Merge pull request #716 from VirtualFlyBrain/development

Development

.travis.yml

@@ -19,7 +19,7 @@ services:
 stages:
   - build
   - name: debug
-    if: branch = debug OR branch = pipeline2 OR branch =~ ^(fix|feature).*
+    if: branch = debug OR branch = vfb_geppetto_application OR branch = pipeline2 OR branch =~ ^(fix|feature).*
   - test
   - deploy
   - name: review

components/VFBMain.js

@@ -912,8 +912,9 @@ class VFBMain extends React.Component {
           }}
           focusTermRef={this.focusTermReference}
           exclude={["ClassQueriesFrom", "Debug"]}
-          order={['Name',
+          order={['Symbol',
                   'Title',
+                  'Name',
                   'Label',
                   'Alternative Names',
                   'Types',
@@ -1193,6 +1194,7 @@ class VFBMain extends React.Component {
 
     window.setTermInfo = function (meta, id) {
       this.handlerInstanceUpdate(meta);
+      this.props.setTermInfo(meta, true);
     }.bind(this);
 
     window.fetchVariableThenRun = function (idsList, cb, label) {
@@ -1238,6 +1240,10 @@ class VFBMain extends React.Component {
         idsList = idList[list].replace("i=","") + idsList;
       } else if (idList[list].indexOf("q=") > -1) {
         this.urlQueryLoader = idList[list].replace("q=","").replace("%20", " ").split(",");
+        // if no other ids are loaded the query target is added.
+        if (idsList.length == 0 && this.urlQueryLoader.length > 1) {
+          idsList = this.urlQueryLoader[0];
+        }
       }
     }
 

components/configuration/VFBListViewer/listViewerConfiguration.js

@@ -36,10 +36,24 @@ const conf = [
   {
     id: "name",
     title: "Name",
-    source : entity => { 
-      let path = entity.path.split(".")[0];
-      return Instances.getInstance(path).getName();
-    }
+    customComponent: component => { 
+      // Retrieve instance path
+      let path = component.value.get("path").split(".")[0];
+
+      let instance = Instances.getInstance(path);
+      var self = this;
+
+      let click = value => {
+        let instance = Instances.getInstance(value.target.id);
+        window.setTermInfo(Instances.getInstance(path)[path + "_meta"], path);
+      };
+      // Create new HTML string with the Type name and tags only
+      let typeHTML = '<a id="' + instance.id + '" style="color:white;text-decoration: none;">' + instance.getName() + "</a>" ;
+
+      // Set HTML string inside div ready for React
+      return <div onClick={e => click(e)} dangerouslySetInnerHTML={{ __html: typeHTML }} />
+    },
+    source : entity => entity
   },
   {
     id: "type",
@@ -67,8 +81,10 @@ const conf = [
       var matchSpan = /<span[^>]*>([\s\S]*?)<\/span>/g
         , tags = html.match(matchSpan);
 
+      // Make anchor open in new tab, and fix path by adding 'geppetto?' to href
+      let textContent = type.join().replace('href="?', 'target="_blank" href="geppetto?');
       // Create new HTML string with the Type name and tags only
-      let typeHTML = "<div>" + type.join('') + tags.join('') + "</div>" ;
+      let typeHTML = "<div>" + textContent + tags.join('') + "</div>" ;
 
       // Set HTML string inside div ready for React
       return <div dangerouslySetInnerHTML={{ __html: typeHTML }} />
@@ -88,8 +104,16 @@ const conf = [
       if ( instance === undefined ) {
         return null;
       }
+
+      let value = GEPPETTO.ModelFactory.getAllVariablesOfMetaType(instance.getType(), 'ImageType')[0].getInitialValues()[0].value;
+      let img = "";
+      if ( value.elements != undefined ) {
+        img = value.elements[0].initialValue.data;
+      } else if ( value.data != undefined ) {
+        img = value.data;
+      }
       // Retrieve thumbnail image from Instance
-      return GEPPETTO.ModelFactory.getAllVariablesOfMetaType(instance.getType(), 'ImageType')[0].getInitialValues()[0].value.data
+      return img;
     }
   }
 ];

components/configuration/VFBMain/queryBuilderConfiguration.js

@@ -75,12 +75,12 @@ var queryResultsColMeta = [
     "sortDirectionCycle": ['asc', 'desc', null]
   },
   {
-    "columnName": "type",
+    "columnName": "gross_type",
     "order": 6,
     "locked": false,
     "visible": true,
-    "displayName": "Type",
-    "cssClassName": "query-results-type-column",
+    "displayName": "Gross_Type",
+    "cssClassName": "query-results-grosstype-column",
     "sortDirectionCycle": ['asc', 'desc', null]
   },
   {
@@ -106,9 +106,27 @@ var queryResultsColMeta = [
     "sortDirectionCycle": ['asc', 'desc', null]
   },
   {
-    "columnName": "controls",
+    "columnName": "template",
     "order": 9,
     "locked": false,
+    "visible": true,
+    "displayName": "Template_Space",
+    "cssClassName": "query-results-template-column",
+    "sortDirectionCycle": ['asc', 'desc', null]
+  },
+  {
+    "columnName": "technique",
+    "order": 10,
+    "locked": false,
+    "visible": true,
+    "displayName": "Imaging_Technique",
+    "cssClassName": "query-results-technique-column",
+    "sortDirectionCycle": ['asc', 'desc', null]
+  },
+  {
+    "columnName": "controls",
+    "order": 11,
+    "locked": false,
     "visible": false,
     "customComponent": QueryResultsControlsComponent,
     "displayName": "Controls",
@@ -118,7 +136,7 @@ var queryResultsColMeta = [
   },
   {
     "columnName": "images",
-    "order": 10,
+    "order": 12,
     "locked": false,
     "visible": true,
     "customComponent": SlideshowImageComponent,
@@ -129,7 +147,7 @@ var queryResultsColMeta = [
   },
   {
     "columnName": "score",
-    "order": 11,
+    "order": 13,
     "locked": false,
     "visible": true,
     "displayName": "Score",
@@ -138,7 +156,7 @@ var queryResultsColMeta = [
   },
   {
     "columnName": "image_count",
-    "order": 12,
+    "order": 14,
     "locked": false,
     "visible": true,
     "displayName": "Image_count",
@@ -148,7 +166,7 @@ var queryResultsColMeta = [
 ];
 
