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Restructuring Genomic Data Loaders #287

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Restructuring Genomic Data Loaders #287

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6aa8ab3
Merge pull request #1 from iVis-at-Bilkent/unstable
gorkemsolun Jul 7, 2023
add9492
Restructuring genomic data loaders & navigator fix
gorkemsolun Jul 10, 2023
6043de9
Undefined percentage #288
gorkemsolun Aug 25, 2023
34f40d0
Socket replacement #280
gorkemsolun Aug 25, 2023
aa0244f
Formatting
gorkemsolun Aug 25, 2023
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2 changes: 1 addition & 1 deletion packages/pathway-mapper/dist/index.es5.js
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2 changes: 1 addition & 1 deletion packages/pathway-mapper/dist/index.es5.js.map
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3 changes: 1 addition & 2 deletions packages/pathway-mapper/dist/managers/EditorActionsManager.d.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -143,10 +143,9 @@ export default class EditorActionsManager {
getGenomicDataSVG(node: any): any;
getOncoprintDataSVG(node: any): any;
removeGenomicData(): void;
addGenomicData(genomicData: any): void;
addGenomicData(genomicData: any, isFromPortal: boolean, groupID?: any, activeGroups?: any[]): void;
adjustVisibilityShareDB(profileId: string, isEnabled: boolean): void;
addToProfiles(profileId: string): void;
addPortalGenomicData(genomicData: any, groupID: any, activeGroups?: any[]): void;
shareDBGenomicDataHandler(op: any): void;
shareDBGenomicDataGroupChangeHandler(op: any): void;
shareDBGenomicDataVisibilityHandler(op: any): void;
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16 changes: 5 additions & 11 deletions packages/pathway-mapper/dist/managers/GenomicDataOverlayManager.d.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -14,24 +14,15 @@ export default class GenomicDataOverlayManager {
private colorScheme;
constructor(cy: any);
getEmptyGroupID(): number;
addGenomicDataLocally(genomicData: any, groupID: any): void;
preparePortalGenomicDataShareDB(genomicData: any): {
genomicDataMap: {};
visibilityMap: {};
};
addGenomicDataLocally(genomicData: any, groupID: any, isFromPortal: boolean, activeGroups?: any[]): void;
addGenomicData(data: any): void;
removeGenomicVisData(): void;
addGenomicDataWithGeneSymbol(geneSymbol: any, data: any): void;
addGenomicGroupData(groupID: any, data: any): void;
addPortalGenomicData(data: any, groupID: any, groupsToBeRendered?: any): void;
clearAllGenomicData: () => void;
removeGenomicData(): void;
removeGenomicDataWithGeneSymbol(geneSymbol: any): void;
addGenomicVisData(key: any, data: any): void;
prepareGenomicDataShareDB: (genomicData: any) => {
genomicDataMap: {};
visibilityMap: {};
};
updateGenomicDataVisibility: (_key: any, isVisible: any) => void;
hideGenomicData: () => void;
countVisibleGenomicDataByType(): number;
Expand All @@ -42,7 +33,10 @@ export default class GenomicDataOverlayManager {
showGenomicData(resizeNodeCallback?: (node: any) => void): void;
generateHTMLContentForComparisonNodeTooltip(ele: any, groupsToBeRendered: any): JQuery<HTMLElement>;
showGroupComparisonData(groupsToBeRendered: any[], resizeNodeCallback?: (node: any) => void): void;
parseGenomicData(genomicData: any, groupID: any): void;
prepareGenomicData: (genomicData: any, groupID: any, isCollaborative: boolean, isFromPortal: boolean) => {
genomicDataMap: any;
visibilityMap: any;
};
registerObserver(observer: any): void;
notifyObservers(): void;
getAlterationCountForPatient(geneData: any): number;
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4 changes: 2 additions & 2 deletions packages/pathway-mapper/package.json
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Expand Up @@ -40,9 +40,9 @@
"cytoscape-fcose": "github:iVis-at-Bilkent/cytoscape.js-fcose#unstable",
"cytoscape-grid-guide": "github:iVis-at-Bilkent/cytoscape.js-grid-guide#unstable",
"cytoscape-layout-utilities": "github:iVis-at-Bilkent/cytoscape.js-layout-utilities#unstable",
"cytoscape-navigator": "^2.0.2",
"cytoscape-navigator": "^1.3.3",
"cytoscape-node-editing": "github:iVis-at-Bilkent/cytoscape.js-node-editing#unstable",
"cytoscape-panzoom": "~2.5.3",
"cytoscape-panzoom": "~2.5.2",
"cytoscape-popper": "^2.0.0",
"cytoscape-undo-redo": "github:iVis-at-Bilkent/cytoscape.js-undo-redo#unstable",
"cytoscape-view-utilities": "github:iVis-at-Bilkent/cytoscape.js-view-utilities#unstable",
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92 changes: 44 additions & 48 deletions packages/pathway-mapper/src/managers/EditorActionsManager.tsx
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Expand Up @@ -1797,34 +1797,52 @@ export default class EditorActionsManager {

