VirtualFlyBrain · Robbie1977 · Feb 26, 2021 · Dec 18, 2020 · Dec 18, 2020 · Dec 18, 2020
diff --git a/components/VFBMain.js b/components/VFBMain.js
@@ -1490,15 +1490,16 @@ class VFBMain extends React.Component {
     }.bind(this));
 
     GEPPETTO.on(GEPPETTO.Events.Websocket_disconnected, function () {
-      if (GEPPETTO.MessageSocket.socketStatus === GEPPETTO.Resources.SocketStatus.CLOSE) {
-        window.ga('vfb.send', 'event', 'reload', 'websocket-disconnect', (window.location.pathname + window.location.search));
-        console.log("Reloading websocket connection by reloading page");
-
-        setTimeout(() => {
-          window.location.reload(true);
-        }, 5000);
-      } else {
-        console.log("%c Websocket reconnection in progress... ", 'background: #444; color: #bada55');
+      window.ga('vfb.send', 'event', 'disconnected', 'websocket-disconnect', (window.location.pathname + window.location.search));
+      if (GEPPETTO.MessageSocket.socketStatus != GEPPETTO.Resources.SocketStatus.OPEN) {
+        if (GEPPETTO.MessageSocket.attempts < 10) {
+          window.ga('vfb.send', 'event', 'reconnect-attempt:' + GEPPETTO.MessageSocket.attempts, 'websocket-disconnect', (window.location.pathname + window.location.search));
+          GEPPETTO.MessageSocket.reconnect();
+        } else {
+          window.ga('vfb.send', 'event', 'reconnect-failed-reloading', 'websocket-disconnect', (window.location.pathname + window.location.search));
+          console.log("%c Websocket reconnection failed reloading content... ", 'background: #444; color: #bada55');
+          window.location.reload();
+        }
       }
     });
   }
@@ -1582,7 +1583,7 @@ class VFBMain extends React.Component {
       }
     }
   }
-  
+
   render () {
     if ((this.state.tutorialWidgetVisible == true) && (this.tutorialRender == undefined)) {
       this.tutorialRender = <TutorialWidget tutorialHandler={this.tutorialHandler} ref="tutorialWidgetRef" />

diff --git a/components/interface/VFBGraph/VFBGraph.js b/components/interface/VFBGraph/VFBGraph.js
@@ -367,7 +367,6 @@ class VFBGraph extends Component {
    */
   queryResults (requestQuery, instance) {
     if ( this.queryRequests.includes(instance.id) ) {
-      alert("yo")
       return;
     }
 

diff --git a/components/interface/VFBListViewer/ListViewerControlsMenu.js b/components/interface/VFBListViewer/ListViewerControlsMenu.js
@@ -209,6 +209,11 @@ class ListViewerControlsMenu extends Component {
         // Replace buttons list in configuration with updated one
         button.list = list;
       }
+      if (self.props.instance.isVisible()) {
+        button.icon.props.className = "fa fa-eye";
+      } else {
+        button.icon.props.className = "fa fa-eye-slash";
+      }
     });
 
     return configuration;
@@ -249,4 +254,4 @@ function mapDispatchToProps (dispatch) {
   return { setTermInfo: (instance, visible) => dispatch(setTermInfo(instance, visible )) }
 }
 
-export default connect(mapStateToProps, mapDispatchToProps)(ListViewerControlsMenu);
+export default connect(mapStateToProps, mapDispatchToProps)(ListViewerControlsMenu);
diff --git a/components/interface/VFBListViewer/VFBListViewer.js b/components/interface/VFBListViewer/VFBListViewer.js
@@ -1,7 +1,6 @@
 import React, { Component } from 'react';
 import ListViewer from '@geppettoengine/geppetto-ui/list-viewer/ListViewer';
 import listViewerConf from '../../configuration/VFBListViewer/listViewerConfiguration';
-import CircularProgress from '@material-ui/core/CircularProgress';
 import { connect } from 'react-redux';
 
 require('../../../css/VFBListViewer.less');

