From 643ddb442059a0b6dd1e58cbb99f93e117cbaf70 Mon Sep 17 00:00:00 2001
From: Bindu Gajria <bindu@sas.upenn.edu>
Date: Mon, 27 Jul 2026 11:35:14 -0400
Subject: [PATCH 1/3] exclude usercomments_userdb_betan.mappedComment and so
 not have communityCount in OrgAbbrev table - this commit is ONLY for the
 dnaseq-merge-experiments branch, and is being tuning for tuning.

---
 Model/lib/xml/tuningManager/apiTuningManager.xml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/Model/lib/xml/tuningManager/apiTuningManager.xml b/Model/lib/xml/tuningManager/apiTuningManager.xml
index 770d9fde9..52c0d7c5e 100644
--- a/Model/lib/xml/tuningManager/apiTuningManager.xml
+++ b/Model/lib/xml/tuningManager/apiTuningManager.xml
@@ -1318,7 +1318,7 @@
     <intermediateTable name="DataSourceCount"/>
     <intermediateTable name="OrganismCentromere"/>
     <intermediateTable name="SequenceCount"/>
-    <intermediateTable name="CommunityCount"/>
+    <!-- intermediateTable name="CommunityCount"/ -->
     <intermediateTable name="ProfileCount"/>
     <!-- <intermediateTable name="PopsetCount"/> -->
     <intermediateTable name="GeneCount"/>
@@ -1396,7 +1396,7 @@
       ]]>
     </sql>
 
-    <sql>
+<!--    <sql>
       <![CDATA[
         CREATE UNLOGGED TABLE CommunityCount AS
         SELECT taxon_id, count(*) as communityCount
@@ -1410,7 +1410,7 @@
         GROUP BY taxon_id
       ]]>
     </sql>
-
+-->
     <sql>
       <![CDATA[
         CREATE UNLOGGED TABLE ProfileCount AS
@@ -1659,7 +1659,7 @@
                    coalesce(sc.contig_num, 0) as contigCount,
                    coalesce(sc.supercont_num, 0) as supercontigCount,
                    coalesce(sc.chrom_num, 0) as chromosomeCount,
-                   coalesce(cc.communityCount, 0) as communityCount,
+                  -- coalesce(cc.communityCount, 0) as communityCount,
                    --coalesce(psc.popsetCount, 0) as popsetCount,
                    coalesce(pc.geneArrayCount, 0) as arrayGeneCount,
                    coalesce(pc.rnaSeqCount, 0) as rnaSeqCount,
@@ -1671,7 +1671,7 @@
               LEFT JOIN DataSourceCount dsc ON o.taxon_id = dsc.taxon_id
               LEFT JOIN OrganismCentromere oc ON o.taxon_id = oc.taxon_id
               LEFT JOIN SequenceCount sc ON o.taxon_id = sc.taxon_id
-              LEFT JOIN CommunityCount cc ON o.taxon_id = cc.taxon_id
+              -- LEFT JOIN CommunityCount cc ON o.taxon_id = cc.taxon_id
               LEFT JOIN GeneCount gc ON o.taxon_id = gc.taxon_id
               --LEFT JOIN popsetCount psc ON o.taxon_id = psc.taxon_id
               LEFT JOIN profileCount pc ON o.taxon_id = pc.taxon_id

From e224f878214bf6e8ec6b4599d887b0b6beebf7f0 Mon Sep 17 00:00:00 2001
From: Bindu Gajria <bindu@sas.upenn.edu>
Date: Wed, 29 Jul 2026 21:20:56 -0400
Subject: [PATCH 2/3] Move communitycount and community_flag to their own
 attribute query

Fix the CommunityCounts join, use @REMOTE_COMMENT_SCHEMA@, and scope
comment counts per project.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
---
 .../records/organismAttributeQueries.xml      | 33 ++++++++++++++++---
 .../lib/wdk/model/records/organismRecords.xml | 23 ++++++-------
 2 files changed, 41 insertions(+), 15 deletions(-)

