Feature/568

.travis.yml

@@ -91,8 +91,7 @@ jobs:
         - echo "$http_status"
         - while [ "$http_status" != "200" ]; do
             echo "Printing logs for debugging purposes";
-            sudo docker cp $CONTAINER_NAME:/home/developer/virgo/serviceability/logs/log.log /etc;
-            tail /etc/log.log;
+            docker logs $CONTAINER_NAME;
             docker stop $(docker ps -a -q);
             echo "Docker container failed to start!";
             travis_terminate 1;
@@ -102,11 +101,10 @@ jobs:
         - travis_wait 41 npm test -- --verbose --colors --forceExit --testPathPattern='tests/jest/vfb/batch1/.*js'
       after_failure:
         - docker ps -a
-        - sudo docker cp $CONTAINER_NAME:/home/developer/virgo/serviceability/logs/log.log /etc
-        - cat /etc/log.log
+        - docker logs $CONTAINER_NAME
         - echo -e "travis_fold:start:Cleanup" || true
-        - docker stop $(docker ps -a -q)
-        - docker rm $(docker ps -a -q)
+        - docker stop $(docker ps -a -q) || true
+        - docker rm $(docker ps -a -q) || true
         - echo -e "travis_fold:end:Cleanup" || true
 
     - stage: test
@@ -132,8 +130,7 @@ jobs:
         - echo "$http_status"
         - while [ "$http_status" != "200" ]; do
             echo "Printing logs for debugging purposes";
-            sudo docker cp $CONTAINER_NAME:/home/developer/virgo/serviceability/logs/log.log /etc;
-            tail /etc/log.log;
+            docker logs $CONTAINER_NAME;
             docker stop $(docker ps -a -q);
             echo "Docker container failed to start!";
             travis_terminate 1;
@@ -143,8 +140,7 @@ jobs:
         - travis_wait 41 npm test -- --verbose --colors --forceExit --testPathPattern='tests/jest/vfb/batch2/.*js'
       after_failure:
         - docker ps -a
-        - sudo docker cp $CONTAINER_NAME:/home/developer/virgo/serviceability/logs/log.log /etc
-        - cat /etc/log.log
+        - docker logs $CONTAINER_NAME
         - echo -e "travis_fold:start:Cleanup" || true
         - docker stop $(docker ps -a -q)
         - docker rm $(docker ps -a -q)
@@ -173,8 +169,7 @@ jobs:
         - echo "$http_status"
         - while [ "$http_status" != "200" ]; do
             echo "Printing logs for debugging purposes";
-            sudo docker cp $CONTAINER_NAME:/home/developer/virgo/serviceability/logs/log.log /etc;
-            tail /etc/log.log;
+            docker logs $CONTAINER_NAME;
             docker stop $(docker ps -a -q);
             echo "Docker container failed to start!";
             travis_terminate 1;
@@ -185,8 +180,7 @@ jobs:
       after_failure:
         - docker ps -a
         - sudo docker cp $CONTAINER_NAME:/home/developer/virgo/serviceability/logs/log.log /etc
-        - cat /etc/log.log
-        - echo -e "travis_fold:start:Cleanup" || true
+        - docker logs $CONTAINER_NAME
         - docker stop $(docker ps -a -q)
         - docker rm $(docker ps -a -q)
         - echo -e "travis_fold:end:Cleanup" || true
@@ -272,8 +266,7 @@ jobs:
         - echo "$http_status"
         - while [ "$http_status" != "200" ]; do
             echo "Printing logs for debugging purposes";
-            sudo docker cp $CONTAINER_NAME:/home/developer/virgo/serviceability/logs/log.log /etc;
-            tail /etc/log.log;
+            docker logs $CONTAINER_NAME;
             docker stop $(docker ps -a -q);
             echo "Docker container failed to start!";
             travis_terminate 1;
@@ -283,8 +276,7 @@ jobs:
         - travis_wait 41 npm test -- --verbose --colors --forceExit --testPathPattern='tests/jest/vfb/review/.*js'
       after_failure:
         - docker ps -a
-        - sudo docker cp $CONTAINER_NAME:/home/developer/virgo/serviceability/logs/log.log /etc
-        - cat /etc/log.log
+        - docker logs $CONTAINER_NAME
         - echo -e "travis_fold:start:Cleanup" || true
         - docker stop $(docker ps -a -q)
         - docker rm $(docker ps -a -q)

components/VFBMain.js

@@ -14,7 +14,7 @@ import HTMLViewer from 'geppetto-client/js/components/interface/htmlViewer/HTMLV
 import ControlPanel from 'geppetto-client/js/components/interface/controlPanel/controlpanel';
 import * as FlexLayout from 'geppetto-client/js/components/interface/flexLayout2/src/index';
 import VFBQuickHelp from './interface/VFBOverview/QuickHelp';
-// import VFBGraph from './interface/VFBGraph/VFBGraph';
+import VFBGraph from './interface/VFBGraph/VFBGraph';
 
 require('../css/base.less');
 require('../css/VFBMain.less');