 // which columns to display in the results
-var queryResultsColumns = ['name', 'expressed_in', 'description', 'reference', 'type', 'stage', 'license', 'images', 'score','image_count'];
+var queryResultsColumns = ['name', 'type', 'expressed_in', 'description', 'reference', 'gross_type', 'stage', 'license', 'template', 'technique', 'controls', 'images', 'score','image_count'];
 
 var queryResultsControlConfig = {
   "Common": {

components/configuration/VFBMain/searchConfiguration.js

@@ -109,6 +109,7 @@ var searchConfiguration = {
       "name": "label",
       "id": "short_form"
     },
+  "filters_expanded": true,
   "filters": [
     {
       "key": "facets_annotation",

components/configuration/VFBOverview/quickHelp.json

@@ -3,7 +3,7 @@
 	"height": "575",
     "width": "900",
 	"steps": [{
-		"title": "This is the Slice Viewer frame",
+		"title": "This is the Slice Viewer tab",
 		"image" : "geppetto/build/slice-viewer.png",
 		"instructions": [{
 			"icon" : "",
@@ -28,7 +28,7 @@
 			"label" : "Toggles the slice position on the 3D Viewer on/off"
 		}]
 	},{
-		"title": "This is the 3D Viewer frame",
+		"title": "This is the 3D Viewer tab",
 		"image" : "geppetto/build/3d-viewer.png",
 		"instructions": [{
 			"icon" : "",
@@ -47,17 +47,17 @@
 			"label" : "Home resets your view"
 		},{
 			"icon" : "fa fa-video-camera",
-			"label" : "The camera icon starts/stops a rotation animation the scene"
+			"label" : "The camera icon starts/stops a rotation animation of the scene"
 		},{
 			"icon" : "gpt-sphere_wireframe-jpg",
 			"label" : "The sphere icon toggles wireframes on/off"
 		}]
 	},{
-		"title": "This is the Term Info frame",
+		"title": "This is the Term Info tab",
 		"image" : "geppetto/build/term-info.png",
 		"instructions": [{
 			"icon" : "",
-			"label" : "Term Info displays information on the currently selected painted anatomy region, neuron or expression pattern"
+			"label" : "Term Info displays information on the currently selected painted anatomy region, neuron, expression pattern or non-image term definitions"
 		},{
 			"icon" : "fa fa-hand-pointer-o",
 			"label" : "Click on thumbnails to add that image to the viewer"

components/configuration/VFBToolbar/vfbtoolbarHTML.js

@@ -13,8 +13,8 @@ var feedback
   + "[<a href='https://github.com/VirtualFlyBrain/VFB2' target='_blank'>VirtualFlyBrain/VFB2</a>].</p>"
   + "<p>If you have a GitHub account you can easily raise a new issue: "
   + "<form id='GitHubIssue' method='get' action='https://github.com/VirtualFlyBrain/VFB2/issues/new' target='_blank'>"
-  + "<input type='hidden' name='body' value=%0A%0A%0A%0A%0A%0ASupport%20info%3A%0A$DATE$%0A$BROWSER$%20$VERSION$%20%5B$SCREEN$%5D%0A$URL$%0A%0A%60%60%60diff%0A$LOG$%0A%60%60%60%0A' />"
-  + "<input type='submit' value='Create GitHub Issue'></form>"
+  + "<input type='hidden' name='body' value='%0A%0A%0A%0A%0A%0ASupport%20info%3A%0A$DATE$%0A$BROWSER$%20$VERSION$%20%5B$SCREEN$%5D%0A$URL$%0A%0A%60%60%60diff%0A$LOG$%0A%60%60%60%0A' />"
+  + "<input type='submit' value='Create GitHub Issue' style='color: black; border-color: darkcyan;'></form>"
   + "</p>"
   + "<p> This could simply be a question or a new feature request, but if you have found a bug we missed please copy in "
   + "the page address and system details listed below to help us resolve any issue as quickly as possible."

components/interface/VFBFocusTerm/VFBFocusTerm.js

@@ -610,4 +610,4 @@ function mapDispatchToProps (dispatch) {
   return { showListViewer: type => dispatch({ type : type }) }
 }
 
-export default connect(mapStateToProps, mapDispatchToProps)(VFBFocusTerm);
+export default connect(mapStateToProps, mapDispatchToProps, null, { forwardRef : true } )(VFBFocusTerm);