diff --git a/Model/lib/wdk/model/records/organismAttributeQueries.xml b/Model/lib/wdk/model/records/organismAttributeQueries.xml
index 31da7de60..4087ae506 100644
--- a/Model/lib/wdk/model/records/organismAttributeQueries.xml
+++ b/Model/lib/wdk/model/records/organismAttributeQueries.xml
@@ -101,7 +101,6 @@
       <column name="tfbscount"/>
       <column name="gocount"/>
       <column name="proteomicscount"/>
-      <column name="communitycount"/>
       <column name="organism_name"/>
       <column name="organism_full"/>
       <column name="isOrganellar_flag"/>
@@ -113,7 +112,6 @@
       <column name="go_flag"/>
       <column name="ec_flag"/>
       <column name="rtpcr_flag"/>
-      <column name="community_flag"/>
       <column name="tfbs_flag"/>
       <column name="hasHTSIsolate_flag"/>
 <!--       <column name="hasPopset_flag"/> -->
@@ -158,7 +156,6 @@
                  nullif(oa.gocount,0) as gocount,
                  nullif(oa.tfbscount,0) as tfbscount,
                  nullif(oa.proteomicscount,0) as proteomicscount,
-                 nullif(oa.communitycount,0) as communitycount, 
                  CASE oa.isOrganellar WHEN 0 THEN 'no' ELSE 'yes' END as isOrganellar_flag,
                  CASE oa.arraygenecount WHEN 0 THEN 'none' ELSE 'yes' END as array_flag,
                  CASE oa.chipchipgenecount WHEN 0 THEN 'none' ELSE 'yes' END as chipchip_flag,
@@ -168,7 +165,6 @@
                  CASE oa.ecnumbercount WHEN 0 THEN 'none' ELSE 'yes' END as ec_flag,
                  CASE oa.gocount WHEN 0 THEN 'none' ELSE 'yes' END as go_flag,
                  CASE oa.rtpcrcount WHEN 0 THEN 'none' ELSE 'yes' END as rtpcr_flag,
-                 CASE oa.communitycount WHEN 0 THEN 'none' ELSE 'yes' END as community_flag,
                  CASE oa.tfbscount WHEN 0 THEN 'none' ELSE 'yes' END as tfbs_flag,
                  CASE oa.hasHTSIsolate WHEN 0 THEN 'none' ELSE 'yes' END as hasHTSIsolate_flag,
                  --CASE oa.hasPopset WHEN 0 THEN 'none' ELSE 'yes' END as hasPopset_flag,
@@ -241,6 +237,35 @@
       </sql>
     </sqlQuery>
 
+
+        <sqlQuery name="CommunityCounts">
+            <column name="source_id"/>
+            <column name="project_id"/>
+            <column name="communitycount"/>
+            <column name="community_flag"/>
+            <sql>
+            <![CDATA[
+              SELECT o.source_id, o.project_id,
+                     nullif(count(comm.stable_id), 0) as communitycount,
+                     CASE WHEN count(comm.stable_id) = 0 THEN 'none' ELSE 'yes' END as community_flag
+              FROM apidbtuning.organismAttributes o
+                   LEFT JOIN apidbtuning.GeneAttributes ga
+                          ON  ga.taxon_id   = o.component_taxon_id
+                          AND ga.project_id = o.project_id
+                   LEFT JOIN (
+                          SELECT distinct stable_id, project_name
+                          FROM   @REMOTE_COMMENT_SCHEMA@MappedComment
+                          WHERE  is_visible = true
+                            AND  comment_target_id = 'gene'
+                   ) comm ON  comm.stable_id    = ga.source_id
+                          AND comm.project_name = ga.project_id
+              where o.project_id = '@PROJECT_ID@' or '@PROJECT_ID@' = 'UniDB'
+              GROUP BY o.source_id, o.project_id
+                ]]>
+           </sql>
+        </sqlQuery>
+
+
         <sqlQuery name="BuscoGenomeCounts">
             <column name="source_id"/>
             <column name="project_id"/>
diff --git a/Model/lib/wdk/model/records/organismRecords.xml b/Model/lib/wdk/model/records/organismRecords.xml
index a1bb762fd..349f27568 100644
--- a/Model/lib/wdk/model/records/organismRecords.xml
+++ b/Model/lib/wdk/model/records/organismRecords.xml
@@ -180,8 +180,6 @@
           help="Number of genes that have evidence of protein expression based on Mass Spectrometry studies" align="right"/>
         <columnAttribute name="tfbscount" type="number" displayName="TFBS" attributeCategory="genemetrics"  
           help="Total number of genes having evidence of expression based on transcription factor binding site identification experiments" align="right" />
-        <columnAttribute name="communitycount" type="number"  displayName="User comments" attributeCategory="genemetrics"  
-          help="Number of genes with comments/notes from the research community" align="right"/>
 
         <columnAttribute name="organism_name" displayName="Organism (text)" inReportMaker="false"/>
         <columnAttribute name="organism_full" displayName="Organism" inReportMaker="false"/>
@@ -302,15 +300,6 @@
            </text>
           </textAttribute>
 
