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<!DOCTYPE sqlMap
PUBLIC "-//ibatis.apache.org//DTD SQL Map 2.0//EN"
"http://ibatis.apache.org/dtd/sql-map-2.dtd">
<sqlMap namespace="FeatureCvTerm">
<cacheModel id="featurecvterm-rank-cache" type ="LRU" readOnly="true">
<flushInterval hours="24"/>
<property name="cache-size" value="15" />
</cacheModel>
<typeAlias alias="FeatureCvTerm"
type="org.gmod.schema.sequence.FeatureCvTerm"/>
<resultMap id="select-featurecvterm-no-rank" class="FeatureCvTerm"
groupBy="featureCvTermId">
<result property="featureCvTermId" column="feature_cvterm_id" />
<result property="feature.featureId" column="feature_id" />
<result property="cvTerm.cvTermId" column="cvterm_id" />
<result property="cvTerm.name" column="cvterm_name" />
<result property="cvTerm.cv.name" column="cv_name" />
<result property="not" column="is_not" />
<result property="featureCvTermProps" resultMap="FeatureCvTermProp.feature_cvtermprop" />
<result property="pub.pubId" column="pub_id" />
<result property="pub.uniqueName" column="uniquename" />
<result property="cvTerm.dbXRef.accession" column="accession" />
<result property="cvTerm.dbXRef.db.name" column="name" />
<result property="featureCvTermDbXRefs" column="feature_cvterm_id"
select="getFeatureCvTermDbXRefByFeatureCvTerm" />
<!-- <result property="pub" column="pub_id" select="selectPub" /> -->
</resultMap>
<resultMap id="select-featurecvterm" class="FeatureCvTerm"
extends="select-featurecvterm-no-rank">
<result property="rank" column="rank" />
</resultMap>
<!-- select feature_cvterm -->
<sql id="sql_select_feature_cvterm">
SELECT
fc.*,
fcp.type_id, fcp.value, fcp.rank AS fcp_rank,
cvterm.name AS cvterm_name,
cv.name AS cv_name,
pub.pub_id,
pub.uniquename,
db.name,
dbxref.accession
FROM feature_cvterm fc
LEFT JOIN feature_cvtermprop fcp ON fc.feature_cvterm_id=fcp.feature_cvterm_id
LEFT JOIN cvterm ON cvterm.cvterm_id=fc.cvterm_id
LEFT JOIN cv ON cvterm.cv_id=cv.cv_id
LEFT JOIN pub ON fc.pub_id=pub.pub_id
LEFT JOIN dbxref ON cvterm.dbxref_id=dbxref.dbxref_id
LEFT JOIN db ON dbxref.db_id=db.db_id
</sql>
<select id="getFeatureCvTermsBySrcFeature" parameterClass="org.gmod.schema.sequence.Feature"
resultMap="select-featurecvterm">
<include refid="sql_select_feature_cvterm"/>
WHERE feature_id IN
(SELECT feature_id FROM featureloc fl WHERE srcfeature_id=$featureId$
<isGreaterThan property="featureLoc.fmin" compareValue="0" prepend="AND">
<![CDATA[ fl.fmin > $featureLoc.fmin$ AND fl.fmax < $featureLoc.fmax$ ]]>
</isGreaterThan>)
ORDER BY fc.feature_cvterm_id, fc.rank, type_id, fcp.rank;
</select>
<select id="getFeatureCvTermsNoRankBySrcFeature" parameterClass="org.gmod.schema.sequence.Feature"
resultMap="select-featurecvterm-no-rank">
<include refid="sql_select_feature_cvterm"/>
WHERE feature_id IN
(SELECT feature_id FROM featureloc fl WHERE srcfeature_id=$featureId$
<isGreaterThan property="featureLoc.fmin" compareValue="0" prepend="AND">
<![CDATA[ fl.fmin > $featureLoc.fmin$ AND fl.fmax < $featureLoc.fmax$ ]]>
</isGreaterThan>)
ORDER BY fc.feature_cvterm_id, type_id, fcp.rank;
</select>
<select id="getFeatureCvTermsByFeature" parameterClass="Feature"
resultMap="select-featurecvterm">
<include refid="sql_select_feature_cvterm"/>
<dynamic>
<isNotNull property="uniqueName" prepend="WHERE">
feature_id IN (SELECT feature_id FROM feature WHERE uniquename=#uniqueName#)
</isNotNull>
</dynamic>
ORDER BY fc.feature_cvterm_id, fc.rank, type_id, fcp.rank;
</select>
<!-- same as getFeatureCvTermsByFeature but without feature_cvterm.rank -->
<select id="getFeatureCvTermsNoRankByFeature" parameterClass="Feature"
resultMap="select-featurecvterm-no-rank">
<include refid="sql_select_feature_cvterm"/>
<dynamic>
<isNotNull property="uniqueName" prepend="WHERE">
feature_id=(SELECT feature_id FROM feature WHERE uniquename=#uniqueName#)
</isNotNull>
</dynamic>
ORDER BY fc.feature_cvterm_id, type_id, fcp.rank;
</select>
<select id="getFeatureCvTermColumnsForASchema" parameterClass="java.lang.String"
resultClass="java.lang.String" cacheModel="featurecvterm-rank-cache">
SELECT pg_attribute.attname
FROM pg_attribute, pg_class, pg_namespace
WHERE pg_namespace.oid=pg_class.relnamespace AND
attrelid=pg_class.oid AND
relname='feature_cvterm' AND
attnum > 0
<!--AND nspname=#value#-->
</select>
<delete id="deleteFeatureCvTerm" parameterClass="FeatureCvTerm">
DELETE FROM feature_cvterm WHERE
feature_cvterm_id=$featureCvTermId$
</delete>
<!-- UPDATE -->
<update id="updateFeatureCvTerm"
parameterClass="FeatureCvTerm">
UPDATE feature_cvterm
SET rank=$rank$
WHERE feature_cvterm_id=$featureCvTermId$
</update>
<!-- INSERT -->
<insert id="insertFeatureCvTerm"
parameterClass="FeatureCvTerm">
INSERT INTO feature_cvterm
( feature_cvterm_id, feature_id, cvterm_id, pub_id, rank, is_not )
VALUES
( nextval('feature_cvterm_feature_cvterm_id_seq'),
(SELECT feature_id FROM feature WHERE uniquename=#feature.uniqueName#),
<isGreaterThan property="cvTerm.cvTermId" compareValue="0">
$cvTerm.cvTermId$,
</isGreaterThan>
<isEqual property="cvTerm.cvTermId" compareValue="0">
(SELECT cvterm_id FROM cvterm WHERE name=#cvTerm.name# AND
cv_id = (SELECT cv_id FROM cv WHERE name=#cvTerm.cv.name#)),
</isEqual>
<dynamic>
<isNotNull property="pub">
<isEqual property="pub.pubId" compareValue="0">
(SELECT pub_id FROM pub WHERE uniquename=#pub.uniqueName#),
</isEqual>
<isGreaterThan property="pub.pubId" compareValue="0">
$pub.pubId$,
</isGreaterThan>
</isNotNull>
<isNull property="pub">
(SELECT pub_id FROM pub WHERE uniquename='null' OR uniquename='NULL'),
</isNull>
</dynamic>
$rank$,
$not$ )
</insert>
</sqlMap>
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