Merge pull request #1457 from VirtualFlyBrain/master-solr-cache

Master solr cache
VirtualFlyBrain · Jan 12, 2024 · 6d44535 · 6d44535
2 parents 9a22372 + 154b944
commit 6d44535
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Showing 5 changed files with 72 additions and 2 deletions.
diff --git a/components/configuration/VFBFocusTerm/focusTermConfiguration.js b/components/configuration/VFBFocusTerm/focusTermConfiguration.js
@@ -115,7 +115,7 @@ var focusTermConfiguration = {
       position: "bottom-start",
       dynamicListInjector: {
         handlerAction: "subMenuGrouping",
-        parameters: ["undefined"]
+        parameters: []
       }
     }
   ]

diff --git a/components/configuration/VFBMain/searchConfiguration.js b/components/configuration/VFBMain/searchConfiguration.js
@@ -194,6 +194,11 @@ var searchConfiguration = {
           "filter_name": "Synaptic Neuropil",
           "enabled": "disabled",
         },
+        {
+          "key": "hasScRNAseq",
+          "filter_name": "Has scRNAseq data",
+          "enabled": "disabled",
+        },
         {
           "key": "DataSet",
           "filter_name": "Dataset",

diff --git a/components/configuration/VFBToolbar/vfbtoolbarMenuConfiguration.js b/components/configuration/VFBToolbar/vfbtoolbarMenuConfiguration.js
@@ -420,6 +420,15 @@ var toolbarMenu = {
                     handlerAction: "openNewTab",
                     parameters: ["https://neuprint.janelia.org/?dataset=hemibrain%3Av1.2.1&qt=findneurons"]
                   }
+                },
+                {
+                  label: "Adult Male VNC (MANC) NeuPRINT+ (FlyEM, Janelia)",
+                  icon: "",
+                  position: "right-start",
+                  action: {
+                    handlerAction: "openNewTab",
+                    parameters: ["https://neuprint.janelia.org/?dataset=manc%3Av1.0&qt=findneurons"]
+                  }
                 }
               ]
             },

diff --git a/components/configuration/VFBTree/VFBTreeConfiguration.js b/components/configuration/VFBTree/VFBTreeConfiguration.js
@@ -9,7 +9,7 @@ var treeCypherQuery = instance => ({
       "statement": "MATCH (root:Class)<-[:INSTANCEOF]-(t:Template {short_form:'" + instance + "'})"
       + "<-[:depicts]-(tc:Template)<-[ie:in_register_with]-(c:Individual)-[:depicts]->(image:"
       + "Individual)-[r:INSTANCEOF]->(anat:Class:Anatomy) WHERE exists(ie.index) WITH root, anat,r,image"
-      + " MATCH p=allshortestpaths((root)<-[:SUBCLASSOF|part_of*..]-(anat)) "
+      + " MATCH p=allshortestpaths((root)<-[:SUBCLASSOF|part_of*..50]-(anat)) "
       + "UNWIND nodes(p) as n UNWIND nodes(p) as m WITH * WHERE id(n) < id(m) "
       + "MATCH path = allShortestPaths( (n)-[:SUBCLASSOF|part_of*..1]-(m) ) "
       + "RETURN collect(distinct { node_id: id(anat), short_form: anat.short_form, image: image.short_form })"

