From 7bece8f8237d7d8bc4de705d50a6c22785582389 Mon Sep 17 00:00:00 2001
From: John Brestelli <jbrestell@gmail.com>
Date: Tue, 14 Apr 2026 15:33:52 -0400
Subject: [PATCH 1/7] Add .worktrees to .gitignore

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 .gitignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitignore b/.gitignore
index a56646eb2..3c07ee7fb 100644
--- a/.gitignore
+++ b/.gitignore
@@ -40,3 +40,4 @@ target
 
 # JBrowse
 /Model/lib/jbrowse/auto_generated/
+.worktrees

From f17d66e757960dbcabf61aa7cc95781ebd37c04a Mon Sep 17 00:00:00 2001
From: John Brestelli <jbrestell@gmail.com>
Date: Tue, 14 Apr 2026 17:08:04 -0400
Subject: [PATCH 2/7] Add 5 EDA DST templates for antibody array WDK support

New templates appended to antibodyArray.dst:
- antibodyArrayEdaAttributeQueriesNumeric: crosstab sqlQuery + meta sqlQuery
  pivoting on sample_stable_id for normalized intensities
- antibodyArrayEdaAttributeRef: attributeQueryRef injection into transcriptRecord.xml
- antibodyArrayEdaAttributeCategory: TSV ontology rows for individuals.txt
- antibodyArrayEdaGeneTableSql: UNION clause linking gene ids via VEUPATHDB_GENE_ID
- antibodyArrayDataTableGeneTableSql: UNION clause for full data table with all attributes

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 Model/lib/dst/antibodyArray.dst | 138 ++++++++++++++++++++++++++++++++
 1 file changed, 138 insertions(+)

diff --git a/Model/lib/dst/antibodyArray.dst b/Model/lib/dst/antibodyArray.dst
index a8284edd8..65a4abb47 100644
--- a/Model/lib/dst/antibodyArray.dst
+++ b/Model/lib/dst/antibodyArray.dst
@@ -226,3 +226,141 @@ Note that changing the sample subset will reset any group assignments you have a
         </dynamicAttributes>
     </question>
 >templateTextEnd<
+
+
+[templateStart]
+name=antibodyArrayEdaAttributeQueriesNumeric
+anchorFile=ApiCommonModel/Model/lib/wdk/model/records/transcriptAttributeQueries.xml
+prop=datasetName
+prop=edaStudyStableId
+prop=edaEntityAbbrev
+prop=includeProjects
+>templateTextStart<
+        <sqlQuery name="AntibodyArrayIntensities${datasetName}"
+                  doNotTest="true"
+                  attributeMetaQueryRef="TranscriptAttributes.MetaAntibodyArrayIntensities${datasetName}"
+                  includeProjects="${includeProjects}">
+            <column name="source_id"/>
+            <column name="gene_source_id"/>
+            <column name="project_id"/>
+            <sql>
+              <![CDATA[
+  SELECT ta.source_id, ta.project_id, ta.gene_source_id, p.*
+  FROM apidbtuning.TranscriptAttributes ta
+    LEFT OUTER JOIN (
+      SELECT * FROM public.crosstab(
+        'SELECT gene_ids.gene_id,
+                CONCAT(''${edaStudyStableId}_'', anc.sample_stable_id) AS sample_col,
+                av_int.number_value AS intensity
+         FROM eda.attributevalue_${edaStudyStableId}_${edaEntityAbbrev} av_int
+         JOIN eda.ancestors_${edaStudyStableId}_${edaEntityAbbrev} anc
+           ON anc.${edaEntityAbbrev}_stable_id = av_int.${edaEntityAbbrev}_stable_id
+         JOIN (SELECT av.${edaEntityAbbrev}_stable_id, MIN(gi.gene) AS gene_id
+               FROM eda.attributevalue_${edaStudyStableId}_${edaEntityAbbrev} av
+               JOIN apidbtuning.GeneId gi ON gi.id = av.string_value
+               WHERE av.attribute_stable_id = ''VEUPATHDB_GENE_ID''
+               GROUP BY av.${edaEntityAbbrev}_stable_id) gene_ids
+           ON gene_ids.${edaEntityAbbrev}_stable_id = av_int.${edaEntityAbbrev}_stable_id
+         WHERE av_int.attribute_stable_id = ''NORMALIZED_INTENSITY''
+         ORDER BY 1, 2',
+        'SELECT CONCAT(''${edaStudyStableId}_'', sample_stable_id) AS sample_col
+         FROM (SELECT DISTINCT sample_stable_id
+               FROM eda.ancestors_${edaStudyStableId}_${edaEntityAbbrev}) s
+         ORDER BY sample_col'
+      ) AS ct(gene_id text, &&META_ATTRIBUTE_COLUMNS_FOR_CROSSTAB&&)
+    ) p ON ta.gene_source_id = p.gene_id
+              ]]>
+            </sql>
+        </sqlQuery>
+
+       <sqlQuery name="MetaAntibodyArrayIntensities${datasetName}" includeProjects="${includeProjects}">
+          <column name="name" />
+          <column name="display_name" />
+          <column name="help" />
+          <column name="reporter_name" />
+          <column name="reporter_display" />
+          <column name="reporter_description" />
+          <column name="reporter_implementation" />
+          <column name="reporter_properties" />
+
+          <sql>
+            <![CDATA[
+           SELECT CONCAT('${edaStudyStableId}_', sample_stable_id) AS name,
+                  sample_stable_id::text AS display_name,
+                  'number' AS column_type,
+                  'Normalized intensity from ${datasetName}' AS help,
+                  'histogram' AS reporter_name,
+                  'Histogram' AS reporter_display,
+                  'Display a histogram of the values' AS reporter_description,
+                  'org.gusdb.wdk.model.report.reporter.HistogramAttributeReporter' AS reporter_implementation,
+                  null AS reporter_properties
+           FROM (SELECT DISTINCT sample_stable_id
+                 FROM eda.ancestors_${edaStudyStableId}_${edaEntityAbbrev}) s
+           ORDER BY sample_stable_id
+            ]]>
+          </sql>
+       </sqlQuery>
+>templateTextEnd<
+
+
+[templateStart]
+name=antibodyArrayEdaAttributeRef
+anchorFile=ApiCommonModel/Model/lib/wdk/model/records/transcriptRecord.xml
+prop=datasetName
+prop=includeProjects
+>templateTextStart<
+              <attributeQueryRef ref="TranscriptAttributes.AntibodyArrayIntensities${datasetName}" attributeMetaQueryRef="TranscriptAttributes.MetaAntibodyArrayIntensities${datasetName}" includeProjects="${includeProjects}">
+              </attributeQueryRef>
+>templateTextEnd<
+
+
+[templateStart]
+name=antibodyArrayEdaAttributeCategory
+anchorFile=ApiCommonModel/Model/lib/wdk/ontology/individuals.txt
+prop=datasetName
+prop=datasetDisplayName
+>templateTextStart<
+AntibodyArrayDataset_${datasetName}	http://edamontology.org/topic_3360	Immunology	DatasetRecordClasses.DatasetRecordClass	dataset	${datasetName}	${datasetDisplayName}	results
+TranscriptAttributes.MetaAntibodyArrayIntensities${datasetName}	AntibodyArrayDataset_${datasetName}		TranscriptRecordClasses.TranscriptRecordClass	attributeMetaQuery	MetaAntibodyArrayIntensities${datasetName}			gene		results	download
+>templateTextEnd<
+
+
+[templateStart]
+name=antibodyArrayEdaGeneTableSql
+anchorFile=ApiCommonModel/Model/lib/wdk/model/records/geneTableQueries.xml
+prop=datasetName
+prop=edaStudyStableId
+prop=edaEntityAbbrev
+>templateTextStart<
+               UNION
+               SELECT '${datasetName}' AS dataset_name , string_value AS source_id
+               FROM eda.ATTRIBUTEvalue_${edaStudyStableId}_${edaEntityAbbrev} av
+               WHERE av.attribute_stable_id = 'VEUPATHDB_GENE_ID'
+>templateTextEnd<
+
+
+[templateStart]
+name=antibodyArrayDataTableGeneTableSql
+anchorFile=ApiCommonModel/Model/lib/wdk/model/records/geneTableQueries.xml
+prop=datasetName
+prop=edaStudyStableId
+prop=edaEntityAbbrev
+>templateTextStart<
+UNION
+SELECT genes.string_value AS gene,
+       ag.display_name AS variable,
+       av.string_value,
+       av.number_value,
+       av.date_value,
+       '${datasetName}' AS dataset_id
+FROM eda.attributevalue_${edaStudyStableId}_${edaEntityAbbrev} av,
+     eda.attributegraph_${edaStudyStableId}_${edaEntityAbbrev} ag,
+     (SELECT av.${edaEntityAbbrev}_stable_id, MIN(gi.gene) as string_value
+      FROM eda.attributevalue_${edaStudyStableId}_${edaEntityAbbrev} av
+      JOIN apidbtuning.GeneId gi ON gi.id = av.string_value
+      WHERE av.attribute_stable_id = 'VEUPATHDB_GENE_ID'
+      GROUP BY av.${edaEntityAbbrev}_stable_id) genes
+WHERE av.attribute_stable_id = ag.stable_id
+  AND av.${edaEntityAbbrev}_stable_id = genes.${edaEntityAbbrev}_stable_id
+  AND av.attribute_stable_id != 'VEUPATHDB_GENE_ID'
+>templateTextEnd<

