Merge pull request #1132 from VirtualFlyBrain/feature/1114

Improve Layout and Links on Circuit Browser
VirtualFlyBrain · Jun 21, 2021 · 4b2f1fb · 4b2f1fb
2 parents eefb5c8 + 15f7cfc
commit 4b2f1fb
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Showing 10 changed files with 233 additions and 183 deletions.
diff --git a/components/configuration/VFBCircuitBrowser/circuitBrowserConfiguration.js b/components/configuration/VFBCircuitBrowser/circuitBrowserConfiguration.js
@@ -1,4 +1,4 @@
-var locationCypherQuery = ( instances, hops, weight ) => ({
+var locationCypherQuery = ( instances, paths, weight ) => ({
   "statements": [
     {
       "statement" : "WITH [" + instances + "] AS neurons"
@@ -7,20 +7,19 @@ var locationCypherQuery = ( instances, hops, weight ) => ({
       + " CALL gds.beta.shortestPath.yens.stream({"
       + "  nodeQuery: 'MATCH (n:Neuron) RETURN id(n) AS id',"
       + "  relationshipQuery: 'MATCH (a:Neuron:has_neuron_connectivity)-[r:synapsed_to]->(b:Neuron) WHERE exists(r.weight) AND r.weight[0] >= "
-      + weight.toString() + " RETURN id(a) AS source, id(b) AS target, type(r) as type, 5000-r.weight[0] as weight_p',"
+      + weight?.toString() + " RETURN id(a) AS source, id(b) AS target, type(r) as type, 5000-r.weight[0] as weight_p',"
       + "  sourceNode: id(source),"
       + "  targetNode: id(target),"
-     + "  k: " + hops.toString() + ","
+      + "  k: " + paths?.toString() + ","
       + "  relationshipWeightProperty: 'weight_p',"
       + "  relationshipTypes: ['*'],"
       + "  path: true"
       + "})"
       + " YIELD index, sourceNode, targetNode, nodeIds, path"
       + " WITH * ORDER BY index DESC"
-     + " OPTIONAL MATCH fp=(source)-[r:synapsed_to*..]->(target) WHERE ALL(n in nodes(fp) WHERE id(n) IN nodeIds)"
-      + " UNWIND r as sr WITH *, collect(id(sr)) as ids, toString(id(sr))+':'+toString(index) as relY OPTIONAL MATCH cp=(source)-[r:synapsed_to*..]-(target)"
-      + " WHERE ALL(n in nodes(cp) WHERE id(n) IN nodeIds) UNWIND ids as id"
-      + " RETURN distinct a as root, collect(distinct fp) as pp, collect(distinct cp) as p, collect(distinct id) as fr, sourceNode as source, targetNode as target, max(length(fp)) as maxHops, collect(distinct relY) as relationshipY ",
+      + " UNWIND relationships(path) as sr"
+      + " OPTIONAL MATCH cp=(x)-[:synapsed_to]-(y) WHERE x=apoc.rel.startNode(sr) AND y=apoc.rel.endNode(sr) OPTIONAL MATCH fp=(x)-[r:synapsed_to]->(y)"
+      + " RETURN distinct a as root, collect(distinct fp) as pp, collect(distinct cp) as p, collect(distinct id(r)) as fr, sourceNode as source, targetNode as target, max(length(path)) as maxHops, collect(distinct toString(id(r))+':'+toString(index)) as relationshipY ",
       "resultDataContents": ["row", "graph"]
     }
   ]
@@ -41,14 +40,16 @@ var configuration = {
       "tooltip" : "label"
     }
   },
-  // Minimum amount of hops allowed
-  minHops : 1,
-  // Maximum amount of hops allowed
-  maxHops : 6,
+  // Minimum amount of paths allowed
+  minPaths : 1,
+  // Maximum amount of paths allowed
+  maxPaths : 6,
   // Minimum amount of neurons allowed
   minNeurons : 2,
   // Maximum amount of neurons allowed
-  maxNeurons : 2
+  maxNeurons : 2,
+  // Curvature of lines, 0 is a straight line
+  linkCurvature : 0
 }
 
 var styling = {
@@ -110,7 +111,7 @@ var styling = {
 }
 
 var restPostConfig = {
-  url: "https://pdb.virtualflybrain.org/db/neo4j/tx/commit",
+  url: "https://pdb-dev.virtualflybrain.org/db/neo4j/tx/commit",
   contentType: "application/json"
 };
 