diff --git a/components/interface/VFBToolbar/VFBToolBar.js b/components/interface/VFBToolbar/VFBToolBar.js
@@ -150,7 +150,7 @@ export default class VFBToolBar extends React.Component {
       majorVersion = parseInt(navigator.appVersion,10);
     }
     // return as much of the log up to the last 10 events < 1000 characters:
-    var logLength = -50;
+    var logLength = -1;
     var limitedLog = window.console.logs.slice(logLength).join('%0A').replace(
       /\&/g,escape('&')
     ).replace(
@@ -160,8 +160,8 @@ export default class VFBToolBar extends React.Component {
     ).replace(
       /\+/g,'%2B'
     );
-    while (limitedLog.length > 1000 && logLength < 0) {
-      logLength += 1;
+    while (limitedLog.length < 1000 && logLength > -50) {
+      logLength -= 1;
       limitedLog = window.console.logs.slice(logLength).join('%0A').replace(
         /\&/g,escape('&')
       ).replace(

diff --git a/css/VFBListViewer.less b/css/VFBListViewer.less
@@ -7,18 +7,19 @@
     flex-direction: column;
     .listviewer-container {
         display: flex;
-        flex-direction: column;
         flex-wrap: wrap;
-        overflow: none;
+        overflow: unset;
         > div {
             flex-grow: 2;
+            overflow : auto !important;
         }    
     }
 
     .griddle-filter {
         padding: 0.5em;
         background-color : #4f4f4f;
         border : none !important;
+        width : 100%;
      }
 