From adf12571de96fa309ceefc74e8997ee6327ae1be Mon Sep 17 00:00:00 2001
From: John Brestelli <jbrestell@gmail.com>
Date: Tue, 14 Apr 2026 17:09:16 -0400
Subject: [PATCH 3/7] Add antibodyArrayEdaAttributeRef TEMPLATE_ANCHOR to
 transcriptRecord.xml

---
 Model/lib/wdk/model/records/transcriptRecord.xml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/Model/lib/wdk/model/records/transcriptRecord.xml b/Model/lib/wdk/model/records/transcriptRecord.xml
index 946385a18..c0fbefb5f 100644
--- a/Model/lib/wdk/model/records/transcriptRecord.xml
+++ b/Model/lib/wdk/model/records/transcriptRecord.xml
@@ -733,6 +733,8 @@
 
             <!-- TEMPLATE_ANCHOR cellularLocalizationEdaAttributeRef -->
 
+            <!-- TEMPLATE_ANCHOR antibodyArrayEdaAttributeRef -->
+
 
           <attributeQueryRef ref="TranscriptAttributes.NaSequenceDatabaseName" >
             <columnAttribute name="sequence_database_name" inReportMaker="false"/>

From 4d4f09178940abf7715226a6c2525526debd737b Mon Sep 17 00:00:00 2001
From: John Brestelli <jbrestell@gmail.com>
Date: Tue, 14 Apr 2026 17:11:14 -0400
Subject: [PATCH 4/7] Add EdaAntibodyArrayDatasets and
 EdaAntibodyArrayGraphsDataTable sqlQuery blocks

Add two new gene record graph table queries for antibody array EDA datasets
targeting PlasmoDB and UniDB. Follows the same pattern as existing EDA phenotype
queries but without the tgonGT1 special case, using category 'Immunology' and
assay_type 'Antibody Array'. Includes TEMPLATE_ANCHOR placeholders for both
the gene table SQL and the data table SQL.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 .../wdk/model/records/geneTableQueries.xml    | 105 ++++++++++++++++++
 1 file changed, 105 insertions(+)

diff --git a/Model/lib/wdk/model/records/geneTableQueries.xml b/Model/lib/wdk/model/records/geneTableQueries.xml
index 309b2a94b..d92be1e3a 100644
--- a/Model/lib/wdk/model/records/geneTableQueries.xml
+++ b/Model/lib/wdk/model/records/geneTableQueries.xml
@@ -1135,6 +1135,111 @@ from (
         </sqlQuery>
 
 
+       <sqlQuery name="EdaAntibodyArrayDatasets" includeProjects="PlasmoDB,UniDB">
+            <column name="source_id" />
+            <column name="project_id" />
+            <column name="project_id_url" />
+            <column name="graph_ids" />
+            <column name="default_graph_id" />
+            <column name="species" />
+            <column name="genus_species" />
+            <column name="mainOpen" />
+            <column name="dataOpen" />
+            <column name="display_name" />
+            <column name="description" />
+            <column name="has_graph_data"/>
+            <column name="has_meta_data"/>
+            <column name="meta_data_categories"/>
+            <column name="dataset_name"/>
+            <column name="dataset_id"/>
+            <column name="summary"/>
+            <column name="short_attribution"/>
+            <column name="assay_type"/>
+            <column name="plot_configs_json"/>
+            <sql>
+
+<![CDATA[
+select g.*
+     , CASE WHEN '@PROJECT_ID@' = 'UniDB' THEN 'EuPathDB' ELSE g.project_id END AS project_id_url
+     , regexp_substr(graph_ids, '[^,]*') as default_graph_id
+from (
+        select ga.source_id, ga.project_id,
+             ga.organism as gene_organism, ga.genus_species ,
+             psgene.profile_graph_id as graph_ids,
+             case when psgene.profile_graph_id is null then 0 else 1 end as has_graph_data,
+             'TRUE' as mainOpen, 'FALSE' as dataOpen,
+             'FALSE' has_meta_data, '' as meta_data_categories,
+             graph_descrip.*, dp.summary, dp.short_attribution, dp.display_name,
+             dp.description, 'Antibody Array' as assay_type, dp.dataset_presenter_id as dataset_id, dp.name as dataset_name
+      from webready.GeneAttributes_p ga,
+           apidbtuning.DatasetDatasource dds,
+           apidbtuning.datasetPresenter dp
+           LEFT JOIN (
+             SELECT dataset_name as graph_dataset_name,
+                    JSON_ARRAYAGG(
+                      JSON_OBJECT(
+                        'plotName' VALUE plot_name,
+                        'plotType' VALUE plot_type,
+                        'xAxisEntityId' VALUE x_axis_entity_id,
+                        'yAxisEntityId' VALUE y_axis_entity_id,
+                        'xAxisVariableId' VALUE x_axis_variable_id,
+                        'yAxisVariableId' VALUE y_axis_variable_id,
+                        'displaySpecVariableId' VALUE 'VEUPATHDB_GENE_ID',
+                        'displayMode' VALUE 'highlight',
+                        'xMin' VALUE x_min,
+                        'xMax' VALUE x_max,
+                        'yMin' VALUE y_min,
+                        'yMax' VALUE y_max
+                       )
+                      ) AS plot_configs_json
+             FROM apidbtuning.edagenegraph
+             GROUP BY graph_dataset_name
+           ) graph_descrip ON graph_descrip.graph_dataset_name = dp.name,
+           (WITH dataset_genes as (
+               SELECT '' as dataset_name, '' as source_id
+               -- TEMPLATE_ANCHOR antibodyArrayEdaGeneTableSql
+           )
+          select ga.source_id, p.dataset_name, p.source_id as profile_graph_id
+          from dataset_genes p
+          join webready.geneid_p gi on gi.id = p.source_id and gi.org_abbrev IN (%%PARTITION_KEYS%%)
+          join webready.GeneAttributes_p ga on ga.source_id = gi.gene and ga.org_abbrev IN (%%PARTITION_KEYS%%)
+            ) psgene
+        where ga.source_id = psgene.source_id
+          and psgene.dataset_name = dds.name
+          and dds.dataset_presenter_id = dp.dataset_presenter_id
+          and dds.category = 'Immunology'
+) g
+ ]]>
+       </sql>
+
+        </sqlQuery>
+
+
+          <sqlQuery name="EdaAntibodyArrayGraphsDataTable" isCacheable="false" includeProjects="PlasmoDB,UniDB">
+            <column name="source_id"/>
+            <column name="project_id"/>
+            <column name="dataset_id"/>
+            <column name="variable"/>
+            <column name="value"/>
+            <sql>
+            <![CDATA[
+SELECT ga.source_id, ga.project_id, gd.variable, coalesce(gd.string_value, coalesce(round(gd.number_value, 4)::text, gd.date_value::text)) AS value, gd.dataset_id
+FROM webready.GeneAttributes_p ga, (
+   SELECT '' as gene,
+          '' as variable,
+          '' as string_value,
+          0 as number_value,
+          DATE '2000-01-01' as date_value,
+          'HAPPY_BIRTHDAY' as dataset_id
+   -- TEMPLATE_ANCHOR antibodyArrayDataTableGeneTableSql
+   ) gd
+   WHERE ga.source_id = gd.gene
+     AND ga.org_abbrev IN (%%PARTITION_KEYS%%)
+        ]]>
+      </sql>
+    </sqlQuery>
+
+
     <sqlQuery name="PhenotypeScoreGraphs" includeProjects="PlasmoDB,UniDB">
       <column name="source_id" />
       <column name="project_id" />

