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Add EdaPhenotypeDataTable and EdaCellularLocalizationDataTable WDK tables #192

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5d7fee8
Add design spec for EdaPhenotypeDataTable and EdaCellularLocalization…
jbrestel May 19, 2026
02546cc
Fix spec: correct stub row columns and ORDER BY placement
jbrestel May 19, 2026
64590bb
Add implementation plan for EDA all-data tables
jbrestel May 19, 2026
3a39bb9
feat: add phenotypeAllDataGeneTableSql template to phenotype.dst
jbrestel May 19, 2026
ff38a50
feat: add cellularLocalizationAllDataGeneTableSql template to cellula…
jbrestel May 19, 2026
dfd5e9a
feat: add EdaPhenotypeDataTable sqlQuery to geneTableQueries.xml
jbrestel May 19, 2026
9f3aed8
feat: add EdaCellularLocalizationDataTable sqlQuery to geneTableQueri…
jbrestel May 19, 2026
b099204
feat: add EdaPhenotypeDataTable and EdaCellularLocalizationDataTable …
jbrestel May 19, 2026
03bf239
feat: add ontology entries for EdaPhenotypeDataTable and EdaCellularL…
jbrestel May 19, 2026
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29 changes: 29 additions & 0 deletions Model/lib/dst/cellularLocalization.dst
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Original file line number Diff line number Diff line change
Expand Up @@ -125,6 +125,35 @@ WHERE av.attribute_stable_id = ag.stable_id
>templateTextEnd<


[templateStart]
name=cellularLocalizationAllDataGeneTableSql
anchorFile=ApiCommonModel/Model/lib/wdk/model/records/geneTableQueries.xml
prop=datasetName
prop=edaStudyStableId
prop=edaEntityAbbrev
prop=datasetDisplayName
prop=shortAttribution
>templateTextStart<
UNION
SELECT genes.string_value AS gene,
'${datasetName}' AS dataset_presenter_id,
'${datasetDisplayName}' AS dataset_presenter_display_name,
'${shortAttribution}' AS short_attribution,
ag.display_name AS variable,
coalesce(av.string_value, coalesce(round(av.number_value::numeric, 4)::text, av.date_value::text)) AS value
FROM eda.attributevalue_${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<


[templateStart]
name=cellularLocalizationEdaAttributeQueriesNumeric
anchorFile=ApiCommonModel/Model/lib/wdk/model/records/transcriptAttributeQueries.xml
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29 changes: 29 additions & 0 deletions Model/lib/dst/phenotype.dst
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Expand Up @@ -110,6 +110,35 @@ WHERE av.attribute_stable_id = ag.stable_id
>templateTextEnd<


[templateStart]
name=phenotypeAllDataGeneTableSql
anchorFile=ApiCommonModel/Model/lib/wdk/model/records/geneTableQueries.xml
prop=datasetName
prop=edaStudyStableId
prop=edaEntityAbbrev
prop=datasetDisplayName
prop=shortAttribution
>templateTextStart<
UNION
SELECT genes.string_value AS gene,
'${datasetName}' AS dataset_presenter_id,
'${datasetDisplayName}' AS dataset_presenter_display_name,
'${shortAttribution}' AS short_attribution,
ag.display_name AS variable,
coalesce(av.string_value, coalesce(round(av.number_value::numeric, 4)::text, av.date_value::text)) AS value
FROM eda.attributevalue_${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<


[templateStart]
name=phenotypeEdaAttributeQueriesNumeric
anchorFile=ApiCommonModel/Model/lib/wdk/model/records/transcriptAttributeQueries.xml
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42 changes: 42 additions & 0 deletions Model/lib/wdk/model/records/geneRecord.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -813,6 +813,48 @@
</table>


<table name="EdaPhenotypeDataTable"
displayName="Phenotype Data"
inReportMaker="false"
includeProjects="ToxoDB,PlasmoDB,TriTrypDB,FungiDB,AmoebaDB,UniDB"
queryRef="GeneTables.EdaPhenotypeDataTable">
<columnAttribute name="dataset_presenter_id" displayName="Dataset ID" internal="true"/>
<columnAttribute name="dataset_presenter_display_name" displayName="Dataset" internal="true"/>
<columnAttribute name="short_attribution" displayName="Attribution"/>
<columnAttribute name="variable" displayName="Variable"/>
<columnAttribute name="value" displayName="Value"/>
<linkAttribute displayName="Dataset" name="presenter_link" internal="false">
<displayText>
<![CDATA[$$dataset_presenter_display_name$$]]>
</displayText>
<url>
<![CDATA[@LEGACY_WEBAPP_BASE_URL@/app/record/dataset/$$dataset_presenter_id$$]]>
</url>
</linkAttribute>
</table>


