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improve proteinattrs performance #73

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1d64aba
improve proteinattrs performance
steve-fischer-200 Apr 21, 2025
3a83adf
add '??' codes
steve-fischer-200 May 5, 2025
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50 changes: 30 additions & 20 deletions Model/lib/xml/tuningManager/apiTuningManager.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -1880,6 +1880,8 @@ create unique index Organism_sourceId_idx&1 ON OrganismAttributes&1 (source_id)
<externalDependency name="sres.EnzymeClass"/>
<ancillaryTable name="GoTermList"/>
<ancillaryTable name="ProteinGoAttributes"/>
<ancillaryTable name="ProteinAttrsEc"/>
<ancillaryTable name="ProteinAttrsEcDerived"/>
<sql>
<![CDATA[
CREATE TABLE &prefixGoTermList&1 AS
Expand Down Expand Up @@ -1963,6 +1965,32 @@ create unique index Organism_sourceId_idx&1 ON OrganismAttributes&1 (source_id)
]]>
</sql>

<sql>
<![CDATA[
CREATE TABLE &prefixtProteinAttrsEc&1 AS
SELECT aa_sequence_id, SUBSTR(string_agg(ec_number, ';' order by ec_number),1, 300) AS ec_numbers
FROM (SELECT DISTINCT asec.aa_sequence_id,
ec.ec_number || ' (' || ec.description || ')' AS ec_number
FROM dots.AaSequenceEnzymeClass asec, sres.EnzymeClass ec
WHERE ec.enzyme_class_id = asec.enzyme_class_id
AND NOT asec.evidence_code = 'OrthoMCLDerived'
) t
GROUP BY aa_sequence_id
]]>
</sql>
<sql>
<![CDATA[
CREATE TABLE &prefixtProteinAttrsEcDerived&1 AS
SELECT aa_sequence_id, SUBSTR(string_agg(ec_number, ';' order by ec_number),1, 300) AS ec_numbers_derived
FROM (SELECT DISTINCT asec.aa_sequence_id,
ec.ec_number || ' (' || ec.description || ')' AS ec_number
FROM dots.AaSequenceEnzymeClass asec, sres.EnzymeClass ec
WHERE ec.enzyme_class_id = asec.enzyme_class_id
AND asec.evidence_code = 'OrthoMCLDerived'
) t
GROUP BY aa_sequence_id
]]>
</sql>
<sql>
<![CDATA[
CREATE TABLE &prefixProteinAttributes&1 AS
Expand Down Expand Up @@ -2029,26 +2057,8 @@ create unique index Organism_sourceId_idx&1 ON OrganismAttributes&1 (source_id)
GROUP BY tmaf.aa_sequence_id) tms
GROUP BY tms.aa_sequence_id
) transmembrane ON tas.aa_sequence_id = transmembrane.aa_sequence_id
LEFT JOIN (
SELECT aa_sequence_id, SUBSTR(string_agg(ec_number, ';' order by ec_number),1, 300) AS ec_numbers
FROM (SELECT DISTINCT asec.aa_sequence_id,
ec.ec_number || ' (' || ec.description || ')' AS ec_number
FROM dots.AaSequenceEnzymeClass asec, sres.EnzymeClass ec
WHERE ec.enzyme_class_id = asec.enzyme_class_id
AND NOT asec.evidence_code = 'OrthoMCLDerived'
) t
GROUP BY aa_sequence_id
) ec ON tas.aa_sequence_id = ec.aa_sequence_id
LEFT JOIN (
SELECT aa_sequence_id, SUBSTR(string_agg(ec_number, ';' order by ec_number),1, 300) AS ec_numbers_derived
FROM (SELECT DISTINCT asec.aa_sequence_id,
ec.ec_number || ' (' || ec.description || ')' AS ec_number
FROM dots.AaSequenceEnzymeClass asec, sres.EnzymeClass ec
WHERE ec.enzyme_class_id = asec.enzyme_class_id
AND asec.evidence_code = 'OrthoMCLDerived'
) t
GROUP BY aa_sequence_id
) ecDerived ON tas.aa_sequence_id = ecDerived.aa_sequence_id
LEFT JOIN &prefixProteinAttrsEc&1 ec ON tas.aa_sequence_id = ec.aa_sequence_id
LEFT JOIN &prefixProteinAttrsEcDerived&1 ecDerived ON tas.aa_sequence_id = ecDerived.aa_sequence_id
LEFT JOIN (
SELECT af.aa_sequence_id,
string_agg(dbref.primary_identifier, ',' order by dbref.primary_identifier) as uniprot_ids
Expand Down
20 changes: 20 additions & 0 deletions Model/lib/xml/tuningManager/tablePruning.txt
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Original file line number Diff line number Diff line change
@@ -1,3 +1,23 @@
MG <tuningTable name="GroupDomainAttribute" prefixEnabled="false">
?? <tuningTable name="SequenceEnzymeClass" prefixEnabled="false">
?? <tuningTable name="AssociatedDataset" prefixEnabled="false">
?? <tuningTable name="TypeAheadCounts" prefixEnabled="false">
?? <tuningTable name="ExternalDbDatasetPresenter" prefixEnabled="false">
?? <tuningTable name="StudyIdDatasetId" prefixEnabled="false">
?? <tuningTable name="ExternalSequenceTaxonRank" prefixEnabled="false">
?? <tuningTable name="EdaGeneGraph" prefixEnabled="false">
?? <tuningTable name="EupathBuildDates" prefixEnabled="false">
?? <tuningTable name="SequenceAttributes" prefixEnabled="false">
?? <tuningTable name="SequencePieceClosure" prefixEnabled="false">
?? <tuningTable name="DomainAssignment" prefixEnabled="false">
?? <tuningTable name="GenomicSeqAttributes" prefixEnabled="false">
?? <tuningTable name="PANResults" prefixEnabled="false">
?? <tuningTable name="PANIO" prefixEnabled="false">
?? <tuningTable name="DatasetDetail" prefixEnabled="false">
?? <tuningTable name="PANExtDbRls" prefixEnabled="false">
?? <tuningTable name="DatasetPresenter" prefixEnabled="false">
?? <tuningTable name="ProjectTaxon" prefixEnabled="false">
?? <tuningTable name="PhyleticPattern" prefixEnabled="false">
MO <tuningTable name="TransmembraneDomains" prefixEnabled="false">
MO <tuningTable name="SignalPeptideDomains" prefixEnabled="true">
MG <tuningTable name="OrganismSelectTaxonRank" prefixEnabled="false">
Expand Down