From 7a50b6db1ebda322f6bda8249cd707c43828dd35 Mon Sep 17 00:00:00 2001
From: John Brestelli <jbrestell@gmail.com>
Date: Tue, 14 Apr 2026 17:12:28 -0400
Subject: [PATCH 5/7] Add EdaAntibodyArrayDatasets and
 EdaAntibodyArrayGraphsDataTable definitions to geneRecord.xml

---
 Model/lib/wdk/model/records/geneRecord.xml | 40 ++++++++++++++++++++++
 1 file changed, 40 insertions(+)

diff --git a/Model/lib/wdk/model/records/geneRecord.xml b/Model/lib/wdk/model/records/geneRecord.xml
index af8f7b216..1ad349dca 100644
--- a/Model/lib/wdk/model/records/geneRecord.xml
+++ b/Model/lib/wdk/model/records/geneRecord.xml
@@ -1343,6 +1343,46 @@ name" internal="true"/>
         </table>
 
 
+        <table name="EdaAntibodyArrayDatasets"
+                 displayName="Antibody Array Datasets"
+                 inReportMaker="false"
+                 includeProjects="PlasmoDB,UniDB"
+                 queryRef="GeneTables.EdaAntibodyArrayDatasets">
+
+            <columnAttribute internal="true" displayName="source_id" name="source_id"/>
+            <columnAttribute internal="true" displayName="project_id" name="project_id"/>
+            <columnAttribute internal="true" displayName="project_id_url" name="project_id_url"/>
+            <columnAttribute internal="true" displayName="graph_ids" name="graph_ids"/>
+            <columnAttribute internal="true" displayName="genus_species" name="genus_species"/>
+            <columnAttribute internal="true" displayName="mainOpen" name="mainOpen"/>
+            <columnAttribute internal="true" displayName="dataOpen" name="dataOpen"/>
+            <columnAttribute displayName="Name" name="display_name"/>
+            <columnAttribute internal="true" displayName="description" name="description"/>
+            <columnAttribute internal="true" displayName="has_graph_data" name="has_graph_data"/>
+            <columnAttribute internal="true" displayName="has_meta_data" name="has_meta_data"/>
+            <columnAttribute internal="true" displayName="meta_data_categories" name="meta_data_categories"/>
+            <columnAttribute internal="true" displayName="dataset_name" name="dataset_name"/>
+            <columnAttribute internal="true" displayName="dataset_id" name="dataset_id"/>
+            <columnAttribute displayName="Summary" name="summary"/>
+            <columnAttribute displayName="Attribution" name="short_attribution"/>
+            <columnAttribute displayName="Assay Type" name="assay_type"/>
+            <columnAttribute internal="true" displayName="DefaultGraphId" name="default_graph_id"/>
+            <columnAttribute internal="true"  displayName="Plots" name="plot_configs_json"/>
+
+            <propertyList name="hideDatasetLink"><value>true</value></propertyList>
+        </table>
+
+
+        <table name="EdaAntibodyArrayGraphsDataTable"
+                inReportMaker="false"
+                displayName="Antibody Array Graphs Data Table"
+                includeProjects="PlasmoDB,UniDB"
+                queryRef="GeneTables.EdaAntibodyArrayGraphsDataTable">
+            <columnAttribute name="dataset_id" displayName="Dataset" internal="true"/>
+            <columnAttribute name="variable" displayName="Variable"/>
+            <columnAttribute name="value" displayName="Value"/>
+        </table>
+
         <table name="PhenotypeScoreGraphs"
                  displayName="Phenotype Graphs"
                  inReportMaker="false"

From b5044757ab69a735f4c9345ad960e94b5eb2ae62 Mon Sep 17 00:00:00 2001
From: John Brestelli <jbrestel@upenn.edu>
Date: Wed, 15 Apr 2026 10:50:35 -0400
Subject: [PATCH 6/7] wip

---
 Model/lib/dst/antibodyArray.dst                            | 6 +++---
 Model/lib/wdk/model/records/transcriptAttributeQueries.xml | 2 ++
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/Model/lib/dst/antibodyArray.dst b/Model/lib/dst/antibodyArray.dst
index 65a4abb47..320e0a200 100644
--- a/Model/lib/dst/antibodyArray.dst
+++ b/Model/lib/dst/antibodyArray.dst
@@ -250,7 +250,7 @@ prop=includeProjects
     LEFT OUTER JOIN (
       SELECT * FROM public.crosstab(
         'SELECT gene_ids.gene_id,
-                CONCAT(''${edaStudyStableId}_'', anc.sample_stable_id) AS sample_col,
+                REPLACE(CONCAT(''${edaStudyStableId}_'', anc.sample_stable_id), ''.'', ''_'') AS sample_col,
                 av_int.number_value AS intensity
          FROM eda.attributevalue_${edaStudyStableId}_${edaEntityAbbrev} av_int
          JOIN eda.ancestors_${edaStudyStableId}_${edaEntityAbbrev} anc
@@ -263,7 +263,7 @@ prop=includeProjects
            ON gene_ids.${edaEntityAbbrev}_stable_id = av_int.${edaEntityAbbrev}_stable_id
          WHERE av_int.attribute_stable_id = ''NORMALIZED_INTENSITY''
          ORDER BY 1, 2',
-        'SELECT CONCAT(''${edaStudyStableId}_'', sample_stable_id) AS sample_col
+        'SELECT REPLACE(CONCAT(''${edaStudyStableId}_'', sample_stable_id), ''.'', ''_'') AS sample_col
          FROM (SELECT DISTINCT sample_stable_id
                FROM eda.ancestors_${edaStudyStableId}_${edaEntityAbbrev}) s
          ORDER BY sample_col'
@@ -285,7 +285,7 @@ prop=includeProjects
 
