Merge branch '2024-refactoring-RF2' of github.com:veg/hivtrace-viz into 2024-refactoring-RF2

Author: stevenweaver

src/clusternetwork.js

@@ -825,7 +825,9 @@ var hivtrace_cluster_network_graph = function (
           .attr("tabindex", "-1")
           .text((d) => "Add this node to the cluster of interest")
           .on("click", (d) => {
-            clustersOfInterest.get_editor().append_node(node.id, true);
+            clustersOfInterest
+              .get_editor()
+              .append_node(self.entity_id(node), true);
           });
       }
 
@@ -2146,8 +2148,8 @@ var hivtrace_cluster_network_graph = function (
                 sort: "value",
               },
               {
-                value: "Nodes",
-                help: "How many nodes are in this cluster of interest",
+                value: "Persons",
+                help: "How many persons are in this cluster of interest",
                 sort: "value",
               },
               {
@@ -2174,7 +2176,9 @@ var hivtrace_cluster_network_graph = function (
               current_node_objects = {};
               _.each(self.defined_priority_groups, (pg) => {
                 if (current_selection.has(pg.name)) {
-                  clusterOITotalNOdes += pg.nodes.length;
+                  clusterOITotalNOdes += self.unique_entity_list(
+                    pg.node_objects
+                  ).length;
                   _.each(pg.nodes, (n) => {
                     current_node_set.add(n.name);
                     current_node_objects[n.name] = {
@@ -2189,9 +2193,10 @@ var hivtrace_cluster_network_graph = function (
                   current_selection.size +
                   " clusterOI with " +
                   clusterOITotalNOdes +
-                  " nodes, creating a new clusterOI with " +
-                  current_node_set.size +
-                  " nodes. <br><small>Note that the clusters of interest being merged will <b>not</b> be automatically deleted</small>"
+                  " persons, creating a new clusterOI with " +
+                  self.unique_entity_list_from_ids([...current_node_set])
+                    .length +
+                  " persons. <br><small>Note that the clusters of interest being merged will <b>not</b> be automatically deleted</small>"
               );
               proceed_btn.attr("disabled", null);
             } else {
@@ -2210,7 +2215,11 @@ var hivtrace_cluster_network_graph = function (
               );
               clustersOfInterest
                 .get_editor()
-                .append_nodes([...current_node_set], current_node_objects);
+                .append_nodes(
+                  [...current_node_set],
+                  current_node_objects,
+                  true
+                );
             }
             $(modal.node()).modal("hide");
           };
@@ -2220,12 +2229,15 @@ var hivtrace_cluster_network_graph = function (
           var rows = [];
           _.each(self.defined_priority_groups, (pg) => {
             const my_overlaps = new Set();
-            _.each(pg.nodes, (n) => {
-              _.each([...self.priority_node_overlap[n.name]], (ps) => {
-                if (ps !== pg.name) {
-                  my_overlaps.add(ps);
+            _.each(pg.node_objects, (n) => {
+              _.each(
+                [...self.priority_node_overlap[self.entity_id(n)]],
+                (ps) => {
+                  if (ps !== pg.name) {
+                    my_overlaps.add(ps);
+                  }
                 }
-              });
+              );
             });
 
             rows.push([
@@ -2243,7 +2255,7 @@ var hivtrace_cluster_network_graph = function (
                 },
               },
               { value: pg.name },
-              { value: pg.nodes.length },
+              { value: self.unique_entity_list(pg.node_objects).length },
               {
                 value: [...my_overlaps],
                 format: (d) => d.join("<br>"),
@@ -4830,17 +4842,17 @@ var hivtrace_cluster_network_graph = function (
       self.legend_svg
         .append("g")
         .classed("hiv-trace-legend", true)
-        .attr("transform", "translate(0," + offset + ")")
+        .attr("transform", "translate(3," + (offset + 5) + ")")
         .append("circle")
-        .attr("cx", "8")
+        .attr("cx", "6")
         .attr("cy", "-4")
-        .attr("r", "8")
+        .attr("r", "6")
         .classed("multi_sequence", true)
         .style("fill", "none");
       self.legend_svg
         .append("g")
         .classed("hiv-trace-legend", true)
-        .attr("transform", "translate(20," + offset + ")")
+        .attr("transform", "translate(20," + (offset + 5) + ")")
         .append("text")
         .text("Represents >1 sequence");
       offset += 24;
@@ -4861,7 +4873,7 @@ var hivtrace_cluster_network_graph = function (
         .classed("legend", true)
         .style(
           "fill",
-          "url(#" + self.generate_cross_hatch_pattern("#ccc") + ")"
+          "url(#" + self.generate_cross_hatch_pattern("#cab") + ")"
         );
       self.legend_svg
         .append("g")

src/clustersOfInterest.js

@@ -655,7 +655,11 @@ function open_editor(
         }
       };
 
