plugin": "^5.3.2",
     "igv": "^2.11.2",
     "imports-loader": "^0.8.0",
@@ -260,6 +261,8 @@
     "react-collapse": "^4.0.3",
     "react-color": "^2.18.1",
     "react-column-resizer": "^1.1.9",
+    "react-date-picker": "^8.4.0",
+    "react-device-detect": "^2.1.2",
     "react-dom": "^16.6",
     "react-draggable": "^3.3.0",
     "react-file-download": "^0.3.2",
@@ -281,7 +284,7 @@
     "react-reveal": "^1.2.2",
     "react-router": "5.2.0",
     "react-router-dom": "^5.2.0",
-    "react-select": "^3.0.4",
+    "react-select": "^5.7.1",
     "react-select1": "npm:[email protected]",
     "react-sortable-hoc": "^1.9.1",
     "react-spinkit": "^3.0.0",

packages/cbioportal-clinical-timeline/src/TimelineTrack.tsx

@@ -209,6 +209,17 @@ function renderRange(
     );
 }
 
+function replaceArray(replaceString: string) {
+    const search = ['ä', 'ü', 'ö', 'Ä', 'Ö', 'Ü', 'ß'];
+    const replace = ['ä', 'ü', 'ö', 'Ä', 'Ö', 'Ü', 'ß'];
+    let regex;
+    for (let i = 0; i < search.length; i++) {
+        regex = new RegExp(search[i], 'g');
+        replaceString = replaceString.replace(regex, replace[i]);
+    }
+    return replaceString;
+}
+
 export const TimelineTrack: React.FunctionComponent<ITimelineTrackProps> = observer(
     function({
         trackData,
@@ -478,7 +489,8 @@ export const EventTooltipContent: React.FunctionComponent<{
                                 <td>{attr.key.replace(/_/g, ' ')}</td>
                                 <td>
                                     <ReactMarkdown
-                                        allowedElements={['p', 'a']}
+                                        allowedElements={['p', 'a', 'br']}
+                                        className="line-break"
                                         linkTarget={'_blank'}
                                         components={{
                                             a: ({ node, ...props }) => {

packages/cbioportal-clinical-timeline/src/timeline.scss

@@ -1,4 +1,4 @@
-$width: 1200px;
+$width: 800px;
 $borderColor: #ccc;
 $tl-fontsize: 12px;
 
@@ -168,6 +168,10 @@ $tl-fontsize: 12px;
     position: relative;
 }
 
+.line-break {
+    white-space: pre-wrap;
+}
+
 .tl-tracklegend {
     z-index: 1000;
     background: #f2f2f2;

packages/cbioportal-utils/src/index.tsx

@@ -21,11 +21,13 @@ export * from './model/Mutation';
 export * from './model/MyCancerGenome';
 export * from './model/MyVariantInfo';
 export * from './model/OncoKB';
+export * from './model/OncoTreeTumorTypes';
 export * from './model/PostTranslationalModification';
 export * from './model/RemoteData';
 export * from './model/SignalMutation';
 export * from './model/SignalMutationStatus';
 export * from './model/SignalGeneFrequencySummary';
+export * from './model/TherapyRecommendation';
 export * from './model/Uniprot';
 
 export * from './mutation/MutationAnnotator';

packages/cbioportal-utils/src/model/OncoTreeTumorTypes.tsx

@@ -0,0 +1,34 @@
+type tumorType = {
+    code?: string;
+    color?: string;
+    name?: string;
+    mainType?: string;
+    externalReferences?: {
+        UMLS?: Array<string>;
+        NCI?: Array<string>;
+    };
+    tissue?: string;
+    children?: object;
+    parent?: string;
+    history?: Array<any>;
+    level?: number;
+    revocations?: Array<any>;
+    precursors?: Array<any>;
+};
+
+let getRequest = new XMLHttpRequest();
+let url = '/tumorTypes.json';
+if (
+    window.location.hostname === 'localhost' ||
+    window.location.port === '3000'
+) {
+    url = 'https://oncotree.info/api/tumorTypes';
+}
+
+getRequest.open('Get', url, false);
+getRequest.send(null);
+const oncoTreeTumorTypes: Array<tumorType> = JSON.parse(
+    getRequest.responseText
+);
+
+export default oncoTreeTumorTypes;

