Merge pull request #2872 from ChrisWakefield/rc

Add "View NG-CHM" button on OncoPrint Heatmap tab

src/config/IAppConfig.ts

@@ -93,6 +93,7 @@ export interface IServerConfig {
     skin_title: string;
     skin_authorization_message: string | null;
     skin_patientview_filter_genes_profiled_all_samples: boolean;
+    show_mdacc_heatmap: boolean;
     quick_search_enabled: boolean;
     default_cross_cancer_study_list: string; // this has a default
     default_cross_cancer_study_list_name: string; // this has a default

src/config/serverConfigDefaults.ts

@@ -21,6 +21,7 @@ const ServerConfigDefaults: Partial<IServerConfig> = {
         'https://bioinformatics.mdanderson.org/study2url?studyid=',
     mdacc_heatmap_study_url:
         'https:// bioinformatics.mdanderson.org/TCGA/NGCHMPortal/?',
+    show_mdacc_heatmap: false,
 
     mygene_info_url:
         'https://mygene.info/v3/gene/<%= entrezGeneId %>?fields=uniprot',

src/pages/resultsView/ResultsViewPageStore.ts

@@ -1390,6 +1390,46 @@ export class ResultsViewPageStore {
         },
     });
 
+
+	// remoteNgchmUrl queries mdanderson.org to test if there are NGCHMs for one selected
+	// study.  The result is either the full URL to a portal page, or an empty string.
+    readonly remoteNgchmUrl = remoteData<string>({
+        await:()=>[this.studyIds],
+        invoke:async()=>{
+            var result = '';
+
+            if (this.studyIds.result!.length === 1) {
+
+                const queryData = {
+                    studyid:this.studyIds.result![0],
+                    format:"json"
+                };
+
+				var urlResponse;
+
+				try {
+                    urlResponse = await request.get("https://bioinformatics.mdanderson.org/study2url")
+                                        .timeout(30000)
+                                        .query(queryData) as any;
+                } catch (err) {
+                    // Just eat the exception. Result will be empty string.
+                }
+
+                if (urlResponse && urlResponse.body.fileContent) {
+                    const parsedUrlResponse = JSON.parse(urlResponse.body.fileContent.trimEnd()) as any;
+
+                    if (parsedUrlResponse.length >= 1) {
+                        // This is faked out for now.  study2url needs mods to include site url
+                        result = "https://bioinformatics.mdanderson.org/TCGA/NGCHMPortal?" + parsedUrlResponse[0];
+                    }
+                }
+            }
+
+            return Promise.resolve (result);
+        }
+    });
+
+
     readonly molecularProfilesWithData = remoteData<MolecularProfile[]>({
         await: () => [
             this.molecularProfilesInStudies,

src/pages/staticPages/tools/oncoprinter/Oncoprinter.tsx

@@ -227,7 +227,8 @@ export default class Oncoprinter extends React.Component<IOncoprinterProps, {}>
             },
             onClickZoomOut:()=>{
                 this.oncoprint.setHorzZoom(this.oncoprint.getHorzZoom()*0.7);
-            }
+            },
+            onClickNGCHM:()=>{}	// do nothing in oncoprinter mode
         };
     }
 

src/pages/studyView/StudyViewPageStore.ts

@@ -2250,11 +2250,13 @@ export class StudyViewPageStore {
         await: () => [this.queriedPhysicalStudyIds],
         onError: (error => {}),
         invoke: async () => {
-            let isSinglePhysicalStudy = this.queriedPhysicalStudyIds.result.length === 1;
-            if (isSinglePhysicalStudy) {
-                return await getHeatmapMeta(getMDAndersonHeatmapStudyMetaUrl(this.queriedPhysicalStudyIds.result[0]));
+            if (AppConfig.serverConfig.show_mdacc_heatmap) {
+                let isSinglePhysicalStudy = this.queriedPhysicalStudyIds.result.length === 1;
+                if (isSinglePhysicalStudy) {
+                    return await getHeatmapMeta(getMDAndersonHeatmapStudyMetaUrl(this.queriedPhysicalStudyIds.result[0]));
+                }
             }
-            return [];
+            return [];  // if not enabled or conditions not met, just return default answer
         }
     }, []);
 

