DO NOT MERGE!!!

Dockerfile

@@ -6,7 +6,7 @@ ARG targetBranch=development
 ARG originBranch=development
 ARG defaultBranch=development
 
-ARG build_type=production
+ARG mvnOpt="-Dhttps.protocols=TLSv1.2 -DskipTests --quiet -Pmaster"
 
 ARG googleAnalyticsSiteCode=UA-45841517-1
 
@@ -32,25 +32,25 @@ WORKDIR $HOME/workspace
 RUN ../copy.sh https://github.com/openworm/org.geppetto.model.git "${targetBranch}" "${originBranch}" "${defaultBranch}" &&\
   cd org.geppetto.model &&\
   /bin/echo -e "\e[96mMaven install org.geppetto.model\e[0m" &&\
-  mvn -Dhttps.protocols=TLSv1.2 -DskipTests --quiet install &&\
+  mvn ${mvnOpt} install &&\
   rm -rf src
 
 RUN ../copy.sh https://github.com/openworm/org.geppetto.core.git "${targetBranch}" "${originBranch}" "${defaultBranch}" &&\
   cd org.geppetto.core &&\
   /bin/echo -e "\e[96mMaven install org.geppetto.core\e[0m" &&\
-  mvn -Dhttps.protocols=TLSv1.2 -DskipTests --quiet install &&\
+  mvn ${mvnOpt} install &&\
   rm -rf src
 
 RUN ../copy.sh https://github.com/openworm/org.geppetto.simulation.git "${targetBranch}" "${originBranch}" "${defaultBranch}" &&\
   cd org.geppetto.simulation &&\
   /bin/echo -e "\e[96mMaven install org.geppetto.simulation\e[0m" &&\
-  mvn -Dhttps.protocols=TLSv1.2 -DskipTests --quiet install &&\
+  mvn ${mvnOpt} install &&\
   rm -rf src
 
 RUN ../copy.sh https://github.com/openworm/org.geppetto.datasources.git "${targetBranch}" "${originBranch}" "${defaultBranch}" &&\
   cd org.geppetto.datasources &&\
   /bin/echo -e "\e[96mMaven install org.geppetto.datasources\e[0m" &&\
-  mvn -Dhttps.protocols=TLSv1.2 -DskipTests --quiet install &&\
+  mvn ${mvnOpt} install &&\
   rm -rf src
 
 RUN ../copy.sh https://github.com/VirtualFlyBrain/uk.ac.vfb.geppetto.git "${targetBranch}" "${originBranch}" "${defaultBranch}"
@@ -60,13 +60,13 @@ RUN export DEBUG=false; if test "$build_type" = "development" ; then export DEBU
 
 RUN cd uk.ac.vfb.geppetto &&\
   /bin/echo -e "\e[96mMaven install uk.ac.vfb.geppetto\e[0m" &&\
-  mvn -Dhttps.protocols=TLSv1.2 -DskipTests --quiet install &&\
+  mvn ${mvnOpt} install &&\
   rm -rf src
 
 RUN ../copy.sh https://github.com/openworm/org.geppetto.model.swc.git "${targetBranch}" "${originBranch}" "${defaultBranch}" &&\
   cd org.geppetto.model.swc &&\
   /bin/echo -e "\e[96mMaven install org.geppetto.model.swc\e[0m" &&\
-  mvn -Dhttps.protocols=TLSv1.2 -DskipTests --quiet install &&\
+  mvn ${mvnOpt} install &&\
   rm -rf src
 
 RUN ../copy.sh https://github.com/openworm/org.geppetto.frontend.git "${targetBranch}" "${originBranch}" "${defaultBranch}"
@@ -85,6 +85,8 @@ COPY dockerFiles/geppetto.plan $HOME/workspace/org.geppetto/geppetto.plan
 COPY dockerFiles/config.json $HOME/workspace/org.geppetto/utilities/source_setup/config.json
 COPY dockerFiles/startup.sh /
 
+RUN if [ "${targetBranch}" == "master" ]; then /startup.sh; fi
+
 WORKDIR $HOME
 RUN mkdir -p $SERVER_HOME/./repository/usr
 

components/configuration/queryBuilderConfiguration.js

@@ -280,14 +280,14 @@ var sorterColumns = [
     column: "score",
     order: "DESC"
   },
-  {
-    column: "name",
-    order: "ASC"
-  },
   {
     column: "images",
     order: "DESC"
   },
+  {
+    column: "name",
+    order: "ASC"
+  }
 ];
 
 module.exports = {

components/interface/TreeWidget.js

@@ -211,7 +211,7 @@ export default class TreeWidget extends React.Component {
     return { nodes: nodesArray, edges: edgesArray };
   }
 
