Times Reported Time consuming queries #1

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SELECT /* ChemConcentrationDao */ cc.chem_id chem_id, t.nm chem, t.nm_html chemNmHtml, t.acc_txt chemAcc, t.secondary_nm casRN, cc.chem_conc || ' ' || cc.chem_conc_uom_nm as concentration, cc.ixn_qualifier_nm vivoVitro, cc.chem_conc_exp_route_nm expRoute, cc.taxon_nm_html organism, cca.anatomyTerms anatomyTerms, cca.anatomyTerms anatomyTermsSort, cc.action_type_cd directEvidence, cc.action_type_cd directEvidenceSort, d.nm diseasenm, d.acc_txt diseaseacc, d.acc_db_cd diseaseaccdbcd, d.id diseaseid, tx.nm taxonnm, tx.secondary_nm taxoncomnm, tx.id taxonid, tx.acc_txt taxonacc, refAcc, COUNT(DISTINCT cc.reference_id) referenceCount, COUNT(*) OVER () fullRowCount FROM chem_conc cc INNER JOIN term t ON cc.chem_id = t.id INNER JOIN term tx ON cc.taxon_id = tx.id LEFT JOIN term d ON cc.disease_id = d.id LEFT JOIN ( SELECT r.id, string_agg(distinct r.acc_txt || '^' || r.abbr_authors_txt || '^' || r.title || '^' || r.pub_start_yr || '^' || r.core_citation_txt, '|') AS refAcc FROM reference r GROUP BY r.id) r ON cc.reference_id = r.id INNER JOIN ( SELECT cca.chem_conc_id, string_agg(distinct cca.anatomy_nm_html || '^' || cca.anatomy_acc_txt || '^' || cca.position_seq || '^' || cca.anatomy_acc_db_id || '^' || cca.anatomy_nm, '|') AS anatomyTerms FROM chem_conc_anatomy cca WHERE cca.chem_conc_id IN ( SELECT chem_conc_id FROM chem_conc_anatomy WHERE anatomy_id = '2199603') GROUP BY cca.chem_conc_id) cca ON cc.id = cca.chem_conc_id GROUP BY chem_id, chem, chemNmHtml, chemAcc, casRN, concentration, vivoVitro, expRoute, organism, anatomyTerms, anatomyTermsSort, directEvidence, directEvidenceSort, diseasenm, diseaseacc, diseaseaccdbcd, diseaseid, taxonnm, taxoncomnm, taxonid, taxonacc, refAcc ORDER BY chem, organism LIMIT 50;

Date: 2026-07-22 08:35:44
Duration: 40s547ms
Bind query: yes

SELECT /* ChemConcentrationDao */ cc.chem_id chem_id, t.nm chem, t.nm_html chemNmHtml, t.acc_txt chemAcc, t.secondary_nm casRN, cc.chem_conc || ' ' || cc.chem_conc_uom_nm as concentration, cc.ixn_qualifier_nm vivoVitro, cc.chem_conc_exp_route_nm expRoute, cc.taxon_nm_html organism, cca.anatomyTerms anatomyTerms, cca.anatomyTerms anatomyTermsSort, cc.action_type_cd directEvidence, cc.action_type_cd directEvidenceSort, d.nm diseasenm, d.acc_txt diseaseacc, d.acc_db_cd diseaseaccdbcd, d.id diseaseid, tx.nm taxonnm, tx.secondary_nm taxoncomnm, tx.id taxonid, tx.acc_txt taxonacc, refAcc, COUNT(DISTINCT cc.reference_id) referenceCount, COUNT(*) OVER () fullRowCount FROM chem_conc cc INNER JOIN term t ON cc.chem_id = t.id INNER JOIN term tx ON cc.taxon_id = tx.id LEFT JOIN term d ON cc.disease_id = d.id LEFT JOIN ( SELECT r.id, string_agg(distinct r.acc_txt || '^' || r.abbr_authors_txt || '^' || r.title || '^' || r.pub_start_yr || '^' || r.core_citation_txt, '|') AS refAcc FROM reference r GROUP BY r.id) r ON cc.reference_id = r.id INNER JOIN ( SELECT cca.chem_conc_id, string_agg(distinct cca.anatomy_nm_html || '^' || cca.anatomy_acc_txt || '^' || cca.position_seq || '^' || cca.anatomy_acc_db_id || '^' || cca.anatomy_nm, '|') AS anatomyTerms FROM chem_conc_anatomy cca WHERE cca.chem_conc_id IN ( SELECT chem_conc_id FROM chem_conc_anatomy WHERE anatomy_id = '2199603') GROUP BY cca.chem_conc_id) cca ON cc.id = cca.chem_conc_id GROUP BY chem_id, chem, chemNmHtml, chemAcc, casRN, concentration, vivoVitro, expRoute, organism, anatomyTerms, anatomyTermsSort, directEvidence, directEvidenceSort, diseasenm, diseaseacc, diseaseaccdbcd, diseaseid, taxonnm, taxoncomnm, taxonid, taxonacc, refAcc ORDER BY chem, organism LIMIT 50;