           <sql>
             <![CDATA[
-           SELECT CONCAT('${edaStudyStableId}_', sample_stable_id) AS name,
+           SELECT REPLACE(CONCAT('${edaStudyStableId}_', sample_stable_id), '.', '_') AS name,
                   sample_stable_id::text AS display_name,
                   'number' AS column_type,
                   'Normalized intensity from ${datasetName}' AS help,
diff --git a/Model/lib/wdk/model/records/transcriptAttributeQueries.xml b/Model/lib/wdk/model/records/transcriptAttributeQueries.xml
index 869b3d98f..1819b760f 100644
--- a/Model/lib/wdk/model/records/transcriptAttributeQueries.xml
+++ b/Model/lib/wdk/model/records/transcriptAttributeQueries.xml
@@ -192,6 +192,8 @@
 
     <!-- TEMPLATE_ANCHOR cellularLocalizationEdaAttributeQueriesString -->
 
+    <!-- TEMPLATE_ANCHOR antibodyArrayEdaAttributeQueriesNumeric -->
+
     <!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
     <!-- Transcripts per gene -->
     <!-- ATTENTION: this SQL cannot be used by a boolean step because it does not have the matched_result dynamic column -->

From 642b3c9d00e75f4fe107b7c7907d544444982177 Mon Sep 17 00:00:00 2001
From: John Brestelli <jbrestel@upenn.edu>
Date: Wed, 15 Apr 2026 17:09:34 -0400
Subject: [PATCH 7/7] Add ByDataset antibody array EDA templates and fix
 individuals.txt category anchors
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

- Add antibodyArrayEdaAttributeQueriesNumericByDataset, antibodyArrayEdaAttributeRefByDataset,
  and antibodyArrayEdaAttributeCategoryByDataset DST templates for datasets split by sub-dataset
- Add TEMPLATE_ANCHOR entries in transcriptAttributeQueries.xml and transcriptRecord.xml for ByDataset variants
- Add TEMPLATE_ANCHOR antibodyArrayEdaAttributeCategory and antibodyArrayEdaAttributeCategoryByDataset
  to individuals.txt — these were missing, causing per-sample intensity columns to have no UI category
- Fix column alignment in antibodyArrayEdaAttributeCategory individuals.txt template

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 Model/lib/dst/antibodyArray.dst               | 436 +++++++++++-------
 .../records/transcriptAttributeQueries.xml    |   2 +
 .../wdk/model/records/transcriptRecord.xml    |   2 +
 Model/lib/wdk/ontology/individuals.txt        |   2 +
 4 files changed, 281 insertions(+), 161 deletions(-)

diff --git a/Model/lib/dst/antibodyArray.dst b/Model/lib/dst/antibodyArray.dst
index 320e0a200..55340f10e 100644
--- a/Model/lib/dst/antibodyArray.dst
+++ b/Model/lib/dst/antibodyArray.dst
@@ -5,15 +5,15 @@ prop=datasetName
 prop=projectName
 >templateTextStart<
       <sqlQuery name="MetadataDataset${datasetName}">
-             <column name="internal"/>
-             <column name="term"/>
-          <sql>
-           <![CDATA[
-             SELECT '${datasetName}' AS term,
-                    '${datasetName}' AS internal
-            ]]>
-          </sql>
-        </sqlQuery>
+	     <column name="internal"/>
+	     <column name="term"/>
+	  <sql>
+	   <![CDATA[
+	     SELECT '${datasetName}' AS term,
+		    '${datasetName}' AS internal
+	    ]]>
+	  </sql>
+	</sqlQuery>
 
 >templateTextEnd<
 
@@ -40,70 +40,70 @@ prop=includeProjectsExcludeEuPathDB
 >templateTextStart<
 
     <question name="GenesByAntibodyArray${datasetName}" includeProjects="${includeProjects}" newBuild="${buildNumberIntroduced}"
-         displayName="${organismAbbrevDisplay} ${datasetDisplayName} Antibody Array (p-value)"
-         shortDisplayName="${datasetShortDisplayName} (p-val)"
-         searchCategory="Host Response"
-         queryRef="GeneId.GenesByTTestWithMetadata"
-         recordClassRef="TranscriptRecordClasses.TranscriptRecordClass">
+	 displayName="${organismAbbrevDisplay} ${datasetDisplayName} Antibody Array (p-value)"
+	 shortDisplayName="${datasetShortDisplayName} (p-val)"
+	 searchCategory="Host Response"
+	 queryRef="GeneId.GenesByTTestWithMetadata"
+	 recordClassRef="TranscriptRecordClasses.TranscriptRecordClass">
 
-        <paramRef ref="sharedParams.metadata_datasets" queryRef="GeneVQ.MetadataDataset${datasetName}" visible="false"/>
+	<paramRef ref="sharedParams.metadata_datasets" queryRef="GeneVQ.MetadataDataset${datasetName}" visible="false"/>
 
 <sqlParamValue name="function">'${function}'</sqlParamValue> 
 	<attributesList includeProjects="${includeProjectsExcludeEuPathDB}"
 	   summary="organism,gene_product,p_value, avg_group_two,avg_group_one,dynamic_graph"
-            sorting="p_value asc" /> 
+	    sorting="p_value asc" /> 
 
