FeatureRelationship.xml

<?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>