From 1d807b016d8b4ddf71961ccbc036ec489b62f61c Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Wed, 19 Sep 2007 12:48:05 +0000
Subject: [PATCH] updates
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@6397 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
artemis_sqlmap/FeatureRelationship.xml | 71 +++++++++++++++++++++++---
1 file changed, 64 insertions(+), 7 deletions(-)
diff --git a/artemis_sqlmap/FeatureRelationship.xml b/artemis_sqlmap/FeatureRelationship.xml
index 8da16d8d7..0d9c4b81f 100644
--- a/artemis_sqlmap/FeatureRelationship.xml
+++ b/artemis_sqlmap/FeatureRelationship.xml
@@ -49,11 +49,12 @@
<result property="featureRelationshipId" column="feature_relationship_id"/>
<result property="featureBySubjectId" column="subject_id"
select="getLazyFeatureById" />
- <result property="featureByObjectId" column="object_id"
- select="getLazyFeatureNameAndTypeById" />
+ <!--<result property="featureByObjectId" column="object_id"
+ select="getLazyFeatureNameAndTypeById" />-->
+ <result property="featureByObjectId" resultMap="Feature.map-feature-name-lazy" />
<result property="value" column="value" />
<result property="rank" column="rank" />
- <result property="cvTerm.name" column="name" />
+ <result property="cvTerm.name" column="fr_name" />
</resultMap>
<!-- select feature_relationship -->
@@ -72,13 +73,69 @@
</select>
<select id="getParentFeatureRelationship" resultMap="map-parent-relationship">
- SELECT feature_relationship_id, subject_id, object_id, type_id, value, rank, cvterm.name
- FROM feature_relationship
- LEFT JOIN cvterm ON cvterm_id=type_id
+ SELECT feature_relationship_id, subject_id, object_id, value, rank,
+ fr_cvterm.name AS fr_name, parent.uniquename, parent_cvterm.name AS name, parent.feature_id AS id
+ FROM feature_relationship AS fr
+ LEFT JOIN cvterm AS fr_cvterm ON fr_cvterm.cvterm_id=fr.type_id
+ LEFT JOIN feature AS parent ON object_id=feature_id
+ LEFT JOIN cvterm AS parent_cvterm ON parent_cvterm.cvterm_id=parent.type_id
WHERE subject_id=#subject_id# AND
- ( cvterm.name='derives_from' OR cvterm.name='part_of' OR cvterm.name='proper_part_of' )
+ ( fr_cvterm.name='derives_from' OR fr_cvterm.name='part_of' OR fr_cvterm.name='proper_part_of' )
+
+ <!--
+ SELECT feature_relationship_id, subject_id, object_id, value, rank,
+ fr_cvterm.name AS fr_name, parent.uniquename, parent_cvterm.name, parent.feature_id AS id
+ FROM feature_relationship AS fr
+ LEFT JOIN cvterm AS fr_cvterm ON fr_cvterm.cvterm_id=fr.type_id
+ LEFT JOIN feature AS parent ON object_id=feature_id
+ LEFT JOIN cvterm AS parent_cvterm ON parent_cvterm.cvterm_id=parent.type_id
+ WHERE
+ ( subject_id=#subject_id#
+ AND (fr_cvterm.name='derives_from' OR fr_cvterm.name='part_of' OR fr_cvterm.name='proper_part_of')
+ AND (parent_cvterm.name='gene' OR parent_cvterm.name='pseudogene'))
+ OR ( subject_id IN (SELECT object_id FROM feature_relationship AS fr2
+ LEFT JOIN cvterm AS fr2_cvterm ON fr2_cvterm.cvterm_id=fr2.type_id
+ WHERE subject_id=#subject_id#
+ AND (fr2_cvterm.name='derives_from' OR fr2_cvterm.name='part_of' OR fr2_cvterm.name='proper_part_of'))
+ AND (fr_cvterm.name='derives_from' OR fr_cvterm.name='part_of' OR fr_cvterm.name='proper_part_of')
+ AND (parent_cvterm.name='gene' OR parent_cvterm.name='pseudogene')) ;
+ -->
+
</select>
+ <select id="getParentFeaturesByChildFeatureIds" resultMap="map-parent-relationship">
+ SELECT feature_relationship_id, subject_id, object_id, value, rank,
+ fr_cvterm.name AS fr_name, parent.uniquename, parent_cvterm.name AS name, parent.feature_id AS id
+ FROM feature_relationship AS fr
+ LEFT JOIN cvterm AS fr_cvterm ON fr_cvterm.cvterm_id=fr.type_id
+ LEFT JOIN feature AS parent ON object_id=feature_id
+ LEFT JOIN cvterm AS parent_cvterm ON parent_cvterm.cvterm_id=parent.type_id
+ WHERE
+ ( subject_id IN <iterate open="(" close=")" conjunction=","> $[]$ </iterate>
+ AND (fr_cvterm.name='derives_from' OR fr_cvterm.name='part_of' OR fr_cvterm.name='proper_part_of') )
+ </select>
+
+ <!--
+ <select id="getGeneFeaturesByChildFeatureIds" resultMap="map-parent-relationship">
+ SELECT feature_relationship_id, subject_id, object_id, value, rank,
+ fr_cvterm.name AS fr_name, parent.uniquename, parent_cvterm.name AS name, parent.feature_id AS id
+ FROM feature_relationship AS fr
+ LEFT JOIN cvterm AS fr_cvterm ON fr_cvterm.cvterm_id=fr.type_id
+ LEFT JOIN feature AS parent ON object_id=feature_id
+ LEFT JOIN cvterm AS parent_cvterm ON parent_cvterm.cvterm_id=parent.type_id
+ WHERE
+ ( subject_id IN <iterate open="(" close=")" conjunction=","> $[]$ </iterate>
+ AND (fr_cvterm.name='derives_from' OR fr_cvterm.name='part_of' OR fr_cvterm.name='proper_part_of')
+ AND (parent_cvterm.name='gene' OR parent_cvterm.name='pseudogene') )
+ OR ( subject_id IN (SELECT object_id FROM feature_relationship AS fr2
+ LEFT JOIN cvterm AS fr2_cvterm ON fr2_cvterm.cvterm_id=fr2.type_id
+ WHERE subject_id IN <iterate open="(" close=")" conjunction=","> $[]$ </iterate>
+ AND (fr2_cvterm.name='derives_from' OR fr2_cvterm.name='part_of' OR fr2_cvterm.name='proper_part_of'))
+ AND (fr_cvterm.name='derives_from' OR fr_cvterm.name='part_of' OR fr_cvterm.name='proper_part_of')
+ AND (parent_cvterm.name='gene' OR parent_cvterm.name='pseudogene') ) ;
+ </select>
+ -->
+
<update id="updateFeatureRelationshipsForSubjectId"
parameterClass="FeatureRelationship">
UPDATE feature_relationship
--
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