        <attributesList includeProjects="EuPathDB"
-              summary="organism,gene_product,p_value, avg_group_two,avg_group_one"
-              sorting="p_value asc"         
-        /> 
-
-        <summary>
-            <![CDATA[ 
-           Find genes based on Immune Response in Clinical Isolates.
-            ]]>
-        </summary>
-
-        <description>
-            <![CDATA[
-             Find genes based on Immune Response in Clinical Isolates. <br />
-             ${optionalQuestionDescription}
-            ]]>
-        </description>
-        <dynamicAttributes>
-           <columnAttribute name="p_value" displayName="P Value" align="center"
-                            help="p-value based on t-test for independent samples with unequal variances">
-	        <reporter name="histogram" displayName="Histogram" scopes=""                                                                     
-                  implementation="org.gusdb.wdk.model.report.reporter.HistogramAttributeReporter">                                               
-                  <description>Display the histogram of the values of this attribute</description>                                               
-                  <property name="type">float</property>
-                </reporter>
+	      summary="organism,gene_product,p_value, avg_group_two,avg_group_one"
+	      sorting="p_value asc"	    
+	/> 
+
+	<summary>
+	    <![CDATA[ 
+	   Find genes based on Immune Response in Clinical Isolates.
+	    ]]>
+	</summary>
+
+	<description>
+	    <![CDATA[
+	     Find genes based on Immune Response in Clinical Isolates. <br />
+	     ${optionalQuestionDescription}
+	    ]]>
+	</description>
+	<dynamicAttributes>
+	   <columnAttribute name="p_value" displayName="P Value" align="center"
+			    help="p-value based on t-test for independent samples with unequal variances">
+		<reporter name="histogram" displayName="Histogram" scopes=""									 
+		  implementation="org.gusdb.wdk.model.report.reporter.HistogramAttributeReporter">						 
+		  <description>Display the histogram of the values of this attribute</description>						 
+		  <property name="type">float</property>
+		</reporter>
 	  </columnAttribute>
-           <columnAttribute name="avg_group_one" displayName="Avg Comp ${function_display}" align="center" 
-                            help="$$function_help$$ comparison samples">
-	        <reporter name="histogram" displayName="Histogram" scopes=""                                                                     
-                  implementation="org.gusdb.wdk.model.report.reporter.HistogramAttributeReporter">                                               
-                  <description>Display the histogram of the values of this attribute</description>                                               
-                  <property name="type">int</property>
-                </reporter>
+	   <columnAttribute name="avg_group_one" displayName="Avg Comp ${function_display}" align="center" 
+			    help="$$function_help$$ comparison samples">
+		<reporter name="histogram" displayName="Histogram" scopes=""									 
+		  implementation="org.gusdb.wdk.model.report.reporter.HistogramAttributeReporter">						 
+		  <description>Display the histogram of the values of this attribute</description>						 
+		  <property name="type">int</property>
+		</reporter>
 	  </columnAttribute>
-           <columnAttribute name="avg_group_two" displayName="Avg Ref ${function_display}" align="center"
-                            help="$$function_help$$ reference samples">
-	        <reporter name="histogram" displayName="Histogram" scopes=""                                                                     
-                  implementation="org.gusdb.wdk.model.report.reporter.HistogramAttributeReporter">                                               
-                  <description>Display the histogram of the values of this attribute</description>                                               
-                  <property name="type">int</property>
-                </reporter>
+	   <columnAttribute name="avg_group_two" displayName="Avg Ref ${function_display}" align="center"
+			    help="$$function_help$$ reference samples">
+		<reporter name="histogram" displayName="Histogram" scopes=""									 
+		  implementation="org.gusdb.wdk.model.report.reporter.HistogramAttributeReporter">						 
+		  <description>Display the histogram of the values of this attribute</description>						 
+		  <property name="type">int</property>
+		</reporter>
 	  </columnAttribute>
-           <textAttribute name="dynamic_graph" displayName="Expression - graph"
-                        inReportMaker="false" truncateTo="100000" sortable="false" includeProjects="${includeProjectsExcludeEuPathDB}">
-           <text>
-                <![CDATA[
-                <img src="/cgi-bin/dataPlotter.pl?type=${graphModule}&project_id=${projectName}&id=$$primary_key$$&template=0&dataset=${datasetName}&fmt=png&thumb=1"/>
-                ]]>
-           </text>
-           </textAttribute>
-        </dynamicAttributes>
+	   <textAttribute name="dynamic_graph" displayName="Expression - graph"
+			inReportMaker="false" truncateTo="100000" sortable="false" includeProjects="${includeProjectsExcludeEuPathDB}">
+	   <text>
+		<![CDATA[
+		<img src="/cgi-bin/dataPlotter.pl?type=${graphModule}&project_id=${projectName}&id=$$primary_key$$&template=0&dataset=${datasetName}&fmt=png&thumb=1"/>
+		]]>
+	   </text>
+	   </textAttribute>
+	</dynamicAttributes>
 
     </question>
 
@@ -123,11 +123,11 @@ prop=includeProjectsExcludeEuPathDB
 			  displayName="${datasetShortDisplayName} - Intensity Graph"
 			  inReportMaker="false" truncateTo="100000" sortable="false"
 			  includeProjects="${includeProjectsExcludeEuPathDB}">
-              <text>
-                <![CDATA[
-                <img src="/cgi-bin/dataPlotter.pl?type=${graphModule}&project_id=${projectName}&template=1&fmt=png&id=$$primary_key$$&dataset=${datasetName}&vp=_LEGEND,xy_scatter&thumb=1"/>
-                ]]>
-              </text>
+	      <text>
+		<![CDATA[
+		<img src="/cgi-bin/dataPlotter.pl?type=${graphModule}&project_id=${projectName}&template=1&fmt=png&id=$$primary_key$$&dataset=${datasetName}&vp=_LEGEND,xy_scatter&thumb=1"/>
+		]]>
+	      </text>
 	   </textAttribute>
 >templateTextEnd<
 
@@ -137,7 +137,7 @@ anchorFile=ApiCommonModel/Model/lib/wdk/model/questions/categories.xml
 prop=datasetName
 prop=includeProjects
 >templateTextStart<
-            <questionRef includeProjects="${includeProjects}">GeneQuestions.GenesByAntibodyArray${datasetName}</questionRef>
+	    <questionRef includeProjects="${includeProjects}">GeneQuestions.GenesByAntibodyArray${datasetName}</questionRef>
 >templateTextEnd<
 
 [templateStart]
@@ -152,27 +152,27 @@ prop=includeProjects
 prop=antibodyArrayWdkAttributes
 >templateTextStart<
     <question name="GenesByAntibodyArrayEdaSubset_${datasetName}" includeProjects="${includeProjects}" newBuild="${buildNumberIntroduced}"
-         displayName="${datasetDisplayName} Antibody Array"
-         shortDisplayName="${datasetShortDisplayName} (QAA)"
-         queryRef="GeneId.GenesByEdaVizWithCompute"
-         recordClassRef="TranscriptRecordClasses.TranscriptRecordClass">
+	 displayName="${datasetDisplayName} Antibody Array"
+	 shortDisplayName="${datasetShortDisplayName} (QAA)"
+	 queryRef="GeneId.GenesByEdaVizWithCompute"
+	 recordClassRef="TranscriptRecordClasses.TranscriptRecordClass">
 
-        <paramRef ref="geneParams.eda_dataset_id" default="${presenterId}" visible="false"/>
-        <paramRef ref="geneParams.eda_analysis_spec" allowEmpty="true" prompt="Filter genes based on antibody array data"/>
+	<paramRef ref="geneParams.eda_dataset_id" default="${presenterId}" visible="false"/>
+	<paramRef ref="geneParams.eda_analysis_spec" allowEmpty="true" prompt="Filter genes based on antibody array data"/>
 
-        <propertyList name="edaNotebookType">
-          <value>antibodyArrayNotebook</value>
-        </propertyList>
+	<propertyList name="edaNotebookType">
+	  <value>antibodyArrayNotebook</value>
+	</propertyList>
 
-         <attributesList
-              summary="organism,gene_product,effectSize,pValue"
-              sorting="effectSize desc" />
+	 <attributesList
+	      summary="organism,gene_product,effectSize,pValue"
+	      sorting="effectSize desc" />
   <!-- TO ADD  ${antibodyArrayWdkAttributes} -->
 
