Merge pull request #1130 from VirtualFlyBrain/pipeline2-sync-00f2

sync: pipeline2 with pipeline2-sync-00f2
VirtualFlyBrain · May 28, 2021 · 88b2a8f · 88b2a8f
2 parents d93d8af + 3b36f0d
commit 88b2a8f
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Showing 6 changed files with 25 additions and 33 deletions.
diff --git a/components/configuration/VFBOverview/quickHelp.json b/components/configuration/VFBOverview/quickHelp.json
@@ -3,16 +3,6 @@
 	"height": "575",
     "width": "900",
 	"steps": [{
-		"title": "Welcome to Virtual Fly Brain",
-		"image" : "https://VirtualFlyBrain.org/data/VFB/screencaps/VFB_3D_400x400.jpg",
-		"instructions": [{
-			"icon" : "fa fa-question-circle-o",
-			"label" : "Hi, we are currently running a VFB User Survey, once you have used the site please consider completing this survey to help us improve it by clicking User Survey in the Help menu above."
-		},{
-			"icon" : "fa fa-fast-forward",
-			"label" : "Just click NEXT below for handy tips on using VFB or SKIP INTRO to close this and jump right into VFB."
-		}]
-	},{
 		"title": "Welcome to Virtual Fly Brain",
 		"image" : "geppetto/build/VFBqHelpMain.jpg",
 		"instructions": [{

diff --git a/components/configuration/VFBToolbar/vfbtoolbarMenuConfiguration.js b/components/configuration/VFBToolbar/vfbtoolbarMenuConfiguration.js
@@ -632,14 +632,6 @@ var toolbarMenu = {
       position: "bottom-start",
       list: [
         {
-          label: "User Survey",
-          icon: "",
-          trailerIcon: "fa fa-external-link",
-          action: {
-            handlerAction: "openNewTab",
-            parameters: ["https://www.surveymonkey.co.uk/r/5HDZZRR"]
-          }
-        },{
           label: "F.A.Q.",
           icon: "",
           trailerIcon: "fa fa-external-link",

diff --git a/components/interface/VFBTermInfo/VFBTermInfo.js b/components/interface/VFBTermInfo/VFBTermInfo.js
@@ -732,12 +732,12 @@ class VFBTermInfoWidget extends React.Component {
       return;
     }
     var Query = require('@geppettoengine/geppetto-core/model/Query');
-    var n = window[path];
     var otherId;
     var otherName;
     var target = widget;
     var that = this;
     var meta = path + "." + path + "_meta";
+    var n = window[meta];
     if (n != undefined) {
       var metanode = Instances.getInstance(meta);
       if ((this.data.length > 0) && (this.data[0] == metanode)) {

diff --git a/css/VFBTermInfo.less b/css/VFBTermInfo.less
@@ -934,3 +934,19 @@
         transition: all 0.50s;
     }
 }
+
+details > summary > i.fa-chevron-circle-right {
+    display: inline-block;
+}
+
+details > summary > i.fa-chevron-circle-down {
+    display: none;
+}
+
+details[open] > summary > i.fa-chevron-circle-down {
+    display: inline-block;
+}
+
+details[open] > summary > i.fa-chevron-circle-right {
+    display: none;
+}
diff --git a/model/vfb.xmi b/model/vfb.xmi
@@ -150,6 +150,9 @@
     <types xsi:type="gep_1:SimpleType"
         id="has_region_connectivity"
         name="Has Region Connectivity"/>
+    <types xsi:type="gep_1:SimpleType"
+        id="NBLASTexp"
+        name="NBLAST to exp"/>
   </libraries>
   <libraries
       id="vfbLibrary"
@@ -550,8 +553,8 @@
           name="NBLAST_anat_image_query"
           description="find has_similar_morphology_to relationships"
           returnType="//@libraries.3/@types.1"
-          query="&quot;statement&quot;: &quot;MATCH (n:Individual)-[nblast:has_similar_morphology_to_part_of]-(c:Class) WHERE n.short_form in [$id] WITH c, nblast OPTIONAL MATCH (c:Class)&lt;-[:INSTANCEOF|SUBCLASSOF*..]-(primary:Individual)&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, 'm20210406' AS version, 'NBLASTexp_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_part_of]-(primary:Class) WHERE n.short_form in [$id] RETURN count(primary) AS count&quot;, &quot;parameters&quot; : { &quot;id&quot; : &quot;$ID&quot; }"/>
+          query="&quot;statement&quot;: &quot;MATCH (n:Neuron)-[nblast:has_similar_morphology_to_part_of]->(primary:Expression_pattern) WHERE n.short_form in [$id] WITH primary, nblast OPTIONAL MATCH (c:Class)&lt;-[:INSTANCEOF]-(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, 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, 'm20210503' AS version, 'NBLASTexp_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_part_of]->(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"
@@ -1040,15 +1043,6 @@
     <matchingCriteria
         type="//@libraries.3/@types.1 //@libraries.3/@types.23"/>
   </queries>
-  <queries xsi:type="gep_2:CompoundRefQuery"
-      id="targeting"
-      name="NBLAST GAL4 targeting"
-      description="NBLAST potential GAL4's targeting $NAME"
-      returnType="//@libraries.3/@types.0"
-      queryChain="//@dataSources.4/@queries.1 //@dataSources.4/@queries.2 //@dataSources.0/@queries.1">
-    <matchingCriteria
-        type="//@libraries.3/@types.0 //@libraries.3/@types.2 //@libraries.3/@types.25 //@libraries.3/@types.1 //@libraries.3/@types.24"/>
-  </queries>
   <queries xsi:type="gep_2:CompoundRefQuery"
       id="AllAlignedImages"
       name="Show all images aligned to template"
@@ -1131,10 +1125,10 @@
   <queries xsi:type="gep_2:CompoundRefQuery"
       id="SimilarMorphologyToPartOf"
       name="has_similar_morphology_to_part_of"
-      description="GAL4 with some neurons with similar morphology to $NAME  [NBLAST mean score]"
+      description="GAL4 with some similar morphology to $NAME  [NBLAST mean score]"
       returnType="//@libraries.3/@types.2"
       queryChain="//@dataSources.0/@queries.19">
     <matchingCriteria
-        type="//@libraries.3/@types.0 //@libraries.3/@types.2 //@libraries.3/@types.40"/>
+        type="//@libraries.3/@types.0 //@libraries.3/@types.2 //@libraries.3/@types.44"/>
   </queries>
 </gep:GeppettoModel>
diff --git a/tests/jest/vfb/batch1/menu-component-tests.js b/tests/jest/vfb/batch1/menu-component-tests.js
@@ -105,7 +105,7 @@ describe('VFB Menu Component Tests', () => {
       await wait4selector(page, "ul.MuiList-root", { visible: true, timeout : 120000 })
       // Check there's four elements in the drop down menu of 'Help'
       const dropDownMenuItems = await page.evaluate(async () => document.getElementsByClassName("MuiListItem-root").length);
-      expect(dropDownMenuItems).toEqual(5);
+      expect(dropDownMenuItems).toEqual(4);
     })
 
     it('Help Modal FAQ Tab Opened', async () => {