Date: 2026-07-22 08:35:54
Duration: 39s999ms
Bind query: yes

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Times Reported Time consuming queries #2

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[ User: editeu - Total duration: 1m20s - Times executed: 4 ]

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select t.ID, t.OBJECT_TYPE_ID, t.ACC_TXT, t.ACC_DB_CD, t.NM, t.NM_SORT, t.SECONDARY_NM, t.DESCRIPTION, t.NOTE, l.NM from pub1.TERM t, pub1.TERM_LABEL l where t.OBJECT_TYPE_ID = 1 and t.id = l.TERM_ID;

Date: 2026-07-22 21:43:39
Duration: 26s126ms
Database: ctddev51
User: editeu
Bind query: yes

select t.ID, t.OBJECT_TYPE_ID, t.ACC_TXT, t.ACC_DB_CD, t.NM, t.NM_SORT, t.SECONDARY_NM, t.DESCRIPTION, t.NOTE, l.NM from pub1.TERM t, pub1.TERM_LABEL l where t.OBJECT_TYPE_ID = 1 and t.id = l.TERM_ID;

Date: 2026-07-22 21:43:35
Duration: 25s970ms
Database: ctddev51
User: editeu
Bind query: yes

select t.ID, t.OBJECT_TYPE_ID, t.ACC_TXT, t.ACC_DB_CD, t.NM, t.NM_SORT, t.SECONDARY_NM, t.DESCRIPTION, t.NOTE, l.NM from pub1.TERM t, pub1.TERM_LABEL l where t.OBJECT_TYPE_ID = 4 and t.id = l.TERM_ID;

Date: 2026-07-22 21:43:25
Duration: 16s44ms
Database: ctddev51
User: editeu
Bind query: yes

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Times Reported Time consuming queries #3

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SELECT /* AdvancedGeneQueryDAO.getData */ g.id geneId, g.acc_txt acc, g.nm nm, g.nm nmHtml, g.secondary_nm secondaryNm, g.has_chems hasChems, g.has_diseases hasDiseases, g.has_exposures hasExposures, g.has_phenotypes hasPhenotypes, COUNT(*) OVER () fullRowCount FROM term g WHERE g.id IN (( SELECT /* IQH.getMasterGoWhereEquals.Gene */ ai.gene_id FROM dag_path pi INNER JOIN gene_go_annot ai ON pi.descendant_object_id = ai.go_term_id INNER JOIN term_label li ON li.term_id = pi.ancestor_object_id WHERE UPPER(li.nm) LIKE 'APOPTOSIS' AND li.object_type_id = 5)) ORDER BY g.nm_sort, g.id LIMIT 50;

Date: 2026-07-22 21:46:15
Duration: 41s242ms
Bind query: yes

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Times Reported Time consuming queries #4

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SELECT /* AdvancedIxnQueryDAO.getData */ g.nm geneSymbol, g.id geneId, g.acc_txt geneAcc, g.acc_db_cd geneAccDbCd, c.nm chemNm, c.nm_html chemNmhtml, c.acc_txt chemAcc, c.secondary_nm casRN, c.id chemId, i.id ixnId, i.ixn_prose_txt ixnProse, i.ixn_prose_html ixnProseHtml, i.actions_txt ixnActions, COUNT(DISTINCT gcr.reference_id) refCount, COUNT(DISTINCT gcr.taxon_id) taxonCount, ( SELECT STRING_AGG(distinct taxonTerm.nm || '^' || 'taxon' || '^' || taxonTerm.nm_html || '^' || taxonTerm.acc_txt || '^' || taxonTerm.acc_db_cd || '^' || COALESCE(taxonTerm.secondary_nm, ''), '|')) as taxonTerms, ( SELECT STRING_AGG(distinct r.acc_txt, '|')) as references, COUNT(*) OVER () fullRowCount FROM gene_chem_reference gcr INNER JOIN ixn i ON gcr.ixn_id = i.id INNER JOIN term g ON gcr.gene_id = g.id INNER JOIN term c ON gcr.chem_id = c.id INNER JOIN reference r on gcr.reference_id = r.id LEFT OUTER JOIN term taxonTerm on gcr.taxon_id = taxonTerm.id WHERE /* CIQH.getIxnWhereCore */ gcr.gene_id = ANY (ARRAY (( SELECT /* IQH.getMasterPathwayWhereEquals.Name */ tp.term_id FROM term_pathway tp WHERE UPPER(tp.pathway_nm) LIKE 'METABOLISM' AND tp.object_type_id = 4))) AND gcr.id IN ( SELECT gcra.gene_chem_reference_id FROM gene_chem_reference_axn gcra WHERE (gcra.action_degree_type_nm = 'increases')) GROUP BY g.nm, g.nm_sort, g.acc_txt, g.acc_db_cd, g.id, c.nm, c.nm_html, c.nm_sort, c.acc_txt, c.secondary_nm, c.id, i.ixn_prose_txt, i.ixn_prose_html, i.sort_txt, i.actions_txt, i.id ORDER BY g.nm_sort, c.nm_sort, i.sort_txt LIMIT 50;

