Merge pull request #546 from WildMeOrg/issue_291

fix relationship diagram and relationship table display issue

src/main/java/org/ecocean/MarkedIndividual.java

@@ -614,7 +614,7 @@ public boolean isDeceased() {
     //}
     for (int c = 0; c < encounters.size(); c++) {
       Encounter temp = (Encounter) encounters.get(c);
-      if (temp.getLivingStatus().equals("dead")) {
+      if ((temp.getLivingStatus() != null) && temp.getLivingStatus().equals("dead")) {
         return true;
       }
     }
@@ -2258,14 +2258,20 @@ public JSONObject uiJson(HttpServletRequest request, boolean includeEncounters)
     jobj.put("maxYearsBetweenResightings", getMaxNumYearsBetweenSightings());
     // note this does not re-compute thumbnail url (so we can get thumbnails on searchResults in a reasonable time)
     jobj.put("thumbnailUrl", this.thumbnailUrl);
+    jobj.put("livingStatus", this.isDeceased() ? "dead" : "alive");
 
-    if(includeEncounters) {
-      Vector<String> encIDs = new Vector<String>();
-      for (Encounter enc : this.encounters) {
+    Vector<String> encIDs = new Vector<String>();
+    Encounter firstEncounter = null;
+    Encounter lastEncounter = null;
+    for (Encounter enc : this.getDateSortedEncounters()) {
         encIDs.add(enc.getCatalogNumber());
-      }
-      jobj.put("encounterIDs", encIDs.toArray());
+        if (firstEncounter == null) firstEncounter = enc;
+        lastEncounter = enc;
     }
+    if (includeEncounters) jobj.put("encounterIDs", encIDs.toArray());
+    if (firstEncounter != null) jobj.put("firstSightingDate", firstEncounter.getDate());
+    if (lastEncounter != null) jobj.put("mostRecentSightingDate", lastEncounter.getDate());
+
     return sanitizeJson(request,decorateJson(request, jobj));
   }
 

src/main/java/org/ecocean/api/Login.java

@@ -96,6 +96,7 @@ protected void doPost(HttpServletRequest request, HttpServletResponse response)
                     myShepherd.closeDBTransaction();
 		}
             }
+            myShepherd.rollbackAndClose();
         }
 