     .griddle-filter::placeholder {

diff --git a/model/vfb.xmi b/model/vfb.xmi
@@ -201,7 +201,7 @@
           name="anat_image_query"
           description="Get images for individual list"
           runForCount="false"
-          query="&quot;statement&quot;: &quot;MATCH (primary:Individual) WHERE primary.short_form in {ARRAY_ID_RESULTS} WITH primary OPTIONAL MATCH (primary)&lt;-[:depicts]-(channel:Individual)-[irw:in_register_with]->(template:Individual)-[:depicts]->(template_anat:Individual) WITH template, channel, template_anat, irw, primary OPTIONAL MATCH (channel)-[:is_specified_output_of]->(technique:Class) WITH CASE WHEN channel IS NULL THEN [] ELSE collect ({ channel: { short_form: channel.short_form, label: coalesce(channel.label,''), iri: channel.iri, types: labels(channel), symbol: coalesce(channel.symbol[0], '')} , imaging_technique: { short_form: technique.short_form, label: coalesce(technique.label,''), iri: technique.iri, types: labels(technique), symbol: coalesce(technique.symbol[0], '')} ,image: { template_channel : { short_form: template.short_form, label: coalesce(template.label,''), iri: template.iri, types: labels(template), symbol: coalesce(template.symbol[0], '')} , template_anatomy: { short_form: template_anat.short_form, label: coalesce(template_anat.label,''), iri: template_anat.iri, types: labels(template_anat), symbol: coalesce(template_anat.symbol[0], '')} ,image_folder: COALESCE(irw.folder[0], ''), index: coalesce(apoc.convert.toInteger(irw.index[0]), []) + [] }}) END AS channel_image,primary OPTIONAL MATCH (primary)-[:INSTANCEOF]->(typ:Class) WITH CASE WHEN typ is null THEN [] ELSE collect ({ short_form: typ.short_form, label: coalesce(typ.label,''), iri: typ.iri, types: labels(typ), symbol: coalesce(typ.symbol[0], '')} ) END AS types,primary,channel_image RETURN { core : { short_form: primary.short_form, label: coalesce(primary.label,''), iri: primary.iri, types: labels(primary), symbol: coalesce(primary.symbol[0], '')} , description : coalesce(primary.description, []), comment : coalesce(primary.comment, []) } AS term, 'bac066c' AS version, 'anat_image_query' AS query, channel_image, types $EXTRA_RESULT_COLUMNS&quot;, &quot;parameters&quot; : { &quot;ARRAY_ID_RESULTS&quot; : $ARRAY_ID_RESULTS}"
+          query="&quot;statement&quot;: &quot;MATCH (primary:Individual) WHERE primary.short_form in {ARRAY_ID_RESULTS} WITH primary OPTIONAL MATCH (primary)&lt;-[&#xb4;:depicts]-(channel:Individual)-[irw:in_register_with]->(template:Individual)-[:depicts]->(template_anat:Individual) WITH template, channel, template_anat, irw, primary OPTIONAL MATCH (channel)-[:is_specified_output_of]->(technique:Class) WITH CASE WHEN channel IS NULL THEN [] ELSE collect ({ channel: { short_form: channel.short_form, label: coalesce(channel.label,''), iri: channel.iri, types: labels(channel), symbol: coalesce(channel.symbol[0], '')} , imaging_technique: { short_form: technique.short_form, label: coalesce(technique.label,''), iri: technique.iri, types: labels(technique), symbol: coalesce(technique.symbol[0], '')} ,image: { template_channel : { short_form: template.short_form, label: coalesce(template.label,''), iri: template.iri, types: labels(template), symbol: coalesce(template.symbol[0], '')} , template_anatomy: { short_form: template_anat.short_form, label: coalesce(template_anat.label,''), iri: template_anat.iri, types: labels(template_anat), symbol: coalesce(template_anat.symbol[0], '')} ,image_folder: COALESCE(irw.folder[0], ''), index: coalesce(apoc.convert.toInteger(irw.index[0]), []) + [] }}) END AS channel_image,primary OPTIONAL MATCH (primary)-[:INSTANCEOF]->(typ:Class) WITH CASE WHEN typ is null THEN [] ELSE collect ({ short_form: typ.short_form, label: coalesce(typ.label,''), iri: typ.iri, types: labels(typ), symbol: coalesce(typ.symbol[0], '')} ) END AS types,primary,channel_image RETURN { core : { short_form: primary.short_form, label: coalesce(primary.label,''), iri: primary.iri, types: labels(primary), symbol: coalesce(primary.symbol[0], '')} , description : coalesce(primary.description, []), comment : coalesce(primary.comment, []) } AS term, 'bac066c' AS version, 'anat_image_query' AS query, channel_image, types &quot;, &quot;parameters&quot; : { &quot;ARRAY_ID_RESULTS&quot; : $ARRAY_ID_RESULTS}"