Date: 2026-07-22 21:47:07
Duration: 24s72ms
Bind query: yes

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Times Reported Time consuming queries #5

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select distinct /* ChemPhenotypesAssnsDAO */ associatedTerm.nm || '^' || o.cd || '^' || associatedTerm.nm_html || '^' || associatedTerm.acc_txt || '^' || associatedTerm.acc_db_cd as associatedTerm, associatedTerm.id associatedTermId, ptr.ixn_id ixnId, associatedTerm.object_type_id || '|' || associatedTerm.nm_sort associatedTermNmSort, COALESCE(associatedTerm.secondary_nm, '') casRN, phenotypeTerm.nm || '^' || 'go' || '^' || phenotypeTerm.nm_html || '^' || phenotypeTerm.acc_txt || '^' || phenotypeTerm.acc_db_cd as phenotype, phenotypeTerm.id phenotypeId, ( SELECT STRING_AGG(distinct taxonTerm.nm || '^' || 'taxon' || '^' || taxonTerm.nm_html || '^' || taxonTerm.acc_txt || '^' || taxonTerm.acc_db_cd || '^' || COALESCE(taxonTerm.secondary_nm, ''), '|')) as taxonTerms, ( SELECT STRING_AGG(distinct anatomyTerm.nm_html || '^' || anatomyTerm.acc_txt || '^' || ia.level_seq || '^' || anatomyTerm.acc_db_cd || '^' || anatomyTerm.nm, '|')) as anatomyTerms, COUNT(DISTINCT taxonTerm.nm) taxonCount, i.ixn_prose_html ixnProseHtml, i.ixn_prose_txt ixnProse, i.sort_txt ixnSort, ( SELECT STRING_AGG(distinct r.acc_txt, '|')) as references, COUNT(DISTINCT ptr.reference_id) refCount, pt.indirect_term_qty inferredCount, COUNT(*) OVER () fullRowCount from phenotype_term_reference ptr inner join phenotype_term pt on ptr.term_id = pt.term_id and ptr.phenotype_id = pt.phenotype_id inner join term associatedTerm on ptr.term_id = associatedTerm.id inner join term phenotypeTerm on ptr.phenotype_id = phenotypeTerm.id left outer join term taxonTerm on ptr.taxon_id = taxonTerm.id inner join reference r on ptr.reference_id = r.id inner join ixn i on ptr.ixn_id = i.id inner join object_type o on associatedTerm.object_type_id = o.id left outer join ixn_anatomy ia on ptr.ixn_id = ia.ixn_id left outer join term anatomyTerm on ia.anatomy_id = anatomyTerm.id where ptr.term_id IN ( select /* DBConstants.getDAGTermSQL */ distinct dp.descendant_object_id from dag_path dp WHERE dp.ancestor_object_id in ( select distinct id from term baseTerm where object_type_id = 2 and upper(baseTerm.nm) LIKE 'ZINC')) and ptr.term_object_type_id = 2 and ptr.phenotype_id IN ( select /* DBConstants.getDAGTermSQL */ distinct dp.descendant_object_id from dag_path dp WHERE dp.ancestor_object_id in ( select distinct id from term baseTerm where object_type_id = 5 and baseTerm.id in ( select object_id from db_link l where l.acc_txt = 'GO:0006915' AND l.type_cd = 'A' AND l.object_type_id = 5))) and taxonTerm.id in ( select /* DBConstants.getDAGTermSQL */ distinct dp.descendant_object_id from dag_path dp WHERE dp.ancestor_object_id in ( select distinct id from term baseTerm where object_type_id = 1 and baseTerm.id in ( select object_id from db_link l where l.acc_txt = '9606' AND l.type_cd = 'A' AND l.object_type_id = 1))) and i.id in ( select ixn_id from ixn_axn where action_type_nm = 'phenotype' and action_degree_type_nm in ('increases')) group by associatedTerm, associatedTermNmSort, phenotype, casRN, ixnId, ixnProseHtml, ixnProse, ixnSort, associatedTermId, phenotypeId, inferredCount ORDER BY associatedTermNmSort asc, pt.indirect_term_qty desc LIMIT 50;

