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FeatureRelationship.xml
FeatureRelationship.xml 8.90 KiB
<?xml version="1.0" encoding="UTF-8" ?>
<!DOCTYPE sqlMap
PUBLIC "-//ibatis.apache.org//DTD SQL Map 2.0//EN"
"http://ibatis.apache.org/dtd/sql-map-2.dtd">
<sqlMap namespace="FeatureRelationship">
<typeAlias alias="FeatureRelationship"
type="org.gmod.schema.sequence.FeatureRelationship"/>
<resultMap id="map-basic-feature-relationship" class="FeatureRelationship">
<result property="featureRelationshipId" column="feature_relationship_id"/>
<result property="cvTerm.cvTermId" column="relation_type_id"/>
<result property="rank" column="rank"/>
<result property="value" column="relation_value" />
</resultMap>
<resultMap id="map-feature-relationship-for-objectId" class="FeatureRelationship"
extends="map-basic-feature-relationship">
<result property="featureByObjectId.featureId" column="object_id"/>
</resultMap>
<resultMap id="map-feature-relationship-for-subjectId" class="FeatureRelationship">
<result property="cvTerm.name" column="fr_name"/>
<result property="featureBySubjectId.featureId" column="subject_id"/>
<result property="featureBySubjectId.uniqueName" column="subject_name"/>
<result property="featureBySubjectId.organism.commonName" column="subject_common_name"/>
<result property="featureBySubjectId.cvTerm.name" column="subject_cvterm" />
<result property="featureBySubjectId.featureCvTerms"
column="{{uniqueName=subject_name}}"
select="getFeatureCvTermsByFeature"/>
<result property="featureBySubjectId.featureRelationshipsForSubjectId"
column="{{subject_id=subject_id}}"
select="getParentFeatureRelationship" />
</resultMap>
<resultMap id="select-relationship" class="FeatureRelationship">
<result property="featureRelationshipId" column="feature_relationship_id"/>
<result property="featureBySubjectId" column="subject_id"
select="getLazyFeatureNoResiduesById" />
<result property="featureByObjectId" column="object_id"
select="getLazyFeatureNoResiduesById" />
<result property="value" column="value" />
<result property="rank" column="rank" />
<result property="cvTerm" column="type_id" select="getCvtermByCvTermId" />
</resultMap>
<resultMap id="map-parent-relationship" class="FeatureRelationship">
<result property="featureRelationshipId" column="feature_relationship_id"/>
<result property="featureBySubjectId.featureId" column="subject_id" />
<!--<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="fr_name" />
</resultMap>
<!-- select feature_relationship -->
<select id="getFeatureRelationship" resultMap="select-relationship">
SELECT feature_relationship_id, subject_id, object_id, type_id, value, rank
FROM feature_relationship
WHERE
<dynamic>
<isNotNull property="object_id">
object_id=#object_id#
</isNotNull> <isNotNull property="subject_id">
subject_id=#subject_id#
</isNotNull>
</dynamic>
</select>
<select id="getParentFeatureRelationship" 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=#subject_id# AND
( 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
SET
rank=$rank$, type_id=$cvTerm.cvTermId$
WHERE subject_id=
( SELECT feature_id FROM feature WHERE uniquename=#featureBySubjectId.uniqueName# )
AND object_id=
( SELECT feature_id FROM feature WHERE uniquename=#featureByObjectId.uniqueName# )
</update>
<insert id="insertFeatureRelationship"
parameterClass="FeatureRelationship">
INSERT INTO feature_relationship
( subject_id, object_id, type_id, rank )
VALUES
( (SELECT feature_id FROM feature WHERE uniquename=#featureBySubjectId.uniqueName#),
(SELECT feature_id FROM feature WHERE uniquename=#featureByObjectId.uniqueName#),
$cvTerm.cvTermId$, $rank$ )
</insert>
<delete id="deleteFeatureRelationship"
parameterClass="FeatureRelationship">
DELETE FROM feature_relationship WHERE
object_id=(SELECT feature_id FROM feature WHERE uniquename=#featureByObjectId.uniqueName#)
AND
subject_id=(SELECT feature_id FROM feature WHERE uniquename=#featureBySubjectId.uniqueName#)
AND type_id=$cvTerm.cvTermId$;
</delete>
</sqlMap>