         if (success) {

src/main/webapp/encounters/relatedIndividuals.jsp

@@ -0,0 +1,121 @@
+<%@ page contentType="application/json; charset=utf-8" language="java" import="org.joda.time.LocalDateTime,
+org.joda.time.format.DateTimeFormatter,
+org.joda.time.format.ISODateTimeFormat,java.net.*,
+org.ecocean.grid.*,org.ecocean.ia.*,java.util.*,
+java.io.*,java.util.*, java.io.FileInputStream, 
+
+org.datanucleus.api.rest.orgjson.JSONArray,
+org.datanucleus.api.rest.orgjson.JSONException,
+org.datanucleus.api.rest.orgjson.JSONObject,
+org.datanucleus.api.rest.RESTUtils,
+org.datanucleus.ExecutionContext,
+java.util.Set, java.util.HashSet,
+java.lang.reflect.Method,
+org.datanucleus.api.jdo.JDOPersistenceManager,
+org.ecocean.cache.*,
+org.ecocean.social.Relationship,
+java.util.zip.GZIPOutputStream,
+java.io.File, java.io.FileNotFoundException, org.ecocean.*,org.ecocean.servlet.*,javax.jdo.*, java.lang.StringBuffer, java.util.Vector, java.util.Iterator, java.lang.NumberFormatException"%>
+<%!
+
+// Returns a somewhat rest-like JSON object containing the metadata
+public JSONObject uiJson(MarkedIndividual indy, HttpServletRequest request) throws JSONException {
+  JSONObject jobj = new JSONObject();
+
+  jobj.put("individualID", indy.getIndividualID());
+  jobj.put("displayName", indy.getDisplayName(request));
+  jobj.put("sex", indy.getSex());
+  jobj.put("nickname", indy.getNickName());
+  jobj.put("nickname", indy.getNickName());
+  jobj.put("timeOfBirth", indy.getTimeOfBirth());
+  jobj.put("timeOfDeath", indy.getTimeofDeath());
+  jobj.put("dateFirstIdentified", indy.getDateFirstIdentified());
+  jobj.put("dateTimeLatestSighting", indy.getDateLatestSighting());
+  jobj.put("genus", request.getParameter("genus"));
+  jobj.put("specificEpithet", request.getParameter("specificEpithet"));
+  jobj.put("numberEncounters", indy.getNumEncounters());
+
+  	JSONArray jArray =new JSONArray();
+    for (Encounter enc : indy.getEncounterList()) {
+    	JSONObject jobjEnc = new JSONObject();
+		jobjEnc.put("lifeStage", enc.getLifeStage());
+		jobjEnc.put("dateInMilliseconds", enc.getDateInMilliseconds());
+		jobjEnc.put("decimalLatitude", enc.getDecimalLatitude());
+		jobjEnc.put("decimalLongitude", enc.getDecimalLongitude());
+		jobjEnc.put("year", enc.getYear());
+		jobjEnc.put("month", enc.getMonth());
+		jobjEnc.put("day", enc.getDay());
+    	jArray.put(jobjEnc);
+    }
+    jobj.put("encounters",jArray);
+  	return jobj;
+}
+
+%>
+<%!
+
+void tryCompress(HttpServletRequest req, HttpServletResponse resp, JSONArray jo, boolean useComp) throws IOException, JSONException {
+	//System.out.println("??? TRY COMPRESS ??");
+    //String s = scrubJson(req, jo).toString();
+    String s = jo.toString();
+    if (!useComp || (s.length() < 3000)) {  //kinda guessing on size here, probably doesnt matter
+        resp.getWriter().write(s);
+    } else {
+        resp.setHeader("Content-Encoding", "gzip");
+    OutputStream o = resp.getOutputStream();
+    GZIPOutputStream gz = new GZIPOutputStream(o);
+        gz.write(s.getBytes());
+        gz.flush();
+        gz.close();
+        o.close();
+    }
+}
+
+%>
+<%
+
+response.setHeader("Access-Control-Allow-Origin", "*"); 
+
+String context="context0";
+context=ServletUtilities.getContext(request);
+
+Shepherd myShepherd=new Shepherd(context);
+myShepherd.setAction("relatedIndividuals.jsp");
+
+
+
+
+
+
+
+MarkedIndividual indiv = myShepherd.getMarkedIndividual(request.getParameter("individualID"));
+if (indiv == null) {
+	response.setStatus(404);
+	myShepherd.rollbackDBTransaction();
+	myShepherd.closeDBTransaction();
+	return;
+}
+
+
+Set<MarkedIndividual> already = new HashSet<MarkedIndividual>();
+try {
+	JSONArray jarr = new JSONArray();
+        jarr.put(uiJson(indiv, request));
+	for (Relationship rel : indiv.getAllRelationships(myShepherd)) {
+		MarkedIndividual other = rel.getMarkedIndividual1();
+		if (other.getId().equals(indiv.getId())) other = rel.getMarkedIndividual2();
+		if (already.contains(other)) continue;
+		already.add(other);
+		jarr.put(uiJson(other, request));
+	}
+	out.println(jarr.toString());
+
+} catch(Exception e){
+	e.printStackTrace();
+}
+finally{
+	myShepherd.rollbackDBTransaction();
+	myShepherd.closeDBTransaction();
+
+}
+%>