 	<summary><![CDATA[
-        Find genes with differential expression in antibody array data based on EDA analysis.
-          ]]>
-        </summary>
+	Find genes with differential expression in antibody array data based on EDA analysis.
+	  ]]>
+	</summary>
     <description> <![CDATA[
 Find proteins with differential abundance between two groups of samples in an antibody array experiment.
 This search uses a guided notebook within the site that runs Limma, a widely-used statistical method for analysing microarray and antibody array data (Ritchie et al., 2015).
@@ -206,24 +206,24 @@ A lower p-value (raw or adjusted) indicates a more statistically confident call.
 <u>Removing outliers</u>: If the PCA plot reveals samples that cluster away from the rest (potential outliers or contaminated arrays), you can exclude them using the <b>Select Samples</b> step at the top of the notebook.
 Apply a filter on the sample identifier or a metadata variable to remove those samples before running Limma.
 Note that changing the sample subset will reset any group assignments you have already made in the Limma step, so it is best to check the PCA first before defining your groups.
-          ]]>
-        </description>
-        <dynamicAttributes>
-           <columnAttribute name="effectSize" displayName="Effect Size" align="center">
-                <reporter name="histogram" displayName="Histogram" scopes=""
-                  implementation="org.gusdb.wdk.model.report.reporter.HistogramAttributeReporter">
-                  <description>Display the histogram of the values of this attribute</description>
-                  <property name="type">float</property>
-                </reporter>
-           </columnAttribute>
-           <columnAttribute name="pValue" displayName="P-Value" align="center">
-                <reporter name="histogram" displayName="Histogram" scopes=""
-                  implementation="org.gusdb.wdk.model.report.reporter.HistogramAttributeReporter">
-                  <description>Display the histogram of the values of this attribute</description>
-                  <property name="type">float</property>
-                </reporter>
-          </columnAttribute>
-        </dynamicAttributes>
+	  ]]>
+	</description>
+	<dynamicAttributes>
+	   <columnAttribute name="effectSize" displayName="Effect Size" align="center">
+		<reporter name="histogram" displayName="Histogram" scopes=""
+		  implementation="org.gusdb.wdk.model.report.reporter.HistogramAttributeReporter">
+		  <description>Display the histogram of the values of this attribute</description>
+		  <property name="type">float</property>
+		</reporter>
+	   </columnAttribute>
+	   <columnAttribute name="pValue" displayName="P-Value" align="center">
+		<reporter name="histogram" displayName="Histogram" scopes=""
+		  implementation="org.gusdb.wdk.model.report.reporter.HistogramAttributeReporter">
+		  <description>Display the histogram of the values of this attribute</description>
+		  <property name="type">float</property>
+		</reporter>
+	  </columnAttribute>
+	</dynamicAttributes>
     </question>
 >templateTextEnd<
 
@@ -236,69 +236,69 @@ prop=edaStudyStableId
 prop=edaEntityAbbrev
 prop=includeProjects
 >templateTextStart<
-        <sqlQuery name="AntibodyArrayIntensities${datasetName}"
-                  doNotTest="true"
-                  attributeMetaQueryRef="TranscriptAttributes.MetaAntibodyArrayIntensities${datasetName}"
-                  includeProjects="${includeProjects}">
-            <column name="source_id"/>
-            <column name="gene_source_id"/>
-            <column name="project_id"/>
-            <sql>
-              <![CDATA[
+	<sqlQuery name="AntibodyArrayIntensities${datasetName}"
+		  doNotTest="true"
+		  attributeMetaQueryRef="TranscriptAttributes.MetaAntibodyArrayIntensities${datasetName}"
+		  includeProjects="${includeProjects}">
+	    <column name="source_id"/>
+	    <column name="gene_source_id"/>
+	    <column name="project_id"/>
+	    <sql>
+	      <![CDATA[
   SELECT ta.source_id, ta.project_id, ta.gene_source_id, p.*
   FROM apidbtuning.TranscriptAttributes ta
     LEFT OUTER JOIN (
       SELECT * FROM public.crosstab(
-        'SELECT gene_ids.gene_id,
-                REPLACE(CONCAT(''${edaStudyStableId}_'', anc.sample_stable_id), ''.'', ''_'') AS sample_col,
-                av_int.number_value AS intensity
-         FROM eda.attributevalue_${edaStudyStableId}_${edaEntityAbbrev} av_int
-         JOIN eda.ancestors_${edaStudyStableId}_${edaEntityAbbrev} anc
-           ON anc.${edaEntityAbbrev}_stable_id = av_int.${edaEntityAbbrev}_stable_id
-         JOIN (SELECT av.${edaEntityAbbrev}_stable_id, MIN(gi.gene) AS gene_id
-               FROM eda.attributevalue_${edaStudyStableId}_${edaEntityAbbrev} av
-               JOIN apidbtuning.GeneId gi ON gi.id = av.string_value
-               WHERE av.attribute_stable_id = ''VEUPATHDB_GENE_ID''
-               GROUP BY av.${edaEntityAbbrev}_stable_id) gene_ids
-           ON gene_ids.${edaEntityAbbrev}_stable_id = av_int.${edaEntityAbbrev}_stable_id
-         WHERE av_int.attribute_stable_id = ''NORMALIZED_INTENSITY''
-         ORDER BY 1, 2',
-        'SELECT REPLACE(CONCAT(''${edaStudyStableId}_'', sample_stable_id), ''.'', ''_'') AS sample_col
-         FROM (SELECT DISTINCT sample_stable_id
-               FROM eda.ancestors_${edaStudyStableId}_${edaEntityAbbrev}) s
-         ORDER BY sample_col'
+	'SELECT gene_ids.gene_id,
+		REPLACE(CONCAT(''${edaStudyStableId}_'', anc.sample_stable_id), ''.'', ''_'') AS sample_col,
+		av_int.number_value AS intensity
+	 FROM eda.attributevalue_${edaStudyStableId}_${edaEntityAbbrev} av_int
+	 JOIN eda.ancestors_${edaStudyStableId}_${edaEntityAbbrev} anc
+	   ON anc.${edaEntityAbbrev}_stable_id = av_int.${edaEntityAbbrev}_stable_id
+	 JOIN (SELECT av.${edaEntityAbbrev}_stable_id, MIN(gi.gene) AS gene_id
+	       FROM eda.attributevalue_${edaStudyStableId}_${edaEntityAbbrev} av
+	       JOIN apidbtuning.GeneId gi ON gi.id = av.string_value
+	       WHERE av.attribute_stable_id = ''VEUPATHDB_GENE_ID''
+	       GROUP BY av.${edaEntityAbbrev}_stable_id) gene_ids
+	   ON gene_ids.${edaEntityAbbrev}_stable_id = av_int.${edaEntityAbbrev}_stable_id
+	 WHERE av_int.attribute_stable_id = ''NORMALIZED_INTENSITY''
+	 ORDER BY 1, 2',
+	'SELECT REPLACE(CONCAT(''${edaStudyStableId}_'', sample_stable_id), ''.'', ''_'') AS sample_col
+	 FROM (SELECT DISTINCT sample_stable_id
+	       FROM eda.ancestors_${edaStudyStableId}_${edaEntityAbbrev}) s
+	 ORDER BY sample_col'
       ) AS ct(gene_id text, &&META_ATTRIBUTE_COLUMNS_FOR_CROSSTAB&&)
     ) p ON ta.gene_source_id = p.gene_id
-              ]]>
-            </sql>
-        </sqlQuery>
+	      ]]>
+	    </sql>
+	</sqlQuery>
 