components/configuration/VFBGraph/graphConfiguration.js

@@ -1,3 +1,14 @@
+var locationCypherQuery = instance => ({
+  "statements": [
+    {
+      "statement": "MATCH p=(n:Entity)-[r:INSTANCEOF|part_of|has_synaptic_terminal_in|has_presynaptic_terminal_in"
+      + "has_postsynaptic_terminal_in|overlaps*..]->(x)"
+      + "WHERE n.short_form = '" + instance + "' return distinct n,r,x,n.short_form as root",
+      "resultDataContents": ["graph"]
+    }
+  ]
+});
+
 var configuration = {
   resultsMapping:
   {
@@ -34,28 +45,50 @@ var styling = {
   // Title bar (in node) background color
   nodeTitleBackgroundColor : "#11bffe",
   // Description area (in node) background color
-  nodeDescriptionBackgroundColor : "white"
+  nodeDescriptionBackgroundColor : "white",
+  icons : {
+    home : "fa fa-home",
+    zoomIn : "fa fa-search-plus",
+    zoomOut : "fa fa-search-minus",
+    sync : "fa fa-refresh",
+    dropdown : "fa fa-bars",
+  },
+  defaultRefreshIconColor : "white",
+  outOfSyncIconColor : "red",
+  dropDownQueries : [
+    {
+      label : instance => "Show classification of " + instance,
+      query : instance => ({
+        "statements": [
+          {
+            "statement": "MATCH p=(n:Entity)-[:INSTANCEOF|:SUBCLASSOF*..]->(x)"
+            + "WHERE 'Anatomy' IN  labels(x)"
+            + "AND n.short_form = '" + instance + "'" 
+            + "RETURN  p, n.short_form as root",
+            "resultDataContents": ["graph"]
+          }
+        ]
+      })
+    },
+    {
+      label : instance => "Show location of " + instance ,
+      query : instance => locationCypherQuery(instance)
+    }
+  ],
+  dropDownHoverBackgroundColor : "#11bffe",
+  dropDownHoverTextColor : "black",
+  dropDownBackgroundColor : "#4f4f4f",
+  dropDownTextColor : "white"
 }
 
 var restPostConfig = {
   url: "https://pdb-alpha.virtualflybrain.org/db/data/transaction/commit",
   contentType: "application/json"
 };
 
-var cypherQuery = instance => ({
-  "statements": [
-    {
-      "statement": "MATCH p=(n:Entity)-[r:INSTANCEOF|part_of|has_synaptic_terminal_in|has_presynaptic_terminal_in"
-      + "has_postsynaptic_terminal_in|overlaps*..]->(x)"
-      + "WHERE n.short_form = '" + instance + "' return distinct n,r,x,n.short_form as root",
-      "resultDataContents": ["graph"]
-    }
-  ]
-});
-
 module.exports = { 
   configuration,
   styling,
   restPostConfig,
-  cypherQuery
+  locationCypherQuery
 };

components/configuration/VFBMain/layoutModel.js

@@ -61,6 +61,11 @@ var modelJson = {
             "type": "tab",
             "name": "Template ROI Browser",
             "component": "treeBrowser"
+          },
+          {
+            "type": "tab",
+            "name": "Graph",
+            "component": "vfbGraph"
           }
         ]
       },

components/configuration/VFBTree/VFBTreeConfiguration.js

@@ -17,8 +17,71 @@ var treeCypherQuery = instance => ({
   ]
 });
 
+var styling = {
+  // Font Awesome Icons to display as Tree's controls
+  icons : {
+    sync : "fa fa-refresh",
+    dropdown : "fa fa-bars",
+  },
+  // Drop down menu options, consists of label and query
+  dropDownQueries : [
+    {
+      label : "Load Tree for 'adult protocerebrum'",
+      query : () => ({
+        "statements": [
+          {
+            "statement": "MATCH (root:Class)<-[:INSTANCEOF]-(t:Individual {short_form:'FBbt_00007145'})"
+            + "<-[: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)) "
+            + "RETURN collect(distinct { node_id: id(anat), short_form: anat.short_form, image: image.short_form })"
+            + " AS image_nodes, id(root) AS root, collect(p)",
+            "resultDataContents": ["row", "graph"]
+          }
+        ]
+      })
+    },
+    {
+      label : "Load Tree for 'adult brain template JFRC2'",
+      query : () => ({
+        "statements": [
+          {
+            "statement": "MATCH (root:Class)<-[:INSTANCEOF]-(t:Individual {short_form:'VFB_00017894'})"
+            + "<-[: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)) "
+            + "RETURN collect(distinct { node_id: id(anat), short_form: anat.short_form, image: image.short_form })"
+            + " AS image_nodes, id(root) AS root, collect(p)",
+            "resultDataContents": ["row", "graph"]
+          }
+        ]
+      })
+    },
+    {
+      label : "Load Tree for 'Adult Cerebrum'",
+      query : () => ({
+        "statements": [
+          {
+            "statement": "MATCH (root:Class)<-[:INSTANCEOF]-(t:Individual {short_form:'FBbt_00007050'})"
+            + "<-[: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)) "
+            + "RETURN collect(distinct { node_id: id(anat), short_form: anat.short_form, image: image.short_form })"
+            + " AS image_nodes, id(root) AS root, collect(p)",
+            "resultDataContents": ["row", "graph"]
+          }
+        ]
+      })
+    }
+  ],
+  dropDownHoverBackgroundColor : "#11bffe",
+  dropDownHoverTextColor : "black",
+  dropDownBackgroundColor : "#4f4f4f",
+  dropDownTextColor : "white"
+}
 
 module.exports = {
   restPostConfig,
-  treeCypherQuery
+  treeCypherQuery,
+  styling
 };