src/main/webapp/javascript/bubbleDiagram/encounter-calls.js

@@ -426,7 +426,7 @@ var makeRelTable = function(items, tableHeadLocation, tableBodyLocation, sortOn)
 				    	return "<button type='button' name='button' value='" + d[1] + "' class='btn btn-sm btn-block deleteRelationshipBtn' id='remove" + d[1] + "'>Remove</button><div class='confirmDelete' value='" + d[1] + "'><p>Are you sure you want to delete this relationship?</p><button class='btn btn-sm btn-block yesDelete' type='button' name='button' value='" +d[1]+ "'>Yes</button><button class='btn btn-sm btn-block cancelDelete' type='button' name='button' value='" + d[1] + "'>No</button></div>";
 					}
 					if(d.length > 2) {
-						return "<a href='individuals.jsp?number=" + d[0] + "'>" + d[5] + "</a><br><span>" + dict['nickname'] + " : " + d[1]+ "</span><br><span>" + dict['alternateID'] + ": " + d[2] + "</span><br><span>" + dict['sex'] + ": " + d[3] + "</span><br><span>" + dict['haplotype'] +": " + d[4] + "</span>";
+						return "<a href='individuals.jsp?number=" + d[0] + "'>" + d[5] + "</a><br><span>" + dict['nickname'] + " : " + (d[1] ?? "")+ "</span><br><span>" + dict['alternateID'] + ": " + (d[2] ?? "") + "</span><br><span>" + dict['sex'] + ": " + (d[3] ?? "") + "</span><br><span>" + dict['haplotype'] +": " + (d[4] ?? "") + "</span>";
 			    	}
 					return d[0].italics() + "-" + d[1];
 			    	//}
@@ -687,48 +687,53 @@ var getRelationshipTableData = function(individualID) {
 	    	relationship = {"roles": [markedIndividualRole, relationshipWithRole], "relationshipWith": [whaleID], "type": type, "socialUnit": relatedSocialUnitName, "edit": ["edit", relationshipID], "remove": ["remove", relationshipID]};
 	    	relationshipArray.push(relationship);
 		}
-		getIndividualData(relationshipArray);
-		console.log("gonna makeRelTable");
-		makeRelTable(relationshipArray, "#relationshipHead", "#relationshipBody", "text");
+		getIndividualData(relationshipArray, function (relationshipTableData) {
+			console.log("All data has been processed:", JSON.stringify(relationshipTableData));
+			makeRelTable(relationshipTableData, "#relationshipHead", "#relationshipBody", "text");
+		});
+
     });
 }
 
-var getIndividualData = function(relationshipArray) {
-	console.log("getIndividualData");
-    var relationshipTableData = [];
-    for(var i=0; i < relationshipArray.length; i++) {
-	d3.json(wildbookGlobals.baseUrl + "/api/org.ecocean.MarkedIndividual/" + relationshipArray[i].relationshipWith[0], function(error, json) {
-	    if(error) {
-		console.log("error")
-	    }
-	    //console.log("json: "+JSON.stringify(json));
-	    let jsonData = json;
-	    var individualInfo = relationshipArray.filter(function(obj) {
-		return obj.relationshipWith[0] === jsonData.individualID;
-	    })[0];
-	    console.log(individualInfo.relationshipWith);
-	    individualInfo.relationshipWith[1] = jsonData.nickName;
-	    individualInfo.relationshipWith[2] = jsonData.alternateid;
-	    individualInfo.relationshipWith[3] = jsonData.sex;
-	    individualInfo.relationshipWith[4] = jsonData.localHaplotypeReflection;
-	    individualInfo.relationshipWith[5] = jsonData.displayName;
-	    relationshipTableData.push(individualInfo);
-
-	    if(relationshipTableData.length == relationshipArray.length) {
-		for(var j = 0; j < relationshipArray.length; j++) {
-		    if(relationshipArray[j].relationshipWith.length == 1) {
-			relationshipArray[j].relationshipWith[1] = jsonData.nickName;
-			relationshipArray[j].relationshipWith[2] = jsonData.alternateid;
-			relationshipArray[j].relationshipWith[3] = jsonData.sex;
-			relationshipArray[j].relationshipWith[4] = jsonData.localHaplotypeReflection;
-			relationshipArray[j].relationshipWith[5] = jsonData.displayName;
-		    }
-		}
-
-	    }
-	});
-    }
+var getIndividualData = function (relationshipArray, onComplete) {
+	var relationshipTableData = [];
+	var completedRequests = 0;
+
+	for (var i = 0; i < relationshipArray.length; i++) {
+		d3.json(wildbookGlobals.baseUrl + "/api/org.ecocean.MarkedIndividual/" + relationshipArray[i].relationshipWith[0], function (error, json) {
+			if (error) {
+				console.log("Error loading data");
+				return;
+			}
 
+			let jsonData = json;
+			var individualInfo = relationshipArray.filter(function (obj) {
+				return obj.relationshipWith[0] === jsonData.individualID;
+			})[0];
+
+			individualInfo.relationshipWith[1] = jsonData.nickName;
+			individualInfo.relationshipWith[2] = jsonData.alternateid;
+			individualInfo.relationshipWith[3] = jsonData.sex;
+			individualInfo.relationshipWith[4] = jsonData.localHaplotypeReflection;
+			individualInfo.relationshipWith[5] = jsonData.displayName;
+
+			relationshipTableData.push(individualInfo);
+			completedRequests++;
+
+			if (completedRequests === relationshipArray.length) {
+				for (var j = 0; j < relationshipArray.length; j++) {
+					if (relationshipArray[j].relationshipWith.length == 1) {
+						relationshipArray[j].relationshipWith[1] = jsonData.nickName;
+						relationshipArray[j].relationshipWith[2] = jsonData.alternateid;
+						relationshipArray[j].relationshipWith[3] = jsonData.sex;
+						relationshipArray[j].relationshipWith[4] = jsonData.localHaplotypeReflection;
+						relationshipArray[j].relationshipWith[5] = jsonData.displayName;
+					}
+				}
+				onComplete(relationshipTableData);
+			}
+		});
+	}
 }
 