           countQuery="&quot;statement&quot;: &quot;MATCH(i:Individual) WHERE i.short_form IN {ARRAY_ID_RESULTS} RETURN count(i) as count&quot;, &quot;parameters&quot; : { &quot;ARRAY_ID_RESULTS&quot; : $ARRAY_ID_RESULTS}"/>
       <queryChain
           xsi:type="gep_2:ProcessQuery"
@@ -236,13 +236,13 @@
           name="Fetch all example individuals for Class"
           description="Fetch all example Individual instances of this Class or subclasses"
           returnType="//@libraries.3/@types.0"
-          query="&quot;statement&quot;: &quot;MATCH p=(n:Class { short_form: {ID} } )&lt;-[r:expresses|SUBCLASSOF|INSTANCEOF*..]-(i:Individual)&lt;-[:depicts]-(j:Individual)-[k:in_register_with]->(m:Individual:Template) WITH i, k ORDER BY length(p) asc OPTIONAL MATCH (i)-[:INSTANCEOF]->(c:Class) RETURN distinct i.short_form as id, CASE WHEN not i.synonym is null THEN i.label+replace(' ('+reduce(a='',n in i.synonym|a+n+', ')+')',', )',')') ELSE i.label END as name, i.description[0] as def, COLLECT(DISTINCT c.label) as type, COLLECT(DISTINCT replace(k.folder[0],'http:','https:') + '/thumbnailT.png') as file&quot;, &quot;parameters&quot; : { &quot;ID&quot; : &quot;$ID&quot; }"
-          countQuery="&quot;statement&quot;: &quot;MATCH (n:VFB:Class { short_form: {ID} } )&lt;-[r:expresses|SUBCLASSOF|INSTANCEOF*..]-(i:Individual)&lt;-[:depicts]-(j:Individual)-[k:in_register_with]->(m:Individual:Template) RETURN count(i) as count&quot;, &quot;parameters&quot; : { &quot;ID&quot; : &quot;$ID&quot; }"/>
+          query="&quot;statement&quot;: &quot;MATCH (c:Class)&lt;-[:INSTANCEOF]-(primary:Individual)&lt;-[:depicts]-(channel:Individual)-[irw:in_register_with]->(template:Individual)-[:depicts]->(template_anat:Individual) WHERE c.short_form in [{ID}] WITH template, channel, template_anat, irw, primary OPTIONAL MATCH (channel)-[:is_specified_output_of]->(technique:Class) WITH CASE WHEN channel IS NULL THEN [] ELSE collect ({ channel: { short_form: channel.short_form, label: coalesce(channel.label,''), iri: channel.iri, types: labels(channel), symbol: coalesce(channel.symbol[0], '')} , imaging_technique: { short_form: technique.short_form, label: coalesce(technique.label,''), iri: technique.iri, types: labels(technique), symbol: coalesce(technique.symbol[0], '')} ,image: { template_channel : { short_form: template.short_form, label: coalesce(template.label,''), iri: template.iri, types: labels(template), symbol: coalesce(template.symbol[0], '')} , template_anatomy: { short_form: template_anat.short_form, label: coalesce(template_anat.label,''), iri: template_anat.iri, types: labels(template_anat), symbol: coalesce(template_anat.symbol[0], '')} ,image_folder: COALESCE(irw.folder[0], ''), index: coalesce(apoc.convert.toInteger(irw.index[0]), []) + [] }}) END AS channel_image,primary OPTIONAL MATCH (primary)-[:INSTANCEOF]->(typ:Class) WITH CASE WHEN typ is null THEN [] ELSE collect ({ short_form: typ.short_form, label: coalesce(typ.label,''), iri: typ.iri, types: labels(typ), symbol: coalesce(typ.symbol[0], '')} ) END AS types,primary,channel_image RETURN { core : { short_form: primary.short_form, label: coalesce(primary.label,''), iri: primary.iri, types: labels(primary), symbol: coalesce(primary.symbol[0], '')} , description : coalesce(primary.description, []), comment : coalesce(primary.comment, []) } AS term, 'm20210224' AS version, 'EXAMPLES_anat_image_query' AS query, channel_image, types&quot;, &quot;parameters&quot; : { &quot;ID&quot; : &quot;$ID&quot; }"