-      panel_object.append_nodes = function (nodes_to_add, existing_attributes) {
+      panel_object.append_nodes = function (
+        nodes_to_add,
+        existing_attributes,
+        mspp_raw
+      ) {
         if (!panel_object.can_add_nodes()) {
           return;
         }
@@ -667,6 +671,7 @@ function open_editor(
 
         let need_update = false;
         let valid_ids = {};
+
         _.each(self.json["Nodes"], (n) => {
           if (!existing_ids[n.id]) {
             if (existing_attributes) {
@@ -677,16 +682,19 @@ function open_editor(
           }
         });
 
-        nodes_to_add = _.flatten(
-          _.map(nodes_to_add, (d) => self.fetch_sequences_for_pid(d))
-        );
+        if (!mspp_raw) {
+          nodes_to_add = _.flatten(
+            _.map(nodes_to_add, (d) => self.fetch_sequences_for_pid(d))
+          );
+        }
 
         _.each(nodes_to_add, (n) => {
           if (!(n in existing_ids) && n in valid_ids) {
-            console.log(n);
             panel_object._append_node(valid_ids[n]);
             existing_ids[n] = 1;
             need_update = true;
+          } else {
+            console.log("***", n);
           }
         });
 

src/hiv_tx_network.js

@@ -675,9 +675,15 @@ class HIVTxNetwork {
   generate_cross_hatch_pattern(color) {
     let id = "id" + this.dom_prefix + "_diagonalHatch_" + color.substr(1, 10);
     if (this.network_svg.select("#" + id).empty()) {
-      this.network_svg
-        .append("defs")
-        .append("pattern")
+      function getComplementaryColor(backgroundColor) {
+        const color = d3.rgb(backgroundColor);
+        const luminance = color.r * 0.299 + color.g * 0.587 + color.b * 0.114;
+        return luminance > 128 ? "#000000" : "#ffffff";
+      }
+
+      let defs = this.network_svg.append("defs");
+
+      /*defs.append("pattern")
         .attr("id", id)
         .attr("patternUnits", "userSpaceOnUse")
         .attr("width", "2")
@@ -687,6 +693,29 @@ class HIVTxNetwork {
         .attr("d", "M -1,2 l 6,0")
         .attr("stroke", color)
         .attr("stroke-width", "3"); //this is actual shape for arrowhead
+        */
+
+      let pattern = defs
+        .append("pattern")
+        .attr("id", id)
+        .attr("patternUnits", "userSpaceOnUse")
+        .attr("width", "6")
+        .attr("height", "6")
+        .attr("patternTransform", "rotate(45)");
+
+      pattern
+        .append("rect")
+        .attr("width", "3")
+        .attr("height", "6")
+        .attr("fill", color)
+        .attr("transform", "translate(0,0)");
+
+      pattern
+        .append("rect")
+        .attr("width", "3")
+        .attr("height", "6")
+        .attr("fill", getComplementaryColor(color))
+        .attr("transform", "translate(3,0)");
     }
     return id;
   }

src/hivtrace.css

@@ -1,17 +1,17 @@
 @keyframes selected_object_animation {
   from {
-    stroke-width: 1px;
-    stroke: #ccc;
+    stroke-width: 3px;
+    stroke: #350e6b;
   }
 
   50% {
     stroke-width: 5px;
-    stroke: #000;
+    stroke: #350e6b;
   }
 
   to {
-    stroke-width: 1px;
-    stroke: #ccc;
+    stroke-width: 3px;
+    stroke: #350e6b;
   }
 }
 
@@ -100,13 +100,13 @@ circle.cluster {
 }
 
 .link {
-  stroke: #aaaaaa;
+  stroke: #cccccc;
   stroke-width: 1.5px;
   fill: none;
 }
 
 .mspp-link {
-  stroke: #666666;
+  stroke: #aaaaaa;
   stroke-width: 2px;
   fill: none;
 }
@@ -194,8 +194,11 @@ circle.selected_object {
 g.multi_sequence,
 path.multi_sequence,
 circle.multi_sequence {
-  stroke-width: 3px;
+  stroke-width: 1px;
   stroke: #350e6b;
+  border-radius: 50%;
+  outline: 8px dotted black;
+  outline-offset: -0.2rem;
   /*stroke-dasharray: 10 1;*/
 }
 

src/network.js

@@ -224,7 +224,7 @@ function handle_cluster_click(self, cluster, release) {
         .on("click", (d) => {
           clustersOfInterest
             .get_editor()
-            .append_nodes(_.map(cluster.children, (c) => c.id));
+            .append_nodes(_.map(cluster.children, (c) => self.entity_id(c)));
         });
     }