 function whatIsIt(object) {
@@ -753,4 +758,4 @@ function whatIsIt(object) {
     {
         return "don't know";
     }
-}
+}

src/main/webapp/javascript/relationshipDiagrams/jsonParser.js

@@ -97,6 +97,7 @@ class JSONQuerier {
      */
     async preFetchData(iId, genus, epithet, callbacks, diagramIds, parsers=[]) {
 	await this.queryIndividualIDNodeData(iId);
+	await this.queryIndividualIDRelatedNodeData(iId);
 	await this.queryIndividualIDRelationshipData(iId);
 	await this.queryIndividualIDOccurrences(iId);
 
@@ -139,6 +140,16 @@ class JSONQuerier {
 	return this.queryData("nodeData", query, this.storeQueryAsDict);
     }
 
+	queryIndividualIDRelatedNodeData(individualID) {
+		let query;
+		if (!this.localFiles) {
+			query = wildbookGlobals.baseUrl  + "/encounters/relatedIndividuals.jsp?";
+			if (individualID) query += "individualID=" + individualID;
+		}
+		else query = "./MarkedIndividual.json";
+		return this.queryData("relatedNodeData", query, this.storeQueryAsDict);
+	}
+
 
     /**
      * Query wrapper for the storage of Relationship data
@@ -316,7 +327,7 @@ class JSONParser {
      */
     processNodeData(iId, isCoOccurrence) {
 	//Generate a two way mapping of all node relationships
-	let nodes = this.getNodeSelection();
+	let nodes = this.getNodeSelection(isCoOccurrence);
 	let relationships = this.mapRelationships(nodes);
 	let [graphNodes, groupNum] = this.traverseRelationshipTree(iId, nodes, relationships, isCoOccurrence);
 
@@ -613,17 +624,31 @@ class JSONParser {
      * Return node data as filtered by selected nodes
      * @return {nodeData} [array] - Any node data matching {selectedNodes} ids
      */
-    getNodeSelection() {
-	if (this.selectedNodes) {
-	    let nodes = {};
-	    Object.entries(JSONParser.nodeData).forEach(([key, data]) => {
-		if (this.selectedNodes.has(key)) { //Filter out any keys not in {selectedNodes}
-		    nodes[key] = data;
+    getNodeSelection(isCoOccurrence) {
+		if (isCoOccurrence) {
+			if (this.selectedNodes) {
+				let nodes = {};
+				Object.entries(JSONParser.nodeData).forEach(([key, data]) => {
+				if (this.selectedNodes.has(key)) { //Filter out any keys not in {selectedNodes}
+					nodes[key] = data;
+				}
+				});
+				return nodes;
+			}
+			return JSONParser.nodeData;
+		}else {
+			if (this.selectedNodes) {
+				let nodes = {};
+				Object.entries(JSONParser.relatedNodeData).forEach(([key, data]) => {
+				if (this.selectedNodes.has(key)) { //Filter out any keys not in {selectedNodes}
+					nodes[key] = data;
+				}
+				});
+				return nodes;
+			}
+			return JSONParser.relatedNodeData;
 		}
-	    });
-	    return nodes;
-	}
-	return JSONParser.nodeData;
+
     }
 
     /**

src/main/webapp/javascript/relationshipDiagrams/socialGraph.js

@@ -28,7 +28,7 @@ class SocialGraph extends ForceLayoutAbstract {
      * Wrapper function to gather species data from the Wildbook DB and generate a graph
      */
     applySocialData() {
-	this.parser.processJSON((nodes, links) => this.graphSocialData(nodes, links), this.id);
+	this.parser.processJSON((nodes, links) => this.graphSocialData(nodes, links), this.id, false);
     }
 
     /**