Fix #260, #257

iVis-at-Bilkent · Jun 24, 2021 · a7a7de7 · a7a7de7
1 parent 8033784
commit a7a7de7
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Showing 8 changed files with 59 additions and 36 deletions.
diff --git a/packages/pathway-mapper/dist/index.es5.js b/packages/pathway-mapper/dist/index.es5.js
diff --git a/packages/pathway-mapper/dist/index.es5.js.map b/packages/pathway-mapper/dist/index.es5.js.map
diff --git a/packages/pathway-mapper/dist/utils/PathwayActions.d.ts b/packages/pathway-mapper/dist/utils/PathwayActions.d.ts
@@ -64,6 +64,7 @@ export default class PathwayActions {
     processFile(file: File, isMerge: boolean): void;
     saveAs(type: string): void;
     editorHandler(editor: any, eh: any, undoRedoManager: any, viewOperationsManager: ViewOperationsManager, gridOptionsManager: GridOptionsManager): void;
+    exists(profileId: string): boolean;
     loadSampleData(): void;
     performLayout(): void;
 }
diff --git a/packages/pathway-mapper/src/managers/EditorActionsManager.tsx b/packages/pathway-mapper/src/managers/EditorActionsManager.tsx
@@ -216,8 +216,6 @@ export default class EditorActionsManager{
     {
         args.ele.data('w', args.newWidth);
         args.ele.data('h', args.newHeight);
-        args.ele.style('width', args.newWidth);
-        args.ele.style('height', args.newHeight);
 
         return args;
     };
@@ -226,9 +224,6 @@ export default class EditorActionsManager{
     {
         args.ele.data('w', args.oldWidth);
         args.ele.data('h', args.oldHeight);
-        args.ele.style('width', args.oldWidth);
-        args.ele.style('height', args.oldHeight);
-
         return args;
     };
 
@@ -955,9 +950,6 @@ export default class EditorActionsManager{
         //his.cy.add(newNode);
         this.cy.nodes().updateCompoundBounds();
         this.undoRedoManager.do("add", newNode);
-        //Width was not properly updated only by changing data property
-        var thatEle = this.cy.getElementById(nodeData.id);
-        thatEle.style('width', thatEle.data('w'));
     };
 
     shareDBNodeAddRemoveEventCallBack(op: any)
@@ -1767,6 +1759,17 @@ export default class EditorActionsManager{
             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++;
+                }
+            });
+
             this.shareDBManager.addGenomicVisibilityData(parsedGenomicData.visibilityMap);
         }
         else

diff --git a/packages/pathway-mapper/src/managers/GenomicDataOverlayManager.ts b/packages/pathway-mapper/src/managers/GenomicDataOverlayManager.ts
@@ -199,6 +199,11 @@ export default class GenomicDataOverlayManager {
   };
 
   hideGenomicData = function() {
+
+    this.cy.nodes('[type="GENE"]').forEach(node => {
+      node.data('w', this.getRequiredWidthForGenomicData(0));
+    })
+
     this.cy
       .style()
       .selector('node[type="GENE"]')
@@ -528,7 +533,7 @@ export default class GenomicDataOverlayManager {
 
     this.cy.nodes('[type="GENE"]').forEach(node => {
       node.data('w', this.getRequiredWidthForGenomicData(genomicDataBoxCount));
-    })
+    });
 
     this.cy
       .style()
@@ -568,8 +573,9 @@ export default class GenomicDataOverlayManager {
     // Parse cancer types
     for (let i = 1; i < metaLineColumns.length; i++) {
       cancerTypes.push(metaLineColumns[i]);
+      const visibleGenomicDataCount = Object.keys(this.visibleGenomicDataMapByType).length;
       // Update initially visible genomic data boxes !
-      if (i - 1 < this.DEFAULT_VISIBLE_GENOMIC_DATA_COUNT) {
+      if (visibleGenomicDataCount < this.DEFAULT_VISIBLE_GENOMIC_DATA_COUNT) {
         this.visibleGenomicDataMapByType[cancerTypes[i - 1]] = true;
       } else {
         this.visibleGenomicDataMapByType[cancerTypes[i - 1]] = false;

