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Genomic colocation: declare Short Variant as input, search, and category node #220

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Merged
jbrestel merged 7 commits into from
Aug 17, 2026
Merged

Genomic colocation: declare Short Variant as input, search, and category node #220

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e8a14ec
Design: genomic colocation for the Short Variant record
jbrestel Aug 15, 2026
44f8b02
Plan: genomic colocation for the Short Variant record
jbrestel Aug 15, 2026
05259ea
Allow Short Variant results as genomic colocation inputs
jbrestel Aug 15, 2026
7565ef8
Add VariantsBySpanLogic, replacing the commented SNP span questions
jbrestel Aug 15, 2026
32ae02f
Place VariantsBySpanLogic in the category ontology
jbrestel Aug 15, 2026
16097fa
Design: record the four Oracle-isms and the temp-table schema decision
jbrestel Aug 15, 2026
9e4964a
Docs: name getStartStop, not the nonexistent makeRegion
jbrestel Aug 17, 2026
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2 changes: 2 additions & 0 deletions Model/lib/wdk/model/questions/params/spanParams.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -175,6 +175,7 @@
<recordClass ref="SnpChipRecordClasses.SnpChipRecordClass" includeProjects="PlasmoDB" />
<recordClass ref="PopsetRecordClasses.PopsetRecordClass" excludeProjects="FungiDB,TrichDB,HostDB,VectorBase" />
-->
<recordClass ref="VariantRecordClasses.VariantRecordClass" includeProjects="AmoebaDB,CryptoDB,FungiDB,MicrosporidiaDB,PiroplasmaDB,PlasmoDB,TriTrypDB,ToxoDB,UniDB" />
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jbrestel marked this conversation as resolved.
<recordClass ref="DynSpanRecordClasses.DynSpanRecordClass" />
</answerParam>

Expand Down Expand Up @@ -262,6 +263,7 @@
<recordClass ref="SnpChipRecordClasses.SnpChipRecordClass" includeProjects="PlasmoDB" />
<recordClass ref="PopsetRecordClasses.PopsetRecordClass" excludeProjects="FungiDB,TrichDB,HostDB" />
-->
<recordClass ref="VariantRecordClasses.VariantRecordClass" includeProjects="AmoebaDB,CryptoDB,FungiDB,MicrosporidiaDB,PiroplasmaDB,PlasmoDB,TriTrypDB,ToxoDB,UniDB" />
<recordClass ref="DynSpanRecordClasses.DynSpanRecordClass" />
</answerParam>

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53 changes: 10 additions & 43 deletions Model/lib/wdk/model/questions/spanQuestions.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -365,26 +365,25 @@
-->

<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
<!-- SNPs -->
<!-- Short Variants -->
<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->

<!-- UNCOMMENT WHEN SNPS are AVAILABLE
<question name="SnpsBySpanLogic"
displayName="SNPs By Relative Location"
shortDisplayName="SNPs by Rel Loc"
<question name="VariantsBySpanLogic"
displayName="Short Variants By Relative Location"
shortDisplayName="Variants by Rel Loc"
queryRef="SpanId.RecordsBySpanLogic"
recordClassRef="SnpRecordClasses.SnpRecordClass"
includeProjects="FungiDB,AmoebaDB,CryptoDB,PlasmoDB,ToxoDB,TriTrypDB,UniDB">
recordClassRef="VariantRecordClasses.VariantRecordClass"
includeProjects="AmoebaDB,CryptoDB,FungiDB,MicrosporidiaDB,PiroplasmaDB,PlasmoDB,TriTrypDB,ToxoDB,UniDB">
<attributesList
summary="snp_location,linkedGeneId,position_in_protein,matched_count,feature_region,matched_regions"
sorting="snp_location asc"
summary="variant_location,gene_ids,variant_type,matched_count,feature_region,matched_regions"
sorting="chromosome_order_num asc,location asc"
/>
<summary>
Get SNPs with span logic operation against other results
Get short variants with span logic operation against other results
</summary>
<description>
<![CDATA[
Get SNPs with span logic operation against other results
Get short variants with span logic operation against other results
]]>
</description>

Expand All @@ -394,39 +393,7 @@
<columnAttribute name="matched_regions" displayName="Matched Regions" truncateTo="4000"/>
</dynamicAttributes>
</question>
-->


<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
<!-- SNPs Chips -->
<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
<!--
<question name="SnpsChipsBySpanLogic"
displayName="SNPs By Relative Location"
shortDisplayName="SNPs by Rel Loc"
queryRef="SpanId.RecordsBySpanLogic"
recordClassRef="SnpChipRecordClasses.SnpChipRecordClass"
includeProjects="PlasmoDB">
<attributesList
summary="snp_location,linkedGeneId,position_in_protein,matched_count,feature_region,matched_regions"
sorting="snp_location asc"
/>
<summary>
Get SNPs with span logic operation against other results
</summary>
<description>
<![CDATA[
Get SNPs with span logic operation against other results
]]>
</description>

<dynamicAttributes>
<columnAttribute name="matched_count" displayName="Match Count" align="center"/>
<columnAttribute name="feature_region" displayName="Region" align="center"/>
<columnAttribute name="matched_regions" displayName="Matched Regions" truncateTo="4000"/>
</dynamicAttributes>
</question>
-->
<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
<!-- DynSpans -->
<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
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3 changes: 1 addition & 2 deletions Model/lib/wdk/ontology/individuals.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -204,8 +204,7 @@ DynSpanRecordClasses.DynSpanRecordClass.SpanQuestions.DynSpansBySpanLogic DynS
DynSpanRecordClasses.DynSpanRecordClass.SpanQuestions.DynSpansByWeightFilter DynSpanRecordClasses.DynSpanRecordClass search SpanQuestions.DynSpansByWeightFilter
DynSpanRecordClasses.DynSpanRecordClass.SpanQuestions.GenesBySpanLogic DynSpanRecordClasses.DynSpanRecordClass search SpanQuestions.GenesBySpanLogic
DynSpanRecordClasses.DynSpanRecordClass.SpanQuestions.OrfsBySpanLogic DynSpanRecordClasses.DynSpanRecordClass search SpanQuestions.OrfsBySpanLogic
DynSpanRecordClasses.DynSpanRecordClass.SpanQuestions.SnpsBySpanLogic DynSpanRecordClasses.DynSpanRecordClass search SpanQuestions.SnpsBySpanLogic
DynSpanRecordClasses.DynSpanRecordClass.SpanQuestions.SnpsChipsBySpanLogic DynSpanRecordClasses.DynSpanRecordClass search SpanQuestions.SnpsChipsBySpanLogic
DynSpanRecordClasses.DynSpanRecordClass.SpanQuestions.VariantsBySpanLogic DynSpanRecordClasses.DynSpanRecordClass search SpanQuestions.VariantsBySpanLogic
SampleRecordClasses.SampleRecordClass.record_overview http://edamontology.org/topic_0219 Curation and Annotation SampleRecordClasses.SampleRecordClass attribute record_overview record-internal
SampleRecordClasses.SampleRecordClass.Characteristics http://edamontology.org/topic_0219 annotation and curation SampleRecordClasses.SampleRecordClass table Characteristics 3 record download
SampleRecordClasses.SampleRecordClass.Protocols http://edamontology.org/topic_0219 annotation and curation SampleRecordClasses.SampleRecordClass table Protocols 2 record download
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