        <sqlQuery name="MetaAntibodyArrayIntensities${datasetName}" includeProjects="${includeProjects}">
-          <column name="name" />
-          <column name="display_name" />
-          <column name="help" />
-          <column name="reporter_name" />
-          <column name="reporter_display" />
-          <column name="reporter_description" />
-          <column name="reporter_implementation" />
-          <column name="reporter_properties" />
-
-          <sql>
-            <![CDATA[
-           SELECT REPLACE(CONCAT('${edaStudyStableId}_', sample_stable_id), '.', '_') AS name,
-                  sample_stable_id::text AS display_name,
-                  'number' AS column_type,
-                  'Normalized intensity from ${datasetName}' AS help,
-                  'histogram' AS reporter_name,
-                  'Histogram' AS reporter_display,
-                  'Display a histogram of the values' AS reporter_description,
-                  'org.gusdb.wdk.model.report.reporter.HistogramAttributeReporter' AS reporter_implementation,
-                  null AS reporter_properties
-           FROM (SELECT DISTINCT sample_stable_id
-                 FROM eda.ancestors_${edaStudyStableId}_${edaEntityAbbrev}) s
-           ORDER BY sample_stable_id
-            ]]>
-          </sql>
+	  <column name="name" />
+	  <column name="display_name" />
+	  <column name="help" />
+	  <column name="reporter_name" />
+	  <column name="reporter_display" />
+	  <column name="reporter_description" />
+	  <column name="reporter_implementation" />
+	  <column name="reporter_properties" />
+
+	  <sql>
+	    <![CDATA[
+	   SELECT REPLACE(CONCAT('${edaStudyStableId}_', sample_stable_id), '.', '_') AS name,
+		  sample_stable_id::text AS display_name,
+		  'number' AS column_type,
+		  'Normalized intensity from ${datasetName}' AS help,
+		  'histogram' AS reporter_name,
+		  'Histogram' AS reporter_display,
+		  'Display a histogram of the values' AS reporter_description,
+		  'org.gusdb.wdk.model.report.reporter.HistogramAttributeReporter' AS reporter_implementation,
+		  null AS reporter_properties
+	   FROM (SELECT DISTINCT sample_stable_id
+		 FROM eda.ancestors_${edaStudyStableId}_${edaEntityAbbrev}) s
+	   ORDER BY sample_stable_id
+	    ]]>
+	  </sql>
        </sqlQuery>
 >templateTextEnd<
 
@@ -309,8 +309,98 @@ anchorFile=ApiCommonModel/Model/lib/wdk/model/records/transcriptRecord.xml
 prop=datasetName
 prop=includeProjects
 >templateTextStart<
-              <attributeQueryRef ref="TranscriptAttributes.AntibodyArrayIntensities${datasetName}" attributeMetaQueryRef="TranscriptAttributes.MetaAntibodyArrayIntensities${datasetName}" includeProjects="${includeProjects}">
-              </attributeQueryRef>
+	      <attributeQueryRef ref="TranscriptAttributes.AntibodyArrayIntensities${datasetName}" attributeMetaQueryRef="TranscriptAttributes.MetaAntibodyArrayIntensities${datasetName}" includeProjects="${includeProjects}">
+	      </attributeQueryRef>
+>templateTextEnd<
+
+
+[templateStart]
+name=antibodyArrayEdaAttributeQueriesNumericByDataset
+anchorFile=ApiCommonModel/Model/lib/wdk/model/records/transcriptAttributeQueries.xml
+prop=datasetName
+prop=edaStudyStableId
+prop=edaEntityAbbrev
+prop=includeProjects
+prop=subDatasetSuffix
+prop=subDatasetFilterValue
+prop=subDatasetAttributeStableId
+>templateTextStart<
+	<sqlQuery name="AntibodyArrayIntensities${datasetName}_${subDatasetSuffix}"
+		  doNotTest="true"
+		  attributeMetaQueryRef="TranscriptAttributes.MetaAntibodyArrayIntensities${datasetName}_${subDatasetSuffix}"
+		  includeProjects="${includeProjects}">
+	    <column name="source_id"/>
+	    <column name="gene_source_id"/>
+	    <column name="project_id"/>
+	    <sql>
+	      <![CDATA[
+  SELECT ta.source_id, ta.project_id, ta.gene_source_id, p.*
+  FROM apidbtuning.TranscriptAttributes ta
+    LEFT OUTER JOIN (
+      SELECT * FROM public.crosstab(
+	'SELECT gene_ids.gene_id,
+		REPLACE(CONCAT(''${edaStudyStableId}_'', anc.sample_stable_id), ''.'', ''_'') AS sample_col,
+		av_int.number_value AS intensity
+	 FROM eda.attributevalue_${edaStudyStableId}_${edaEntityAbbrev} av_int
+	 JOIN eda.ancestors_${edaStudyStableId}_${edaEntityAbbrev} anc
+	   ON anc.${edaEntityAbbrev}_stable_id = av_int.${edaEntityAbbrev}_stable_id
+	 JOIN (SELECT av.${edaEntityAbbrev}_stable_id, MIN(gi.gene) AS gene_id
+	       FROM eda.attributevalue_${edaStudyStableId}_${edaEntityAbbrev} av
+	       JOIN apidbtuning.GeneId gi ON gi.id = av.string_value
+	       WHERE av.attribute_stable_id = ''VEUPATHDB_GENE_ID''
+	       GROUP BY av.${edaEntityAbbrev}_stable_id) gene_ids
+	   ON gene_ids.${edaEntityAbbrev}_stable_id = av_int.${edaEntityAbbrev}_stable_id
+	 JOIN eda.attributevalue_${edaStudyStableId}_${edaEntityAbbrev} av_dataset
+	   ON av_dataset.${edaEntityAbbrev}_stable_id = av_int.${edaEntityAbbrev}_stable_id
+	  AND av_dataset.attribute_stable_id = ''${subDatasetAttributeStableId}''
+	  AND av_dataset.string_value = ''${subDatasetFilterValue}''
+	 WHERE av_int.attribute_stable_id = ''NORMALIZED_INTENSITY''
+	 ORDER BY 1, 2',
+	'SELECT REPLACE(CONCAT(''${edaStudyStableId}_'', s.sample_stable_id), ''.'', ''_'') AS sample_col
+	 FROM (SELECT DISTINCT anc.sample_stable_id
+	       FROM eda.ancestors_${edaStudyStableId}_${edaEntityAbbrev} anc
+	       JOIN eda.attributevalue_${edaStudyStableId}_${edaEntityAbbrev} av_dataset
+		 ON av_dataset.${edaEntityAbbrev}_stable_id = anc.${edaEntityAbbrev}_stable_id
+		AND av_dataset.attribute_stable_id = ''${subDatasetAttributeStableId}''
+		AND av_dataset.string_value = ''${subDatasetFilterValue}'') s
+	 ORDER BY sample_col'
+      ) AS ct(gene_id text, &&META_ATTRIBUTE_COLUMNS_FOR_CROSSTAB&&)
+    ) p ON ta.gene_source_id = p.gene_id
+	      ]]>
+	    </sql>
+	</sqlQuery>
+
+       <sqlQuery name="MetaAntibodyArrayIntensities${datasetName}_${subDatasetSuffix}" includeProjects="${includeProjects}">
+	  <column name="name" />
+	  <column name="display_name" />
+	  <column name="help" />
+	  <column name="reporter_name" />
+	  <column name="reporter_display" />
+	  <column name="reporter_description" />
+	  <column name="reporter_implementation" />
+	  <column name="reporter_properties" />
+
+	  <sql>
+	    <![CDATA[
+	   SELECT REPLACE(CONCAT('${edaStudyStableId}_', s.sample_stable_id), '.', '_') AS name,
+		  s.sample_stable_id::text AS display_name,
+		  'number' AS column_type,
+		  'Normalized intensity from ${datasetName} (${subDatasetSuffix})' AS help,
+		  'histogram' AS reporter_name,
+		  'Histogram' AS reporter_display,
+		  'Display a histogram of the values' AS reporter_description,
+		  'org.gusdb.wdk.model.report.reporter.HistogramAttributeReporter' AS reporter_implementation,
+		  null AS reporter_properties
+	   FROM (SELECT DISTINCT anc.sample_stable_id
+		 FROM eda.ancestors_${edaStudyStableId}_${edaEntityAbbrev} anc
+		 JOIN eda.attributevalue_${edaStudyStableId}_${edaEntityAbbrev} av_dataset
+		   ON av_dataset.${edaEntityAbbrev}_stable_id = anc.${edaEntityAbbrev}_stable_id
+		  AND av_dataset.attribute_stable_id = '${subDatasetAttributeStableId}'
+		  AND av_dataset.string_value = '${subDatasetFilterValue}') s
+	   ORDER BY s.sample_stable_id
+	    ]]>
+	  </sql>
+       </sqlQuery>
 >templateTextEnd<
 