-         <columnAttribute name="community_flag" inReportMaker="false"/>
-         <textAttribute name="hasCommunity" displayName="Community" align="center" inReportMaker="false" >
-           <text>
-             <![CDATA[
-             <img width="8" border="0" alt="$$community_flag$$" src="/a/images/reddot.gif" style="display:$$community_flag$$"/>
-             ]]>
-           </text>
-          </textAttribute>
-
          <columnAttribute name="ec_flag" inReportMaker="false"/>
          <textAttribute name="hasEC" displayName="EC#" align="center" inReportMaker="false" >
            <text>
@@ -434,6 +423,18 @@
                        help ="VectorBase genomes initial annotation source (version 1.0) is either from NCBI RefSeq or from the genome authors own pipeline. Subsequent annotations are provided by VectorBase, either by the community (currently via Apollo) or by the EBI pipeline (via predictions and alignments to external databases)." />
      </attributeQueryRef>
 
+     <attributeQueryRef ref="OrganismAttributes.CommunityCounts">
+       <columnAttribute name="communitycount" type="number" displayName="User comments" attributeCategory="genemetrics"
+          help="Number of genes with comments/notes from the research community" align="right"/>
+       <columnAttribute name="community_flag" inReportMaker="false"/>
+       <textAttribute name="hasCommunity" displayName="Community" align="center" inReportMaker="false" >
+         <text>
+           <![CDATA[
+           <img width="8" border="0" alt="$$community_flag$$" src="/a/images/reddot.gif" style="display:$$community_flag$$"/>
+           ]]>
+         </text>
+       </textAttribute>
+     </attributeQueryRef>
 
      <attributeQueryRef ref="OrganismAttributes.BuscoProteinCounts" excludeProjects="HostDB,EuPathDB">
        <columnAttribute name="busco_protein"  displayName="BUSCO Protein"

From 9f22c4eed3a5f737eddfda224194a00f2ce60215 Mon Sep 17 00:00:00 2001
From: Bindu Gajria <bindu@sas.upenn.edu>
Date: Wed, 29 Jul 2026 21:40:37 -0400
Subject: [PATCH 3/3] Remove dead CommunityCount tuning code

Superseded by the CommunityCounts attribute query.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
---
 .../lib/xml/tuningManager/apiTuningManager.xml | 18 ------------------
 1 file changed, 18 deletions(-)

diff --git a/Model/lib/xml/tuningManager/apiTuningManager.xml b/Model/lib/xml/tuningManager/apiTuningManager.xml
index 52c0d7c5e..5f5fd2618 100644
--- a/Model/lib/xml/tuningManager/apiTuningManager.xml
+++ b/Model/lib/xml/tuningManager/apiTuningManager.xml
@@ -1318,7 +1318,6 @@
     <intermediateTable name="DataSourceCount"/>
     <intermediateTable name="OrganismCentromere"/>
     <intermediateTable name="SequenceCount"/>
-    <!-- intermediateTable name="CommunityCount"/ -->
     <intermediateTable name="ProfileCount"/>
     <!-- <intermediateTable name="PopsetCount"/> -->
     <intermediateTable name="GeneCount"/>
@@ -1396,21 +1395,6 @@
       ]]>
     </sql>
 
-<!--    <sql>
-      <![CDATA[
-        CREATE UNLOGGED TABLE CommunityCount AS
-        SELECT taxon_id, count(*) as communityCount
-        FROM Geneattributes
-        WHERE (source_id, project_id) IN (
-              SELECT distinct stable_id, project_name
-              FROM usercomments_userdb_betan.mappedComment
-              WHERE is_visible = '1'
-                AND comment_target_id = 'gene'
-          )
-        GROUP BY taxon_id
-      ]]>
-    </sql>
--->
     <sql>
       <![CDATA[
         CREATE UNLOGGED TABLE ProfileCount AS
@@ -1659,7 +1643,6 @@
                    coalesce(sc.contig_num, 0) as contigCount,
                    coalesce(sc.supercont_num, 0) as supercontigCount,
                    coalesce(sc.chrom_num, 0) as chromosomeCount,
-                  -- coalesce(cc.communityCount, 0) as communityCount,
                    --coalesce(psc.popsetCount, 0) as popsetCount,
                    coalesce(pc.geneArrayCount, 0) as arrayGeneCount,
                    coalesce(pc.rnaSeqCount, 0) as rnaSeqCount,
@@ -1671,7 +1654,6 @@
               LEFT JOIN DataSourceCount dsc ON o.taxon_id = dsc.taxon_id
               LEFT JOIN OrganismCentromere oc ON o.taxon_id = oc.taxon_id
               LEFT JOIN SequenceCount sc ON o.taxon_id = sc.taxon_id
-              -- LEFT JOIN CommunityCount cc ON o.taxon_id = cc.taxon_id
               LEFT JOIN GeneCount gc ON o.taxon_id = gc.taxon_id
               --LEFT JOIN popsetCount psc ON o.taxon_id = psc.taxon_id
               LEFT JOIN profileCount pc ON o.taxon_id = pc.taxon_id