<table name="EdaCellularLocalizationDataTable"
displayName="Cellular Localization Data"
inReportMaker="false"
includeProjects="ToxoDB,TriTrypDB,UniDB"
queryRef="GeneTables.EdaCellularLocalizationDataTable">
<columnAttribute name="dataset_presenter_id" displayName="Dataset ID" internal="true"/>
<columnAttribute name="dataset_presenter_display_name" displayName="Dataset" internal="true"/>
<columnAttribute name="short_attribution" displayName="Attribution"/>
<columnAttribute name="variable" displayName="Variable"/>
<columnAttribute name="value" displayName="Value"/>
<linkAttribute displayName="Dataset" name="presenter_link" internal="false">
<displayText>
<![CDATA[$$dataset_presenter_display_name$$]]>
</displayText>
<url>
<![CDATA[@LEGACY_WEBAPP_BASE_URL@/app/record/dataset/$$dataset_presenter_id$$]]>
</url>
</linkAttribute>
</table>


<table name="PhenotypeScoreGraphsDataTable"
inReportMaker="false"
displayName="Phenotype Score Graphs Data Table"
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74 changes: 74 additions & 0 deletions Model/lib/wdk/model/records/geneTableQueries.xml
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Expand Up @@ -4599,6 +4599,80 @@ FROM webready.GeneAttributes_p ga, (
</sqlQuery>


<sqlQuery name="EdaPhenotypeDataTable" isCacheable="false"
includeProjects="ToxoDB,PlasmoDB,TriTrypDB,FungiDB,AmoebaDB,UniDB">
<column name="source_id"/>
<column name="project_id"/>
<column name="dataset_presenter_id"/>
<column name="dataset_presenter_display_name"/>
<column name="short_attribution"/>
<column name="variable"/>
<column name="value"/>
<sql>
<![CDATA[
SELECT ga.source_id, ga.project_id, gd.dataset_presenter_id,
gd.dataset_presenter_display_name, gd.short_attribution,
gd.variable, gd.value
FROM webready.GeneAttributes_p ga, (
WITH raw_data AS (
SELECT '' AS gene,
'' AS dataset_presenter_id,
'' AS dataset_presenter_display_name,
'' AS short_attribution,
'' AS variable,
'' AS value
-- TEMPLATE_ANCHOR phenotypeAllDataGeneTableSql
)
SELECT rsog.ref_source_id AS gene, rd.dataset_presenter_id,
rd.dataset_presenter_display_name, rd.short_attribution,
rd.variable, rd.value
FROM webready.RefSynOrthologousGenes_P rsog, raw_data rd
WHERE rsog.source_id = rd.gene
AND rsog.org_abbrev IN ('tgonGT1')
UNION
SELECT rd.gene, rd.dataset_presenter_id, rd.dataset_presenter_display_name,
rd.short_attribution, rd.variable, rd.value
FROM raw_data rd
) gd
WHERE ga.source_id = gd.gene
AND ga.org_abbrev IN (%%PARTITION_KEYS%%)
ORDER BY gd.dataset_presenter_display_name, gd.variable, gd.value
]]>
</sql>
</sqlQuery>


<sqlQuery name="EdaCellularLocalizationDataTable" isCacheable="false"
includeProjects="ToxoDB,TriTrypDB,UniDB">
<column name="source_id"/>
<column name="project_id"/>
<column name="dataset_presenter_id"/>
<column name="dataset_presenter_display_name"/>
<column name="short_attribution"/>
<column name="variable"/>
<column name="value"/>
<sql>
<![CDATA[
SELECT ga.source_id, ga.project_id, gd.dataset_presenter_id,
gd.dataset_presenter_display_name, gd.short_attribution,
gd.variable, gd.value
FROM webready.GeneAttributes_p ga, (
SELECT '' AS gene,
'' AS dataset_presenter_id,
'' AS dataset_presenter_display_name,
'' AS short_attribution,
'' AS variable,
'' AS value
-- TEMPLATE_ANCHOR cellularLocalizationAllDataGeneTableSql
) gd
WHERE ga.source_id = gd.gene
AND ga.org_abbrev IN (%%PARTITION_KEYS%%)
ORDER BY gd.dataset_presenter_display_name, gd.variable, gd.value
]]>
</sql>
</sqlQuery>