diff --git a/model/vfb.xmi b/model/vfb.xmi
@@ -162,6 +162,9 @@
     <types xsi:type="gep_1:SimpleType"
         id="hasScRNAseq"
         name="has Single Cell RNA Seq Results"/>
+    <types xsi:type="gep_1:SimpleType"
+        id="Gene"
+        name="Gene"/>
   </libraries>
   <libraries
       id="vfbLibrary"
@@ -622,6 +625,41 @@
           returnType="//@libraries.3/@types.0"
           queryProcessorId="neo4jQueryProcessor"/>
     </queries>
+    <queries
+        xsi:type="gep_2:CompoundQuery"
+        id="dataset_scRNAseq_query_compound"
+        name="dataset_scRNAseq_query">
+      <queryChain
+          xsi:type="gep_2:SimpleQuery"
+          name="Get JSON for dataset scRNAseq query"
+          description="Get JSON for dataset scRNAseq query"
+          query="&quot;statement&quot;: &quot;MATCH (c:Individual)-[:has_source]->(ds:scRNAseq_DataSet) WHERE ds.short_form = $id OPTIONAL MATCH (ds)-[:has_reference]->(p:pub) WITH COLLECT({ core: { short_form: p.short_form, label: coalesce(p.label,''), iri: p.iri, types: labels(p), unique_facets: apoc.coll.sort(coalesce(p.uniqueFacets, [])), symbol: coalesce(([]+p.symbol)[0], '')} , PubMed: coalesce(([]+p.PMID)[0], ''), FlyBase: coalesce(([]+p.FlyBase)[0], ''), DOI: coalesce(([]+p.DOI)[0], '') }) AS pubs, c RETURN { core : { short_form: c.short_form, label: coalesce(c.label,''), iri: c.iri, types: labels(c), unique_facets: apoc.coll.sort(coalesce(c.uniqueFacets, [])), symbol: coalesce(([]+c.symbol)[0], '')} , description : coalesce(c.description, []), comment : coalesce(c.comment, []) } AS term, 'Get JSON for dataset scRNAseq query' AS query, 'ma3c0d68' AS version, pubs&quot;, &quot;parameters&quot; : { &quot;id&quot; : &quot;$ID&quot; }"
+          countQuery="&quot;statement&quot;: &quot;MATCH (c:Individual)-[:has_source]->(ds:scRNAseq_DataSet) WHERE ds.short_form = $id RETURN count(c) as count&quot;, &quot;parameters&quot; : { &quot;id&quot; : &quot;$ID&quot; }"/>
+      <queryChain
+          xsi:type="gep_2:ProcessQuery"
+          name="Process Images"
+          returnType="//@libraries.3/@types.0"
+          queryProcessorId="neo4jQueryProcessor"/>
+    </queries>
+    <queries
+        xsi:type="gep_2:CompoundQuery"
+        id="expression_cluster_query_compound"
+        name="expression_cluster_query"
+        description="Get JSON for expression in cluster query">
+      <queryChain
+          xsi:type="gep_2:SimpleQuery"
+          id="cluster_expression_query"
+          name="Get JSON for cluster expression query"
+          description="Get JSON for cluster expression query"
+          query="&quot;statement&quot;: &quot;MATCH (primary:Individual:Cluster)-[e:expresses]->(g:Gene:Class) WHERE g.short_form in [$id] WITH e.expression_level[0] as expression_level, e.expression_extent[0] as expression_extent, { short_form: g.short_form, label: coalesce(g.label,''), iri: g.iri, types: labels(g), unique_facets: apoc.coll.sort(coalesce(g.uniqueFacets, [])), symbol: coalesce(([]+g.symbol)[0], '')}  AS gene,primary MATCH (a:Anatomy)&lt;-[:composed_primarily_of]-(primary) WITH { short_form: a.short_form, label: coalesce(a.label,''), iri: a.iri, types: labels(a), unique_facets: apoc.coll.sort(coalesce(a.uniqueFacets, [])), symbol: coalesce(([]+a.symbol)[0], '')}  AS anatomy,primary,expression_level,expression_extent,gene  RETURN { core : { short_form: primary.short_form, label: coalesce(primary.label,''), iri: primary.iri, types: labels(primary), unique_facets: apoc.coll.sort(coalesce(primary.uniqueFacets, [])), symbol: coalesce(([]+primary.symbol)[0], '')} , description : coalesce(primary.description, []), comment : coalesce(primary.comment, []) } AS term, 'Get JSON for expression in cluster query' AS query, 'ma3c0d68' AS version , expression_level, expression_extent, anatomy&quot;, &quot;parameters&quot; : { &quot;id&quot; : &quot;$ID&quot; }"
+          countQuery="&quot;statement&quot;: &quot;MATCH (primary:Individual:Cluster)-[e:expresses]->(g:Gene:Class) WHERE g.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"
+          id="vfb_query_schema_processor"
+          name="Process clusters"
+          description="vfb_query_schema_processor"
+          queryProcessorId="neo4jQueryProcessor"/>
+    </queries>
     <fetchVariableQuery
         xsi:type="gep_2:CompoundQuery"
         name="Compound query for collating term information"
@@ -1250,6 +1288,24 @@
     <matchingCriteria
         type="//@libraries.3/@types.0 //@libraries.3/@types.22"/>
   </queries>
+  <queries xsi:type="gep_2:CompoundRefQuery"
+      id="scRNAdatasetData"
+      name="Show all data for a scRNAseq dataset"
+      description="List all data for $NAME"
+      returnType="//@libraries.3/@types.0"
+      queryChain="//@dataSources.0/@queries.23">
+    <matchingCriteria
+        type="//@libraries.3/@types.24 //@libraries.3/@types.47"/>
+  </queries>
+  <queries xsi:type="gep_2:CompoundRefQuery"
+      id="expressionCluster"
+      name="expression_cluster"
+      description="scRNAseq clusters expressing $NAME"
+      returnType="//@libraries.3/@types.0"
+      queryChain="//@dataSources.0/@queries.24">
+    <matchingCriteria
+        type="//@libraries.3/@types.1 //@libraries.3/@types.48 //@libraries.3/@types.47"/>
+  </queries>
   <queries xsi:type="gep_2:CompoundRefQuery"
       id="terminfotest"
       name="Term Info Test"