-  searchChildren (array, key, target){
+  searchChildren (array, key, target, label){
     // Define Start and End Index
     let startIndex = 0;
     let endIndex = array.length - 1;
@@ -222,7 +222,13 @@ export default class TreeWidget extends React.Component {
       let middleIndex = Math.floor((startIndex + endIndex) / 2);
       // Compare Middle Index with Target for match
       if (this.isNumber(array[middleIndex][key]) === this.isNumber(target[key])) {
-        return middleIndex;
+        // check for target relationship (label)
+        if (array[middleIndex].label === label){
+          return middleIndex;
+        } else {
+          // move on if not matching target relationship (label)
+          startIndex = middleIndex + 1; 
+        }
       }
       // Search Right Side Of Array
       if (this.isNumber(target[key]) > this.isNumber(array[middleIndex][key])) {
@@ -237,9 +243,9 @@ export default class TreeWidget extends React.Component {
     return undefined;
   }
 
-  findChildren (parent, key, familyList) {
+  findChildren (parent, key, familyList, label) {
     var childrenList = [];
-    var childKey = this.searchChildren(familyList, key, parent);
+    var childKey = this.searchChildren(familyList, key, parent, label);
     if (childKey !== undefined) {
       childrenList.push(childKey);
       var i = childKey - 1;
@@ -257,18 +263,19 @@ export default class TreeWidget extends React.Component {
   }
 
   insertChildren (nodes, edges, child) {
-    var childrenList = this.findChildren({ from: child.id }, "from", edges);
+    var childrenList = this.findChildren({ from: child.id }, "from", edges, "part of");
+    // child.images = this.findChildren({ from: child.id }, "from", edges, "INSTANCEOF");
     var nodesList = [];
     for ( var i = 0; i < childrenList.length; i++) {
       nodesList.push(edges[childrenList[i]].to)
     }
     var uniqNodes = [...new Set(nodesList)];
     for ( var j = 0; j < uniqNodes.length; j++) {
-      var node = nodes[this.findChildren({ id: uniqNodes[j] }, "id", nodes)[0]];
+      var node = nodes[this.findChildren({ id: uniqNodes[j] }, "id", nodes, "part of")[0]];
       child.children.push({
         title: node.title,
         subtitle: node.instanceId,
-        description: node.instanceId + " \n- " + node.info,
+        description: node.info,
         instanceId: node.instanceId,
         id: node.id,
         children: []
@@ -284,11 +291,12 @@ export default class TreeWidget extends React.Component {
         refinedDataTree.push({
           title: nodes[i].title,
           subtitle: nodes[i].instanceId,
-          description: "- " + nodes[i].instanceId + " \n- " + nodes[i].info,
+          description: nodes[i].info,
           instanceId: nodes[i].instanceId,
           id: nodes[i].id,
           isSelected: true,
-          children: []
+          children: [],
+          images: []
         });
         break;
       }
@@ -341,13 +349,7 @@ export default class TreeWidget extends React.Component {
     this.restPost({
       "statements": [
         {
-          "statement": "MATCH (root:Class)<-[:INSTANCEOF]-(t:Individual { short_form : '" + instance + "'})"
-                            + "<-[:depicts]-(tc:Individual)<-[ie:in_register_with]-(c:Individual)-[:depicts]->"
-                            + "(image:Individual)-[:INSTANCEOF]->(ac:Class) WHERE has(ie.index) WITH root, COLLECT"
-                            + " (ac.short_form) as tree_nodes, COLLECT (DISTINCT{ image: image.short_form, anat_ind:"
-                            + " image.short_form, type: ac.short_form}) AS domain_map MATCH p=allShortestPaths((root)"
-                            + "<-[:SUBCLASSOF|part_of*..]-(anat:Class)) WHERE anat.short_form IN tree_nodes RETURN p,"
-                            + " domain_map",
+          "statement": "MATCH (root:Class)<-[:INSTANCEOF]-(t:Individual {short_form:'" + instance + "'})<-[:depicts]-(tc:Individual)<-[ie:in_register_with]-(c:Individual)-[:depicts]->(image:Individual)-[r:INSTANCEOF]->(anat:Class) WHERE has(ie.index) WITH root, anat,r,image MATCH p=allShortestPaths((root)<-[:SUBCLASSOF|part_of*..]-(anat:Class)) RETURN p,r,image",
           "resultDataContents": ["graph"]
         }
       ]

dockerFiles/startup.sh

@@ -18,7 +18,7 @@ grep -rls '"useSsl":' $HOME/workspace/org.geppetto.frontend/src/main/webapp | xa
 # Frontend final build
 cd $HOME/workspace/org.geppetto.frontend 
 /bin/echo -e "\e[96mMaven install org.geppetto.frontend\e[0m"
-mvn -Dhttps.protocols=TLSv1.2 -DcontextPath=org.geppetto.frontend -DuseSsl=false -DskipTests install
+mvn ${mvnOpt} -DcontextPath=org.geppetto.frontend -DuseSsl=false install
 rm -rf src
 
 # Start a logfile