Date: 2026-07-22 21:50:16
Duration: 18s100ms
Bind query: yes

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Times Reported Time consuming queries #6

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SELECT /* AdvancedGeneQueryDAO.getData */ g.id geneId, g.acc_txt acc, g.nm nm, g.nm nmHtml, g.secondary_nm secondaryNm, g.has_chems hasChems, g.has_diseases hasDiseases, g.has_exposures hasExposures, g.has_phenotypes hasPhenotypes, COUNT(*) OVER () fullRowCount FROM term g WHERE g.id IN (( SELECT /* IQH.getMasterDiseaseWhereEquals.Name.Gene */ gd.gene_id FROM term t INNER JOIN dag_path dp ON t.id = dp.ancestor_object_id INNER JOIN gene_disease gd ON dp.descendant_object_id = gd.disease_id WHERE UPPER(t.nm) LIKE 'ASTHMA' AND t.object_type_id = 3)) ORDER BY g.nm_sort, g.id LIMIT 50;

Date: 2026-07-22 21:46:28
Duration: 13s44ms
Bind query: yes

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Times Reported Time consuming queries #7

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SELECT /* BasicCountsDAO gen */ ii.cd, COUNT(ii.id) cnt FROM ( SELECT ot.cd, tl.term_id id FROM object_type ot INNER JOIN term_label tl ON ot.id = tl.object_type_id WHERE tl.nm_fts @@ to_tsquery('common.english_nostops', 'DDT') UNION SELECT 'reference', r.id FROM reference r WHERE r.title_abstract_fts @@ to_tsquery('pg_catalog.english', 'DDT') OR r.id IN ( SELECT rpr.reference_id FROM reference_party_role rpr INNER JOIN reference_party rp ON rpr.reference_party_id = rp.id WHERE (SUBSTR(get_reference_party_nm_sort (rp.required_nm), 1, 128) LIKE 'DDT')) UNION SELECT ot.cd, l.object_id FROM db_link l INNER JOIN object_type ot on l.object_type_id = ot.id WHERE l.type_cd = 'A' AND (upper(l.acc_txt) LIKE 'DDT')) ii GROUP BY ii.cd;

Date: 2026-07-22 21:45:17
Duration: 7s606ms
Bind query: yes

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Times Reported Time consuming queries #8

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select p.ancestor_object_id, p.descendant_object_id from DAG_PATH p where p.descendant_object_id in ( select go_term_id from GENE_GO_ANNOT gga where gga.taxon_id = ( select id from TERM where acc_txt = '9606' and object_type_id = ( select id from OBJECT_TYPE where cd = 'taxon')) AND gga.is_not = 'f') and p.ancestor_object_id NOT in ( SELECT c.id FROM TERM c WHERE c.acc_txt in ('ALL') AND c.object_type_id = ( select id from OBJECT_TYPE where cd = 'go'));

Date: 2026-07-22 21:43:37
Duration: 7s571ms
Bind query: yes

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Times Reported Time consuming queries #9

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[ User: pubeu - Total duration: 7s7ms - Times executed: 1 ]

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select count(distinct gene_id) from GENE_TAXON where taxon_id = 597275;

Date: 2026-07-22 21:43:24
Duration: 7s7ms
Database: ctddev51
User: pubeu
Bind query: yes

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Times Reported Time consuming queries #10

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[ User: pubeu - Total duration: 6s405ms - Times executed: 1 ]

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SELECT /* TermBrowseIndexDAO */ DISTINCT REGEXP_REPLACE(UPPER(SUBSTRING(t.nm, 1, 1)), '[^A-Z]', '#') indexChar FROM term t WHERE t.object_type_id = '4' ORDER BY 1;

Date: 2026-07-22 21:43:33
Duration: 6s405ms
Database: ctddev51
User: pubeu
Bind query: yes

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Times Reported Time consuming queries #11