diff --git a/components/configuration/VFBOverview/quickHelp.json b/components/configuration/VFBOverview/quickHelp.json
@@ -3,16 +3,6 @@
 	"height": "575",
     "width": "900",
 	"steps": [{
-		"title": "Welcome to Virtual Fly Brain",
-		"image" : "https://VirtualFlyBrain.org/data/VFB/screencaps/VFB_3D_400x400.jpg",
-		"instructions": [{
-			"icon" : "fa fa-question-circle-o",
-			"label" : "Hi, we are currently running a VFB User Survey, once you have used the site please consider completing this survey to help us improve it by clicking User Survey in the Help menu above."
-		},{
-			"icon" : "fa fa-fast-forward",
-			"label" : "Just click NEXT below for handy tips on using VFB or SKIP INTRO to close this and jump right into VFB."
-		}]
-	},{
 		"title": "Welcome to Virtual Fly Brain",
 		"image" : "geppetto/build/VFBqHelpMain.jpg",
 		"instructions": [{

diff --git a/components/configuration/VFBToolbar/vfbtoolbarMenuConfiguration.js b/components/configuration/VFBToolbar/vfbtoolbarMenuConfiguration.js
@@ -632,14 +632,6 @@ var toolbarMenu = {
       position: "bottom-start",
       list: [
         {
-          label: "User Survey",
-          icon: "",
-          trailerIcon: "fa fa-external-link",
-          action: {
-            handlerAction: "openNewTab",
-            parameters: ["https://www.surveymonkey.co.uk/r/5HDZZRR"]
-          }
-        },{
           label: "F.A.Q.",
           icon: "",
           trailerIcon: "fa fa-external-link",

diff --git a/components/interface/VFBCircuitBrowser/Controls.js b/components/interface/VFBCircuitBrowser/Controls.js
@@ -115,11 +115,11 @@ const searchConfiguration = require('./../../configuration/VFBMain/searchConfigu
 const datasourceConfiguration = require('./../../configuration/VFBMain/searchConfiguration').datasourceConfiguration;
 
 /**
- * Create custom marks for Hops slider.
- * Only show the label for the minimum and maximum hop, hide the rest
+ * Create custom marks for Paths slider.
+ * Only show the label for the minimum and maximum paths, hide the rest
  */
 const customMarks = () => {
-  let marks = new Array(configuration.maxHops);
+  let marks = new Array(configuration.maxPaths);
   for ( var i = 0; i < marks.length; i++ ) {
     if ( i == 0 || i == marks.length - 1 ) {
       marks[i] = { value : i + 1, label : (i + 1).toString() };
@@ -203,7 +203,7 @@ class Controls extends Component {
       key : 1
     };
     this.weight = this.props.weight;
-    this.hops = this.props.hops;
+    this.paths = this.props.paths;
     this.addNeuron = this.addNeuron.bind(this);
     this.reverseNeurons = this.reverseNeurons.bind(this);
     this.neuronTextfieldModified = this.neuronTextfieldModified.bind(this);
@@ -330,7 +330,7 @@ class Controls extends Component {
       clearTimeout(this.typingTimeout);
     }
     // Create a setTimeout interval, to avoid performing searches on every stroke
-    setTimeout(this.typingTimeout, 500, event.target);
+    setTimeout(this.typingTimeout, 10, event.target);
   }
 
   /**
@@ -355,10 +355,10 @@ class Controls extends Component {
   }
 
   /**
-   * Hops slider has been dragged, value has changed
+   * Paths slider has been dragged, value has changed
    */
   sliderChange (event, value ) {
-    this.hops = value;
+    this.paths = value;
   }
 
   weightChange (event ) {
@@ -528,13 +528,13 @@ class Controls extends Component {
                   <Grid item sm={9}>
                     <Slider
                       aria-labelledby="discrete-slider-always"
-                      defaultValue={this.hops}
+                      defaultValue={this.paths}
                       onChangeCommitted={this.sliderChange}
                       step={1}
                       marks={customMarks()}
                       valueLabelDisplay="auto"
-                      min={configuration.minHops}
-                      max={configuration.maxHops}
+                      min={configuration.minPaths}
+                      max={configuration.maxPaths}
                     />  
                   </Grid>
                 </Grid>
@@ -580,7 +580,7 @@ function mapStateToProps (state) {
 }
 
 function mapDispatchToProps (dispatch) {
-  return { vfbCircuitBrowser: (type, path) => dispatch ( { type : type, data : { instance : path } }), }
+  return { vfbCircuitBrowser: (type, neurons) => dispatch ( { type : type, data : { instance : neurons } }), }
 }
 
 export default connect(mapStateToProps, mapDispatchToProps, null, { forwardRef : true } )(withStyles(styles)(Controls));