src/shared/components/oncoprint/ResultsViewOncoprint.tsx

@@ -389,6 +389,11 @@ export default class ResultsViewOncoprint extends React.Component<IResultsViewOn
             get heatmapIsDynamicallyQueried () {
                 return self.heatmapIsDynamicallyQueried;
             },
+            get ngchmButtonActive() {
+                return (AppConfig.serverConfig.show_mdacc_heatmap &&
+                        (self.props.store.remoteNgchmUrl.result &&
+                        self.props.store.remoteNgchmUrl.result != '') ? true : false);
+            },
             get heatmapGeneInputValue() {
                 return self.heatmapGeneInputValue;
             },
@@ -583,6 +588,9 @@ export default class ResultsViewOncoprint extends React.Component<IResultsViewOn
             onClickAddTreatmentsToHeatmap:(treatmentIds:string[])=>{
                 this.addHeatmapTracks(this.selectedHeatmapProfile, treatmentIds);
             },
+            onClickNGCHM:()=>{
+            	window.open(this.props.store.remoteNgchmUrl.result, '_blank');
+            },
             onClickDownload:(type:string)=>{
                 switch(type) {
                     case "pdf":

src/shared/components/oncoprint/controls/ConfirmNgchmModal.tsx

@@ -0,0 +1,53 @@
+import * as React from 'react';
+import { Button, Modal } from 'react-bootstrap';
+import {observer} from "mobx-react";
+import {observable} from "mobx";
+
+//
+// NG-CHM are "Next-Generation Clustered Heat Maps", a highly interactive viewer of
+// even very large heat maps, as described here:
+// https://bioinformatics.mdanderson.org/public-software/ngchm/
+// Source code for the viewer and other tools can be found at
+// https://github.com/MD-Anderson-Bioinformatics
+//
+
+@observer
+export default class ConfirmNgchmModal extends React.Component<{ show:boolean, onHide:()=>void, openNgchmWindow:()=>void }, {}> {
+
+	// CSS properties in img tag below should go in .css file?
+	// margin-right:20px; margin-bottom:20px;
+
+    render() {
+        return (
+            <Modal show={this.props.show} onHide={this.props.onHide} animation={false}>
+                <Modal.Header closeButton>
+                    <Modal.Title>Open new tab to MD Anderson NG-CHM?</Modal.Title>
+                </Modal.Header>
+                <Modal.Body>
+                	<div className="oncoprint__controls__heatmap_menu mdacc-modal">
+                    <p>Continue will open a tab or window to a different site (not cBioPortal).</p>
+                    <img src={require("./mdandersonlogo260x85.png")} alt="MD Anderson Cancer Center logo" style={{width:153, height:50, margin:2, 'margin-right':20, 'margin-bottom':20, float:'left'}}/>
+                    <p>
+                         The University of Texas MD Anderson Cancer Center has created a 
+                        Next-Generation Clustered Heatmap compendium
+                        based on the same dataset or a very similar dataset containing many of the
+                        same TCGA samples.  Continue will display a page of NG-CHM based on 
+                        this dataset.
+                    </p>
+                    <div style={{clear:'left'}}/>
+                    Read details on the data processing used for this TCGA compendium <a
+                        href="https://bioinformatics.mdanderson.org/public-datasets/about-the-tcga-compendium/"
+                        target='_blank'
+                        >
+                        here
+                    </a> (opens in a new tab).
+                    </div>
+                </Modal.Body>
+                <Modal.Footer>
+                    <Button onClick={()=>{this.props.openNgchmWindow(); this.props.onHide();}}>Continue</Button>
+                    <Button onClick={this.props.onHide}>Cancel</Button>
+                </Modal.Footer>
+            </Modal>
+        );
+    }
+}