diff --git a/packages/pathway-mapper/src/managers/ShareDBManager.tsx b/packages/pathway-mapper/src/managers/ShareDBManager.tsx
@@ -53,7 +53,7 @@ export default class ShareDBManager {
         var genomicDataGroupCount = this.doc.data[this.GENOMIC_DATA_GROUP_COUNT];
         //Reset all genomic maps
         for (const key of Object.keys(genomicMap)) {
-            ops.push({p: [this.GENOMIC_DATA_GROUP_NAME, key], od: genomicMap[key]});
+            ops.push({p: [this.GENOMIC_DATA_MAP_NAME, key], od: genomicMap[key]});
         }
         for (const key of Object.keys(visMap)) {
             ops.push({p: [this.VISIBLE_GENOMIC_DATA_MAP_NAME, key], od: visMap[key]});
@@ -415,6 +415,7 @@ export default class ShareDBManager {
 
         this.editor.genomicDataOverlayManager.showGenomicData();
         this.editor.genomicDataOverlayManager.notifyObservers();
+        this.editor.cy.style().update();
         this.editor.cy.fit(50);
     };
 

diff --git a/packages/pathway-mapper/src/ui/CytoscapeArea.tsx b/packages/pathway-mapper/src/ui/CytoscapeArea.tsx
@@ -485,10 +485,10 @@ export default class CytoscapeArea extends React.Component<PathwayMapperType, {}
         // so that a data field or something like that will be used to set node dimentions instead of directly calling node.css()
         // is highly recommended (Of course this will require a proper setting in the stylesheet).
         setWidth: function (node, width) {
-            node.style('width', width);
+            node.data('w', width)
         },
         setHeight: function (node, height) {
-            node.style('height', height);
+            node.data('h', height);
         },
         setCompoundMinWidth: function (node, minWidth) {
             node.style('min-width', minWidth);
@@ -687,15 +687,6 @@ export default class CytoscapeArea extends React.Component<PathwayMapperType, {}
       this.editor.postLayout();
     });
 
-    // //TODO fix this when cytoscape is updated !!!
-    // //Due to cytoscape.js bug, only workaround that worked :(
-    // this.cy.on('add', 'node', function(event)
-    // {
-    //     // event.target.select();
-    //     this.cy.style().update();
-    //     this.cy.forceRender();
-    // });
-
     this.cy.on("nodeediting.resizeend", (_e: any, _type: any, node: any) => {
 
       //Updates 'data' properties from 'style'

diff --git a/packages/pathway-mapper/src/utils/PathwayActions.ts b/packages/pathway-mapper/src/utils/PathwayActions.ts
@@ -418,24 +418,45 @@ export default class PathwayActions {
     this.gridOptionsManager = gridOptionsManager;
   }
 
+  @autobind
+  exists(profileId: string){
+
+    let exists = false;
+    this.profiles.forEach((profile: IProfileMetaData) => {
+      if(profile.profileId === profileId){
+        exists = true;
+      }
+    });
+
+    return exists;
+  }
+
   @autobind
   loadSampleData() {
     const data =
-      "gene\tlung\tovarian\tbreast\ty\n" +
-      "PTEN\t-7\t-20\t10\t20\n" +
-      "NF1\t-12\t-4\t30\t20\n" +
-      "PIK3CA\t18\t40\t-50\t20\n" +
-      "KRAS\t11\t-5\t0\t20\n" +
-      "ZIYA\t0\t-2\t0\t20\n" +
-      "AKT1\t3\t30\t-10\t20\n" +
-      "AKT2\t6\t-3\t20\t20\n" +
-      "AKT3\t6\t-3\t20\t20\n" +
+      "gene\tlung\tovarian\tbreast\n" +
+      "PTEN\t-7\t-20\t10\n" +
+      "NF1\t-12\t-4\t30\n" +
+      "PIK3CA\t18\t40\t-50\n" +
+      "KRAS\t11\t-5\t0\n" +
+      "ZIYA\t0\t-2\t0\n" +
+      "AKT1\t3\t30\t-10\n" +
+      "AKT2\t6\t-3\t20\n" +
+      "AKT3\t6\t-3\t20\n" +
       "\n";
+
+    if (this.exists("lung") || this.exists("ovarian") || this.exists("breast")) {
+      return;
+    }    
+
     this.editor.addGenomicData(data);
 
-    this.addProfile({ profileId: "lung", enabled: true });
-    this.addProfile({ profileId: "ovarian", enabled: true });
-    this.addProfile({ profileId: "breast", enabled: true });
+    if (!this.isCollaborative) {
+      this.addProfile({ profileId: "lung", enabled: this.profiles.length < 6 ? true : false });
+      this.addProfile({ profileId: "ovarian", enabled: this.profiles.length < 6 ? true : false });
+      this.addProfile({ profileId: "breast", enabled: this.profiles.length < 6 ? true : false });
+    }
+
   }
 
   @autobind