+          countQuery="&quot;statement&quot;: &quot;MATCH (c:Class)&lt;-[:INSTANCEOF]-(n:Individual)&lt;-[:depicts]-(channel:Individual)-[irw:in_register_with]->(template:Individual)-[:depicts]->(template_anat:Individual) WHERE c.short_form in [{ID}] RETURN count(n) AS count&quot;, &quot;parameters&quot; : { &quot;ID&quot; : &quot;$ID&quot; }"/>
       <queryChain
           xsi:type="gep_2:ProcessQuery"
           name="Process Images"
           returnType="//@libraries.3/@types.0"
-          queryProcessorId="vfbCreateResultListForIndividualsForQueryResultsQueryProcessor"/>
+          queryProcessorId="neo4jQueryProcessor"/>
     </queries>
     <queries
         xsi:type="gep_2:CompoundQuery"
@@ -501,6 +501,26 @@
           runForCount="false"
           queryProcessorId="neo4jQueryProcessor"/>
     </queries>
+    <queries
+        xsi:type="gep_2:CompoundQuery"
+        id="has_similar_morphology_to"
+        name="NBLAST similarity neo Query"
+        description="NBLAST similarity neo Query"
+        returnType="//@libraries.3/@types.0">
+      <queryChain
+          xsi:type="gep_2:SimpleQuery"
+          id="NBLAST_anat_image_query"
+          name="NBLAST_anat_image_query"
+          description="find has_similar_morphology_to relationships"
+          returnType="//@libraries.3/@types.0"
+          query="&quot;statement&quot;: &quot;MATCH (n:Individual)-[nblast:has_similar_morphology_to]-(primary:Individual) WHERE n.short_form in [{ID}] WITH primary, nblast OPTIONAL MATCH (primary)&lt;-[:depicts]-(channel:Individual)-[irw:in_register_with]->(template:Individual)-[:depicts]->(template_anat:Individual) WITH template, channel, template_anat, irw, primary, nblast OPTIONAL MATCH (channel)-[:is_specified_output_of]->(technique:Class) WITH CASE WHEN channel IS NULL THEN [] ELSE collect ({ channel: { short_form: channel.short_form, label: coalesce(channel.label,''), iri: channel.iri, types: labels(channel), symbol: coalesce(channel.symbol[0], '')} , imaging_technique: { short_form: technique.short_form, label: coalesce(technique.label,''), iri: technique.iri, types: labels(technique), symbol: coalesce(technique.symbol[0], '')} ,image: { template_channel : { short_form: template.short_form, label: coalesce(template.label,''), iri: template.iri, types: labels(template), symbol: coalesce(template.symbol[0], '')} , template_anatomy: { short_form: template_anat.short_form, label: coalesce(template_anat.label,''), iri: template_anat.iri, types: labels(template_anat), symbol: coalesce(template_anat.symbol[0], '')} ,image_folder: COALESCE(irw.folder[0], ''), index: coalesce(apoc.convert.toInteger(irw.index[0]), []) + [] }}) END AS channel_image,primary, nblast OPTIONAL MATCH (primary)-[:INSTANCEOF]->(typ:Class) WITH CASE WHEN typ is null THEN [] ELSE collect ({ short_form: typ.short_form, label: coalesce(typ.label,''), iri: typ.iri, types: labels(typ), symbol: coalesce(typ.symbol[0], '')} ) END AS types,primary,channel_image, nblast RETURN { core : { short_form: primary.short_form, label: coalesce(primary.label,''), iri: primary.iri, types: labels(primary), symbol: coalesce(primary.symbol[0], '')} , description : coalesce(primary.description, []), comment : coalesce(primary.comment, []) } AS term, nblast.NBLAST_score[0] as score, 'm20210225' AS version, 'NBLAST_anat_image_query' AS query, channel_image, types&quot;, &quot;parameters&quot; : { &quot;ID&quot; : &quot;$ID&quot; }"
+          countQuery="&quot;statement&quot;: &quot;MATCH (n:Individual)-[nblast:has_similar_morphology_to]-(primary:Individual) WHERE n.short_form in [{ID}] RETURN count(primary) AS count&quot;, &quot;parameters&quot; : { &quot;ID&quot; : &quot;$ID&quot; }"/>
+      <queryChain
+          xsi:type="gep_2:ProcessQuery"
+          name="Process Images"
+          returnType="//@libraries.3/@types.0"
+          queryProcessorId="neo4jQueryProcessor"/>
+    </queries>
     <fetchVariableQuery
         xsi:type="gep_2:CompoundQuery"
