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New query for ud #30

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2f1b0b8
add new search for UD UI
steve-fischer-200 Nov 2, 2023
0f38ade
debug
steve-fischer-200 Nov 4, 2023
812f1dc
Merge branch 'master' into new-query-for-UD
steve-fischer-200 Nov 6, 2023
319c5e4
improve perf of GO Term query
steve-fischer-200 Nov 6, 2023
5660142
Merge branch 'new-query-for-UD' of github.com:VEuPathDB/ApiCommonMode…
steve-fischer-200 Nov 6, 2023
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10 changes: 10 additions & 0 deletions Model/lib/wdk/model/questions/genomicQuestions.xml
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Expand Up @@ -359,6 +359,16 @@
<description>Find all primary sequences to by organisms</description>
</question>

<!--===========================================================================-->
<!-- retrieve sequence record which is the longest sequence in a provided organism -->
<!-- used internally by the User Dataset UI to form browser track URLs -->
<!--===========================================================================-->
<question name="LongestSeqForAnOrganism" excludeProjects="EuPathDB"
displayName="Longest seq for an organism"
queryRef="SequenceIds.ByOrganismNameForFiles"
recordClassRef="SequenceRecordClasses.SequenceRecordClass">
<description>Find longest seq for an organism</description>
</question>



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2 changes: 2 additions & 0 deletions Model/lib/wdk/model/questions/params/genomicParams.xml
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Expand Up @@ -190,6 +190,8 @@
<suggest includeProjects="UniDB,PlasmoDB,ToxoDB,CryptoDB" default="1"/>
</stringParam>

<stringParam name="organismNameForFiles" excludeProjects="EuPathDB" prompt="Org name for files" number="false"/>

<enumParam name="medianOrIndividual" includeProjects="AmoebaDB,TriTrypDB,PlasmoDB,ToxoDB,CryptoDB,FungiDB,UniDB"
prompt="Median Or By Strain/Sample?"
multiPick="false">
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25 changes: 25 additions & 0 deletions Model/lib/wdk/model/questions/queries/genomicQueries.xml
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Expand Up @@ -414,6 +414,31 @@ from apidbtuning.GenomicSeqAttributes s
</sql>
</sqlQuery>

<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
<!-- Retrieves genomic sequence ID of longest sequence in an organism -->
<!-- Used by user datasets UI to build genome browser track URLs -->
<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->

<sqlQuery name="ByOrganismNameForFiles" excludeProjects="EuPathDB">
<paramRef ref="genomicParams.organismNameForFiles"/>
<column name="project_id"/>
<column name="source_id"/>
<sql>
<![CDATA[
SELECT gsa.project_id, gsa.source_id
FROM apidbtuning.genomicseqattributes gsa, apidb.organism o,
(SELECT MAX(length) AS ML, taxon_id
FROM apidbtuning.genomicseqattributes
GROUP BY taxon_id ) info
WHERE info.taxon_id = gsa.taxon_id
AND info.ml = gsa.length
AND gsa.taxon_id = o.taxon_id
AND $$organismNameForFiles$$ = o.name_for_filenames

]]>
</sql>
</sqlQuery>

</querySet>

</wdkModel>