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<?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="Organism">
<cacheModel id="organism-cache" type ="LRU" readOnly="true">
<flushInterval hours="24"/>
<property name="cache-size" value="85" />
</cacheModel>
<resultMap id="map-organism" class="org.gmod.schema.organism.Organism">
<result property="organismId" column="organismId"/>
<result property="abbreviation" column="abbreviation"/>
<result property="commonName" column="commonName"/>
<result property="genus" column="genus"/>
<result property="species" column="species"/>
<result property="comment" column="comment"/>
<result property="organismProps" column="organismId" select="getOrganismPropByOrganismIdLazy"/>
</resultMap>
<select id="getOrganism" resultMap="map-organism" cacheModel="organism-cache">
SELECT organism_id AS organismId, abbreviation, genus, species, common_name AS commonName, comment
FROM organism
<dynamic>
<isNotNull property="organismId">
<isGreaterThan property="organismId" compareValue="0">
WHERE organism_id=#organismId#
<isNotNull prepend="AND" property="commonName">
common_name=#commonName#
</isNotNull>
</isGreaterThan>
<isLessEqual property="organismId" compareValue="0">
<isNotNull prepend="WHERE" property="commonName">
common_name=#commonName#
</isNotNull>
</isLessEqual>
</isNotNull>
<isNull property="organismId">
<isNotNull prepend="WHERE" property="commonName">
common_name=#commonName#
</isNotNull>
</isNull>
<isNull prepend="ORDER BY" property="organismId">
commonName
</isNull>
</dynamic>
</select>
<select id="getOrganismIdBySrcFeatureIdOrFeatureId" resultClass="java.lang.Integer"
parameterClass="org.gmod.schema.sequence.Feature" cacheModel="organism-cache">
SELECT organism_id AS organismId FROM feature f WHERE
<isGreaterThan property="featureLoc.featureBySrcFeatureId.featureId" compareValue="0">
f.feature_id=$featureLoc.featureBySrcFeatureId.featureId$
</isGreaterThan>
<isEqual property="featureLoc.featureBySrcFeatureId.featureId" compareValue="0">
<isGreaterThan property="featureId" compareValue="0">
f.feature_id=$featureId$
</isGreaterThan>
</isEqual>
<isNull property="featureLoc.featureBySrcFeatureId">
f.feature_id=$featureId$
</isNull>
</select>
<select id="getOrganismsContainingSrcFeatures" 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 cvterm on feature.type_id = cvterm.cvterm_id
WHERE residues notnull AND residues != ''
AND ( <include refid="source_feature_cvterm_names"/> )
</select>
<select id="getTopLevelOrganisms" resultMap="map-organism">
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>
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