From e9985025ec2cf25d9fac3db52bdba9168cf05183 Mon Sep 17 00:00:00 2001
From: Rob Court <rcourt@ed.ac.uk>
Date: Mon, 12 Jun 2023 18:58:47 +0100
Subject: [PATCH] Adding Query for scRNAseq datasets to return clusters and
 samples

Ref https://github.com/VirtualFlyBrain/vfb-pipeline-polishing/issues/1
---
 model/vfb.xmi | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/model/vfb.xmi b/model/vfb.xmi
index 3223567ac..0a502c405 100644
--- a/model/vfb.xmi
+++ b/model/vfb.xmi
@@ -622,6 +622,22 @@
           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 c.short_form = $id OPTIONAL MATCH (ds)-[:has_reference]->(p:pub) WITH { 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], '')}  AS cluster, { short_form: ds.short_form, label: coalesce(ds.label,''), iri: ds.iri, types: labels(ds), unique_facets: apoc.coll.sort(coalesce(ds.uniqueFacets, [])), symbol: coalesce(([]+ds.symbol)[0], '')}  AS dataset, 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,primary 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 dataset scRNAseq query' AS query, 'ma3c0d68' AS version , cluster, dataset, pubs&quot;, &quot;parameters&quot; : { &quot;ids&quot; : $ARRAY_ID_RESULTS , &quot;id&quot; : &quot;$ID&quot; }"
+          countQuery="&quot;statement&quot;: &quot;MATCH (c:Individual)-[:has_source]->(ds:scRNAseq_DataSet) WHERE c.short_form = $id RETURN count(c) as count&quot;, &quot;parameters&quot; : { &quot;ids&quot; : $ARRAY_ID_RESULTS , &quot;id&quot; : &quot;$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"
@@ -1242,4 +1258,13 @@
     <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>
 </gep:GeppettoModel>