<sqlQuery name="PhenotypeScoreGraphsDataTable" isCacheable="false" includeProjects="PlasmoDB,UniDB">
<column name="source_id"/>
<column name="project_id"/>
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2 changes: 2 additions & 0 deletions Model/lib/wdk/ontology/individuals.txt
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Expand Up @@ -222,6 +222,7 @@ GeneRecordClasses.GeneRecordClass.Antibody http://edamontology.org/topic_0121 Pr
GeneRecordClasses.GeneRecordClass.CommunityExpComments http://edamontology.org/topic_0219 Curation and Annotation GeneRecordClasses.GeneRecordClass table CommunityExpComments gene record download
GeneRecordClasses.GeneRecordClass.EdaCellularLocalizationDatasets http://edamontology.org/topic_0140 Protein targeting and localization GeneRecordClasses.GeneRecordClass table EdaCellularLocalizationDatasets gene record
GeneRecordClasses.GeneRecordClass.EdaCellularLocalizationGraphsDataTable http://edamontology.org/topic_0140 Protein targeting and localization GeneRecordClasses.GeneRecordClass table EdaCellularLocalizationGraphsDataTable gene record-internal download
GeneRecordClasses.GeneRecordClass.EdaCellularLocalizationDataTable http://edamontology.org/topic_0140 Protein targeting and localization GeneRecordClasses.GeneRecordClass table EdaCellularLocalizationDataTable gene record download
GeneRecordClasses.GeneRecordClass.Products http://edamontology.org/topic_0219 Curation and Annotation GeneRecordClasses.GeneRecordClass table Products transcript record download
GeneRecordClasses.GeneRecordClass.SNPsAlignment http://edamontology.org/topic_0199 Genetic Variation GeneRecordClasses.GeneRecordClass table SNPsAlignment gene record
GeneRecordClasses.GeneRecordClass.MercatorTable http://edamontology.org/topic_3299 EvoBiol Comparison GeneRecordClasses.GeneRecordClass table MercatorTable gene record
Expand Down Expand Up @@ -262,6 +263,7 @@ GeneRecordClasses.GeneRecordClass.eQTLPhenotypeGraphs http://edamontology.org/to
GeneRecordClasses.GeneRecordClass.PhenotypeGraphs http://edamontology.org/topic_3298 phenotype GeneRecordClasses.GeneRecordClass table PhenotypeGraphs gene record
GeneRecordClasses.GeneRecordClass.PhenotypeScoreGraphsDataTable http://edamontology.org/topic_3298 phenotype GeneRecordClasses.GeneRecordClass table PhenotypeScoreGraphsDataTable gene record-internal
GeneRecordClasses.GeneRecordClass.EdaPhenotypeGraphsDataTable http://edamontology.org/topic_3298 phenotype GeneRecordClasses.GeneRecordClass table EdaPhenotypeGraphsDataTable gene record-internal download
GeneRecordClasses.GeneRecordClass.EdaPhenotypeDataTable http://edamontology.org/topic_3298 phenotype GeneRecordClasses.GeneRecordClass table EdaPhenotypeDataTable gene record download
GeneRecordClasses.GeneRecordClass.HostResponseGraphsDataTable http://edamontology.org/topic_0804 Immunology GeneRecordClasses.GeneRecordClass table HostResponseGraphsDataTable gene record-internal download
GeneRecordClasses.GeneRecordClass.RodMalPhenotype http://edamontology.org/topic_3298 phenotype GeneRecordClasses.GeneRecordClass table RodMalPhenotype transcript record download
GeneRecordClasses.GeneRecordClass.Plasmo_eQTL_Table http://edamontology.org/topic_3298 phenotype GeneRecordClasses.GeneRecordClass table Plasmo_eQTL_Table transcript record download
Expand Down
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