 
@@ -320,8 +410,32 @@ anchorFile=ApiCommonModel/Model/lib/wdk/ontology/individuals.txt
 prop=datasetName
 prop=datasetDisplayName
 >templateTextStart<
-AntibodyArrayDataset_${datasetName}	http://edamontology.org/topic_3360	Immunology	DatasetRecordClasses.DatasetRecordClass	dataset	${datasetName}	${datasetDisplayName}	results
-TranscriptAttributes.MetaAntibodyArrayIntensities${datasetName}	AntibodyArrayDataset_${datasetName}		TranscriptRecordClasses.TranscriptRecordClass	attributeMetaQuery	MetaAntibodyArrayIntensities${datasetName}			gene		results	download
+AntibodyArrayDataset_${datasetName}	http://edamontology.org/topic_3360	Immunology	DatasetRecordClasses.DatasetRecordClass	dataset	${datasetName}	${datasetDisplayName}						results
+TranscriptAttributes.MetaAntibodyArrayIntensities${datasetName}	AntibodyArrayDataset_${datasetName}		TranscriptRecordClasses.TranscriptRecordClass	attributeMetaQuery	MetaAntibodyArrayIntensities${datasetName}				gene		results	download
+>templateTextEnd<
+
+
+[templateStart]
+name=antibodyArrayEdaAttributeRefByDataset
+anchorFile=ApiCommonModel/Model/lib/wdk/model/records/transcriptRecord.xml
+prop=datasetName
+prop=subDatasetSuffix
+prop=includeProjects
+>templateTextStart<
+              <attributeQueryRef ref="TranscriptAttributes.AntibodyArrayIntensities${datasetName}_${subDatasetSuffix}" attributeMetaQueryRef="TranscriptAttributes.MetaAntibodyArrayIntensities${datasetName}_${subDatasetSuffix}" includeProjects="${includeProjects}">
+              </attributeQueryRef>
+>templateTextEnd<
+
+
+[templateStart]
+name=antibodyArrayEdaAttributeCategoryByDataset
+anchorFile=ApiCommonModel/Model/lib/wdk/ontology/individuals.txt
+prop=datasetName
+prop=datasetDisplayName
+prop=subDatasetSuffix
+>templateTextStart<
+AntibodyArrayDataset_${datasetName}_${subDatasetSuffix}	http://edamontology.org/topic_3360	Immunology	DatasetRecordClasses.DatasetRecordClass	dataset	${datasetName}	${datasetDisplayName} (${subDatasetSuffix})						results
+TranscriptAttributes.MetaAntibodyArrayIntensities${datasetName}_${subDatasetSuffix}	AntibodyArrayDataset_${datasetName}_${subDatasetSuffix}		TranscriptRecordClasses.TranscriptRecordClass	attributeMetaQuery	MetaAntibodyArrayIntensities${datasetName}_${subDatasetSuffix}				gene		results	download
 >templateTextEnd<
 
 
diff --git a/Model/lib/wdk/model/records/transcriptAttributeQueries.xml b/Model/lib/wdk/model/records/transcriptAttributeQueries.xml
index 1819b760f..a761760a2 100644
--- a/Model/lib/wdk/model/records/transcriptAttributeQueries.xml
+++ b/Model/lib/wdk/model/records/transcriptAttributeQueries.xml
@@ -194,6 +194,8 @@
 
     <!-- TEMPLATE_ANCHOR antibodyArrayEdaAttributeQueriesNumeric -->
 
+    <!-- TEMPLATE_ANCHOR antibodyArrayEdaAttributeQueriesNumericByDataset -->
+
     <!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
     <!-- Transcripts per gene -->
     <!-- ATTENTION: this SQL cannot be used by a boolean step because it does not have the matched_result dynamic column -->
diff --git a/Model/lib/wdk/model/records/transcriptRecord.xml b/Model/lib/wdk/model/records/transcriptRecord.xml
index c0fbefb5f..2bbcd4726 100644
--- a/Model/lib/wdk/model/records/transcriptRecord.xml
+++ b/Model/lib/wdk/model/records/transcriptRecord.xml
@@ -735,6 +735,8 @@
 
             <!-- TEMPLATE_ANCHOR antibodyArrayEdaAttributeRef -->
 
+            <!-- TEMPLATE_ANCHOR antibodyArrayEdaAttributeRefByDataset -->
+
 
           <attributeQueryRef ref="TranscriptAttributes.NaSequenceDatabaseName" >
             <columnAttribute name="sequence_database_name" inReportMaker="false"/>
diff --git a/Model/lib/wdk/ontology/individuals.txt b/Model/lib/wdk/ontology/individuals.txt
index 8d3a2aa60..916ea2d34 100644
--- a/Model/lib/wdk/ontology/individuals.txt
+++ b/Model/lib/wdk/ontology/individuals.txt
@@ -916,6 +916,8 @@ derisi_timeseries_pie	http://purl.obolibrary.org/obo/OBI_0001985		PathwayRecordC
 ## TEMPLATE_ANCHOR profileMinMaxAttributesRnaAntisenseCategory
 ## TEMPLATE_ANCHOR phenotypeEdaAttributeCategory
 ## TEMPLATE_ANCHOR cellularLocalizationEdaAttributeCategory
+## TEMPLATE_ANCHOR antibodyArrayEdaAttributeCategory
+## TEMPLATE_ANCHOR antibodyArrayEdaAttributeCategoryByDataset
 
 ## TEMPLATE_ANCHOR metaboliteGraphTextAttributeCategory													
 ## TEMPLATE_ANCHOR graphTextAttributeCategoryPathwayRecord