packages/cbioportal-utils/src/model/TherapyRecommendation.ts

@@ -0,0 +1,153 @@
+export enum TREvidenceLevel {
+    NA,
+    m1A,
+    m1B,
+    m1C,
+    m2A,
+    m2B,
+    m2C,
+    m3,
+    m4,
+}
+
+export enum EvidenceLevelExtension {
+    NA = '',
+    IS = 'is',
+    IV = 'iv',
+    R = 'R',
+    ZFDA = 'Z(FDA)',
+    ZEMA = 'Z(EMA)',
+}
+
+export enum MtbState {
+    PARTIAL = 'Partial',
+    PRELIMINARY = 'Preliminary',
+    FINAL = 'Final',
+}
+
+export interface IRecommender {
+    credentials: string;
+    full_name?: string;
+    email?: string;
+}
+
+export interface IMtb {
+    id: string;
+    orderId: string;
+    therapyRecommendations: ITherapyRecommendation[];
+    geneticCounselingRecommendation: boolean;
+    rebiopsyRecommendation: boolean;
+    generalRecommendation: string;
+    date: string;
+    mtbState: MtbState;
+    samples: string[];
+    author: string;
+}
+
+export interface ITherapyRecommendation {
+    id: string;
+    comment: string[];
+    reasoning: IReasoning;
+    evidenceLevel: TREvidenceLevel;
+    evidenceLevelExtension?: EvidenceLevelExtension;
+    evidenceLevelM3Text: string;
+    author: string;
+    treatments: ITreatment[];
+    references: IReference[];
+    clinicalTrials: IClinicalTrial[];
+    diagnosis?: string[];
+    studyId?: string;
+    caseId?: string;
+}
+
+export interface IClinicalTrial {
+    name: string;
+    id: string;
+}
+
+export interface IReference {
+    name: string;
+    pmid?: number;
+    comment?: string;
+}
+
+export interface ITreatment {
+    name: string;
+    ncit_code: string;
+    synonyms?: string;
+}
+
+export interface IClinicalData {
+    sampleId?: string;
+    attributeId?: string;
+    attributeName?: string;
+    value: string;
+}
+
+export interface IReasoning {
+    geneticAlterations?: IGeneticAlteration[];
+    clinicalData?: IClinicalData[];
+    tmb?: number;
+    other?: string;
+}
+
+export interface IGeneticAlteration {
+    entrezGeneId?: number;
+    hugoSymbol: string;
+    alteration?: string;
+    chromosome?: string;
+    start?: number;
+    end?: number;
+    ref?: string;
+    alt?: string;
+    aminoAcidChange?: string;
+    alleleFrequency?: number | null;
+    dbsnp?: string;
+    clinvar?: number;
+    cosmic?: string;
+    gnomad?: number;
+    sampleIds?: string[];
+}
+
+export interface IDeletions {
+    mtb: string[];
+    therapyRecommendation: string[];
+    followUp: string[];
+}
+
+export interface IResponseCriteria {
+    cr3: boolean;
+    pr3: boolean;
+    sd3: boolean;
+    pd3: boolean;
+    cr6: boolean;
+    pr6: boolean;
+    sd6: boolean;
+    pd6: boolean;
+    cr12: boolean;
+    pr12: boolean;
+    sd12: boolean;
+    pd12: boolean;
+}
+
+export interface IFollowUp {
+    id: string;
+    therapyRecommendation: ITherapyRecommendation;
+    date: string;
+    author: string;
+    therapyRecommendationRealized: boolean;
+    sideEffect: boolean;
+    response: IResponseCriteria;
+    comment: string;
+}
+
+export interface ISharedTherapyRecommendationData {
+    localTherapyRecommendations: ITherapyRecommendation[];
+    localFollowUps: IFollowUp[];
+    sharedTherapyRecommendations: ITherapyRecommendation[];
+    sharedFollowUps: IFollowUp[];
+    proteinChange?: string;
+    diagnosis?: string[];
+    caseId?: string;
+    studyId?: string;
+}