         name="Compound query for collating term information"
@@ -822,30 +842,6 @@
         description="Keep nothing slimply pass ids and scores"
         queryProcessorId="nblastQueryProcessor"/>
   </dataSources>
-  <dataSources
-      id="opencpuDataSource"
-      name="NBLAST Data Source (vfbnblast)"
-      dataSourceService="opencpuDataSource"
-      url="http://r.virtualflybrain.org/ocpu/library/vfbnblast/R/vfbnblast_neuron/json"
-      dependenciesLibrary="//@libraries.3"
-      targetLibrary="//@libraries.4">
-    <queries
-        xsi:type="gep_2:SimpleQuery"
-        id="vfbnblastSimilarTo"
-        name="VFB NBLAST similar to"
-        description="Find all similar to $NAME"
-        query="&quot;query&quot;:&quot;$ID&quot;,&quot;n&quot;:25"
-        countQuery="">
-      <matchingCriteria
-          type="//@libraries.3/@types.0 //@libraries.3/@types.2"/>
-    </queries>
-    <queries
-        xsi:type="gep_2:ProcessQuery"
-        id="nblastPassIdAndScores"
-        name="NBLAST pass ids and scores"
-        description="Keep nothing slimply pass ids and scores"
-        queryProcessorId="nblastQueryProcessor"/>
-  </dataSources>
   <queries xsi:type="gep_2:CompoundRefQuery"
       id="ListAllAvailableImages"
       name="List all available images for class with examples"
@@ -1007,15 +1003,6 @@
     <matchingCriteria
         type="//@libraries.3/@types.1 //@libraries.3/@types.23"/>
   </queries>
-  <queries xsi:type="gep_2:CompoundRefQuery"
-      id="SimilarTo"
-      name="NBLAST Similar to"
-      description="NBLAST Similar to $NAME"
-      returnType="//@libraries.3/@types.2"
-      queryChain="//@dataSources.4/@queries.0 //@dataSources.4/@queries.2 //@dataSources.0/@queries.1">
-    <matchingCriteria
-        type="//@libraries.3/@types.0 //@libraries.3/@types.2 //@libraries.3/@types.25"/>
-  </queries>
   <queries xsi:type="gep_2:CompoundRefQuery"
       id="targeting"
       name="NBLAST GAL4 targeting"
@@ -1070,15 +1057,6 @@
     <matchingCriteria
         type="//@libraries.3/@types.20"/>
   </queries>
-  <queries xsi:type="gep_2:CompoundRefQuery"
-      id="vfbSimilarTo"
-      name="VFB NBLAST Similar to"
-      description="NBLAST Similar to $NAME"
-      returnType="//@libraries.3/@types.2"
-      queryChain="//@dataSources.5/@queries.0 //@dataSources.4/@queries.2 //@dataSources.0/@queries.1">
-    <matchingCriteria
-        type="//@libraries.3/@types.40 //@libraries.3/@types.0 //@libraries.3/@types.2"/>
-  </queries>
   <queries xsi:type="gep_2:CompoundRefQuery"
       id="ref_neuron_region_connectivity_query"
       name="Show connectivity to regions from Neuron X"
@@ -1095,4 +1073,13 @@
     <matchingCriteria
         type="//@libraries.3/@types.42"/>
   </queries>
+  <queries xsi:type="gep_2:CompoundRefQuery"
+      id="SimilarMorphologyTo"
+      name="has_similar_morphology_to"
+      description="Neurons with similar morphology to $NAME  [NBLAST mean score]"
+      returnType="//@libraries.3/@types.2"
+      queryChain="//@dataSources.0/@queries.17">
+    <matchingCriteria
+        type="//@libraries.3/@types.0 //@libraries.3/@types.2 //@libraries.3/@types.25"/>
+  </queries>
 </gep:GeppettoModel>
diff --git a/tests/jest/vfb/batch1/layer-component-tests.js b/tests/jest/vfb/batch1/layer-component-tests.js
@@ -16,7 +16,7 @@ const openControls = async (page, text) => {
 		let elems = Array.from(document.querySelectorAll('.vfbListViewer .griddle-row'));
 		for (var i = 0; i < elems.length; i++) {
 			if (elems[i].innerText.includes(text)) {
-				elems[1].querySelector(".fa-eye").click()
+				elems[1].querySelector(".fa-angle-down").click()
 				break;
 			}
 		}
-Original file line number
+Diff line change
@@ Expand Up / @@ -367,7 +367,6 @@ class VFBGraph extends Component { @@
        */
       queryResults (requestQuery, instance) {
         if ( this.queryRequests.includes(instance.id) ) {
-          alert("yo")
           return;
         }
@@ Expand Down @@