src/shared/components/oncoprint/controls/OncoprintControls.tsx

@@ -1,7 +1,8 @@
 import * as React from 'react';
 import {observer, Observer} from 'mobx-react';
-import {Button, ButtonGroup} from 'react-bootstrap';
+import {Button, ButtonGroup, Modal} from 'react-bootstrap';
 import CustomDropdown from './CustomDropdown';
+import ConfirmNgchmModal from './ConfirmNgchmModal';
 import ReactSelect from 'react-select1';
 import {MobxPromise} from 'mobxpromise';
 import {action, computed, IObservableObject, observable, ObservableMap, reaction, toJS,} from 'mobx';
@@ -65,13 +66,12 @@ export interface IOncoprintControlsHandlers {
     onChangeSelectedClinicalTracks?: (
         attributeIds: (string | SpecialAttribute)[]
     ) => void;
-
     onClickAddGenesToHeatmap?: () => void;
     onClickAddTreatmentsToHeatmap?: (treatments: string[]) => void;
     onSelectHeatmapProfile?: (molecularProfileId: string) => void;
     onChangeHeatmapGeneInputValue?: (value: string) => void;
     onChangeHeatmapTreatmentInputValue?: (value: string) => void;
-
+    onClickNGCHM: () => void;
     onSetHorzZoom: (z: number) => void;
     onClickZoomIn: () => void;
     onClickZoomOut: () => void;
@@ -116,6 +116,7 @@ export interface IOncoprintControlsState {
     heatmapGeneInputValue?: string;
     heatmapTreatmentInputValue?: string;
     hideHeatmapMenu?: boolean;
+    ngchmButtonActive?: boolean;
 
     customDriverAnnotationBinaryMenuLabel?: string;
     customDriverAnnotationTiersMenuLabel?: string;
@@ -176,6 +177,7 @@ const EVENT_KEY = {
     downloadOrder: '28',
     downloadTabular: '29',
     horzZoomSlider: '30',
+    viewNGCHM: '31',
     addTreatmentsToHeatmap: '32',
 };
 
@@ -189,6 +191,7 @@ export default class OncoprintControls extends React.Component<
     @observable private _selectedTreatmentIds: string[] = [];
     private textareaTreatmentText = '';
     @observable treatmentFilter = '';
+    @observable showConfirmNgchmModal:boolean = false;
 
     constructor(props: IOncoprintControlsProps) {
         super(props);
@@ -444,6 +447,11 @@ export default class OncoprintControls extends React.Component<
                 this.props.handlers.onClickDownload &&
                     this.props.handlers.onClickDownload('tabular');
                 break;
+            case EVENT_KEY.viewNGCHM:
+            	if (this.props.state.ngchmButtonActive && this.props.handlers.onClickNGCHM) {
+                    this.showConfirmNgchmModal = true;
+            	}
+                break;
         }
     }
 
@@ -695,6 +703,16 @@ export default class OncoprintControls extends React.Component<
                                     Add Treatment Response to Heatmap
                                 </button>,
                             ]}
+
+                        {this.props.state.ngchmButtonActive &&
+                            (<DefaultTooltip overlay={<span>Open a new tab for NG-CHM with this study from MD Anderson Cancer Center compendium.</span>}>
+                             <button
+                                 className={classNames("btn", "btn-sm", "btn-default")}
+                                 name={EVENT_KEY.viewNGCHM}
+                                 onClick={this.onButtonClick}
+                             >View Next-Generation Clustered Heat Map (NG-CHM)</button>
+                             </DefaultTooltip>)
+                        }
                     </div>
                 );
             }
@@ -1309,6 +1327,11 @@ export default class OncoprintControls extends React.Component<
                     <Observer>{this.getDownloadMenu}</Observer>
                     <Observer>{this.getHorzZoomControls}</Observer>
                     {this.minimapButton}
+                    <ConfirmNgchmModal 
+                        show={this.showConfirmNgchmModal}
+                        onHide={()=>this.showConfirmNgchmModal=false}
+                        openNgchmWindow={this.props.handlers.onClickNGCHM}
+                        />
                 </ButtonGroup>
             </div>
         );