}

addGenomicData(genomicData: any)
{
const groupID = this.getEmptyGroupID();

if(this.isCollaborative)
{
var parsedGenomicData = this.genomicDataOverlayManager.prepareGenomicDataShareDB(genomicData);
this.shareDBManager.addGenomicData(parsedGenomicData.genomicDataMap);
this.shareDBManager.groupGenomicData(Object.keys(parsedGenomicData.visibilityMap),
groupID);

let currentVisibleGenomicDataCount = this.genomicDataOverlayManager.countVisibleGenomicDataByType();
Object.keys(parsedGenomicData.visibilityMap).forEach(study => {
if (parsedGenomicData.visibilityMap[study] && (currentVisibleGenomicDataCount >= 6)) {
parsedGenomicData.visibilityMap[study] = false;
}
else if(parsedGenomicData.visibilityMap[study]) {
currentVisibleGenomicDataCount++;
}
addGenomicData(genomicData: any, isFromPortal: boolean, groupID?: any, activeGroups?: any[])
{
if (!isFromPortal) {
groupID = this.getEmptyGroupID();
}

if (this.isCollaborative) {
var parsedGenomicData = this.genomicDataOverlayManager.prepareGenomicData(
genomicData,
null,
this.isCollaborative,
isFromPortal
);
this.shareDBManager.addGenomicData(parsedGenomicData.genomicDataMap);
this.shareDBManager.groupGenomicData(
Object.keys(parsedGenomicData.visibilityMap),
groupID
);

if (!isFromPortal) {
let currentVisibleGenomicDataCount =
this.genomicDataOverlayManager.countVisibleGenomicDataByType();
Object.keys(parsedGenomicData.visibilityMap).forEach((study) => {
if (
parsedGenomicData.visibilityMap[study] &&
currentVisibleGenomicDataCount >= 6
) {
parsedGenomicData.visibilityMap[study] = false;
} else if (parsedGenomicData.visibilityMap[study]) {
currentVisibleGenomicDataCount++;
}
});

this.shareDBManager.addGenomicVisibilityData(parsedGenomicData.visibilityMap);
}
else
{
this.genomicDataOverlayManager.addGenomicDataLocally(genomicData, groupID);
}

this.shareDBManager.addGenomicVisibilityData(
parsedGenomicData.visibilityMap
);
} else {
if (activeGroups !== undefined) {
this.genomicDataOverlayManager.addGenomicDataLocally(genomicData, groupID, isFromPortal, activeGroups);
} else {
this.genomicDataOverlayManager.addGenomicDataLocally(genomicData, groupID, isFromPortal);
}

}
}
}

adjustVisibilityShareDB(profileId: string, isEnabled: boolean){
const targetProfileIndex = this.profiles.map(profile => profile.profileId).indexOf(profileId);
Expand All @@ -1846,28 +1864,6 @@ export default class EditorActionsManager {
});
}

addPortalGenomicData(genomicData: any, groupID: any, activeGroups?: any[])
{

if(this.isCollaborative)
{
var parsedGenomicData = this.genomicDataOverlayManager.preparePortalGenomicDataShareDB(genomicData);
this.shareDBManager.addGenomicData(parsedGenomicData.genomicDataMap);
this.shareDBManager.groupGenomicData(Object.keys(parsedGenomicData.visibilityMap),
groupID);
this.shareDBManager.addGenomicVisibilityData(parsedGenomicData.visibilityMap);
}
else
{
if( activeGroups !== undefined){
this.genomicDataOverlayManager.addPortalGenomicData(genomicData, groupID, activeGroups);
}
else {
this.genomicDataOverlayManager.addPortalGenomicData(genomicData, groupID);
}
}
}

shareDBGenomicDataHandler(op: any)
{
var isRemove = Object.keys(op)[1] === 'od';
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