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SELECT /* BatchDiseaseGeneAssnsDAO */ 'asthenia' "Input", d.nm "DiseaseName", d.acc_db_cd || ':' || d.acc_txt "DiseaseID", g.nm "GeneSymbol", g.acc_txt "GeneID", ( SELECT STRING_AGG(stm.slim_term_nm, '|' ORDER BY stm.slim_term_nm) FROM slim_term_mapping stm WHERE stm.mapped_term_id = d.id) "DiseaseCategories", CASE WHEN gdr.via_chem_id IS NULL THEN ( SELECT STRING_AGG(a.action_type_nm, '|') FROM gene_disease_axn a WHERE a.gene_id = gdr.gene_id AND a.disease_id = gdr.disease_id) ELSE NULL END "DirectEvidence", c.nm "InferenceChemicalName", gdr.network_score "InferenceScore", STRING_AGG(gdr.source_acc_txt, '|' ORDER BY gdr.source_acc_txt) "OmimIDs", STRING_AGG(DISTINCT r.acc_txt, '|') "PubMedIDs" FROM gene_disease_reference gdr INNER JOIN term g ON gdr.gene_id = g.id INNER JOIN term d ON gdr.disease_id = d.id LEFT OUTER JOIN reference r ON gdr.reference_id = r.id LEFT OUTER JOIN term c ON gdr.via_chem_id = c.id WHERE (d.id = 2184971) GROUP BY g.nm, g.acc_txt, d.nm, d.id, d.acc_txt, d.acc_db_cd, d.nm_sort, CASE WHEN gdr.via_chem_id IS NULL THEN ( SELECT STRING_AGG(a.action_type_nm, '|') FROM gene_disease_axn a WHERE a.gene_id = gdr.gene_id AND a.disease_id = gdr.disease_id) ELSE NULL END, c.nm, gdr.network_score ORDER BY d.nm_sort, g.nm, "DirectEvidence", c.nm;

Date: 2026-07-22 21:49:25
Duration: 5s601ms
Bind query: yes

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Times Reported Time consuming queries #12

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SELECT /* BatchChemGODAO */ 'ddt' "Input", sqi.chem_nm "ChemicalName", sqi.chem_acc_txt "ChemicalID", sqi.casRN "CasRN", sqi.gene_symbol "GeneSymbol", sqi.gene_acc_txt "GeneID", sqi.ontology_nm "Ontology", sqi.go_term_nm "GoTermName", sqi.go_acc_txt "GoTermID" FROM ( WITH sq AS ( SELECT DISTINCT c.id chem_id, c.nm chem_nm, c.acc_txt chem_acc_txt, c.secondary_nm casRN, c.nm_sort chem_nm_sort, gcr.gene_id, g.nm gene_symbol, g.acc_txt gene_acc_txt, g.nm_sort gene_symbol_sort FROM term c INNER JOIN gene_chem_reference gcr ON c.id = gcr.chem_id INNER JOIN term g ON gcr.gene_id = g.id WHERE (c.id = 1398646)) SELECT DISTINCT sq.chem_nm, sq.chem_acc_txt, sq.casRN, sq.gene_symbol, sq.gene_acc_txt, gt.nm go_term_nm, gt.acc_txt go_acc_txt, sq.chem_nm_sort, sq.gene_symbol_sort, gt.nm_sort, d.nm ontology_nm FROM sq INNER JOIN gene_go_annot gga ON sq.gene_id = gga.gene_id INNER JOIN dag_node gt ON gga.go_term_id = gt.object_id INNER JOIN dag d ON gt.dag_id = d.id WHERE gga.is_not = false AND (d.id = 5 OR d.id = 4) ORDER BY sq.chem_nm_sort, sq.gene_symbol_sort, d.nm, gt.nm_sort) sqi;

Date: 2026-07-22 21:49:19
Duration: 5s454ms
Bind query: yes

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Times Reported Time consuming queries #13

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SELECT /* AdvancedGeneQueryDAO.getData */ g.id geneId, g.acc_txt acc, g.nm nm, g.nm nmHtml, g.secondary_nm secondaryNm, g.has_chems hasChems, g.has_diseases hasDiseases, g.has_exposures hasExposures, g.has_phenotypes hasPhenotypes, COUNT(*) OVER () fullRowCount FROM term g WHERE g.id IN (( SELECT /* IQH.getMasterDiseaseWhereEquals.Label.Gene */ gd.gene_id FROM term_label l INNER JOIN dag_path dp ON l.term_id = dp.ancestor_object_id INNER JOIN gene_disease gd ON dp.descendant_object_id = gd.disease_id WHERE UPPER(l.nm) LIKE 'GLAUCOMA' AND l.object_type_id = 3)) ORDER BY g.nm_sort, g.id LIMIT 50;

Date: 2026-07-22 21:45:34
Duration: 5s9ms
Bind query: yes

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Times Reported Time consuming queries #1