From bbffb240c2fd95226331b7d0794f0e89f44f2319 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Thu, 14 May 2009 15:37:17 +0000
Subject: [PATCH] changes to speed up getOrganismsContainingSrcFeatures
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10812 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
artemis_sqlmap/Organism.xml | 16 +++++++++-------
uk/ac/sanger/artemis/chado/IBatisDAO.java | 2 +-
2 files changed, 10 insertions(+), 8 deletions(-)
diff --git a/artemis_sqlmap/Organism.xml b/artemis_sqlmap/Organism.xml
index 8b03b450a..96f608051 100644
--- a/artemis_sqlmap/Organism.xml
+++ b/artemis_sqlmap/Organism.xml
@@ -81,13 +81,15 @@
</select>
<select id="getTopLevelOrganisms" resultMap="map-organism">
- SELECT DISTINCT ON( feature.organism_id )
- organism.organism_id AS organismId, abbreviation, genus, species, common_name AS commonName, comment
- FROM feature
- join organism using (organism_id)
- JOIN featureprop using (feature_id)
- WHERE featureprop.type_id in
- (SELECT cvterm_id FROM cvterm JOIN cv using (cv_id) WHERE cv.name = 'genedb_misc' AND cvterm.name = 'top_level_seq' )
+ SELECT organism.organism_id AS organismId, abbreviation, genus, species, common_name AS commonName, comment
+ FROM organism
+ WHERE exists (
+ SELECT *
+ FROM organismprop
+ JOIN cvterm on organismprop.type_id = cvterm.cvterm_id
+ JOIN cv using (cv_id)
+ WHERE organism_id = organism.organism_id
+ AND cv.name = 'genedb_misc' and cvterm.name = 'populated' )
</select>
</sqlMap>
diff --git a/uk/ac/sanger/artemis/chado/IBatisDAO.java b/uk/ac/sanger/artemis/chado/IBatisDAO.java
index 2da3faa42..2e9f1c99d 100644
--- a/uk/ac/sanger/artemis/chado/IBatisDAO.java
+++ b/uk/ac/sanger/artemis/chado/IBatisDAO.java
@@ -593,7 +593,7 @@ public class IBatisDAO extends GmodDAO
public List getOrganismsContainingSrcFeatures()
{
- CvTerm cvTerm = getCvTermByNameAndCvName("top_level_seq", "genedb_misc");
+ CvTerm cvTerm = getCvTermByNameAndCvName("populated", "genedb_misc");
if(cvTerm != null)
return sqlMap.queryForList("getTopLevelOrganisms", null);
else
--
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