Feature.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="Feature"> 
 
  <typeAlias alias="Feature"
        type="org.gmod.schema.sequence.Feature"/>
                 
  <parameterMap id="schema-cvlist" 
                class="Feature">
    <parameter property="schema" javaType="java.lang.String"/>
    <parameter property="featureCvTerms" javaType="java.util.List"/>
  </parameterMap> 

  <resultMap id="select-feature" 
             class="Feature" groupBy="featureId">
    <result property="timeLastModified" column="timelastmodified"/>
   	<result property="featureId" column="id"/>
   	<result property="featureRelationshipsForSubjectId" 
   	            resultMap="FeatureRelationship.feature_relationship"  /> 
   <!--	    
  	<result property="featureRelationship.featureByObjectId.featureId" column="object_id"/>
  	<result property="featureRelationship.cvTerm.cvTermId" column="relation_type_id"/>
  	<result property="featureRelationship.rank" column="rank"/>
  	-->
    <result property="featureLoc.strand" column="strand" nullValue="0"/>
    <result property="featureLoc.fmin" column="fmin" nullValue="-1"/>
    <result property="featureLoc.fmax" column="fmax" nullValue="0"/>
    <result property="featureLoc.phase" column="phase"/>
    <result property="uniqueName" column="uniquename"/>
    <result property="cvTerm.cvTermId" column="type_id"/>
    <result property="featureProps" resultMap="FeatureProp.featureprop" />
   <!--
    <result property="featureprop.cvTerm.cvTermId" column="prop_type_id" nullValue="0"/>
    <result property="featureprop.value" column="value"/>
    <result property="featureprop.rank" column="prop_rank" nullValue="0"/> 
    -->
  </resultMap>

  <!-- mapping for feature table and lazy loading of feature_dbxref, feature_relationship,
       featureprop, organism tables -->
  <resultMap id="select-feature-lazy" 
             class="Feature">       
    <result property="timeLastModified" column="timelastmodified"/>
   	<result property="featureId" column="id"/>
    <result property="uniqueName" column="uniquename"/>
    <result property="name" column="name"/>
    <result property="residues" column="residues" />
    <result property="seqLen" column="length" nullValue="-999" />
    <result property="cvTerm" column="type_id" select="selectCvterm" />
    <result property="dbXRef" column="dbXRefId"
                              select="selectDbXRef" />
    <result property="featureLocsForFeatureId" column="{id=id}" 
                                               select="getFeatureLoc" />
    <result property="featureProps" column="{feature_id=id}" 
                                       select="selectFeatureProp" />
    <result property="featureDbXRefs" column="{featureId=id}"
                                      select="getFeatureDbXRef" />
    <result property="featureRelationshipsForObjectId" column="{object_id=id}" 
                                       select="getFeatureRelationship" />  
    <result property="featureRelationshipsForSubjectId" column="{subject_id=id}" 
                                       select="getFeatureRelationship" /> 
    <result property="featureSynonyms" column="{feature.uniqueName=uniqueName}" 
                                       select="getLazyFeatureSynonymsByUniquename" />                          
    <result property="organism" column="{organismId=organismId}" 
                                select="getOrganism" />
  </resultMap>
     
     
  <resultMap id="select-similaritymatch" 
             class="Feature" groupBy="featureId">       
    <result property="timeLastModified" column="timelastmodified"/>
   	<result property="featureId" column="id"/>
    <result property="uniqueName" column="uniquename"/>
    <result property="name" column="name"/>
    <result property="seqLen" column="length" nullValue="-999" />
    <result property="residues" column="residues" />
    <result property="cvTerm" column="type_id" select="selectCvterm" />
    <result property="featureLocsForFeatureId" resultMap="FeatureLoc.select-location" />
    <result property="featureProps" column="{feature_id=id}" 
                                       select="selectFeatureProp" />
    <result property="analysisFeatures" column="{feature_id=id}" 
                                        select="selectAnalysisFeatures" />                                                
  </resultMap>
    
  <resultMap id="select-feature-with-residues-result" 
             class="Feature">
    <result property="name" column="name"/>
    <result property="uniqueName" column="uniquename"/>
    <result property="featureId" column="feature_id"/>
    <result property="cvTerm.cvTermId" column="type_id"/>
  </resultMap>
     
  <!-- SQL --> 
  <!-- get feature -->

     <select id="getFeature" parameterClass="Feature" 
                             resultMap="select-feature">
        SELECT
          timelastmodified, 
          f.feature_id AS id, 
          fr.object_id,
          fr.type_id AS relation_type_id,
          fr.rank,
          fr.value AS relation_value,
          fl.strand, 
          fmin, 
          fmax, 
          uniquename,
          f.type_id,  
          fp.type_id AS prop_type_id,
          fp.rank AS prop_rank,
          fp.value,
          fl.phase
        FROM feature f
        LEFT JOIN feature_relationship fr ON fr.subject_id = f.feature_id
        LEFT JOIN featureprop fp          ON fp.feature_id = f.feature_id
        LEFT JOIN featureloc fl           ON f.feature_id  = fl.feature_id
        WHERE
            <dynamic>
             <isGreaterThan property="featureLoc.featureBySrcFeatureId.featureId" compareValue="0"> 
               srcfeature_id=$featureLoc.featureBySrcFeatureId.featureId$ 
             </isGreaterThan>
             <isNotNull property="uniqueName">                        
               uniquename LIKE #uniqueName# 
             </isNotNull>
           </dynamic>    
        ORDER BY f.type_id,  uniquename
     </select>
 
     <select id="getLazyFeature" resultMap ="select-feature-lazy" 
                                 parameterClass="Feature">
	 SELECT
	    timelastmodified,
	 	f.feature_id AS id,
	 	uniquename,
	 	organism_id AS organismId,
		f.name,
	 	f.type_id,
	 	f.dbxref_id AS dbXRefId,
		seqlen AS length,
		residues
	 FROM feature f
	 <dynamic>
	   <isNotNull property="cvTerm.name">
	     LEFT JOIN cvterm ON f.type_id=cvterm.cvterm_id
	   </isNotNull>
	 </dynamic>
	 WHERE
	   <dynamic>
          <isGreaterThan property="featureId" compareValue="0"> 
            f.feature_id=$featureId$ AND
          </isGreaterThan>
          
          <isNotNull property="uniqueName">                                 
            <isNotNull property="featureSynonyms">
              <iterate property="featureSynonyms" conjunction="OR" open="(" close=") OR">
               f.feature_id=#featureSynonyms[].feature.featureId#
             </iterate>
            </isNotNull>
            ( uniquename LIKE #uniqueName# ESCAPE '/' OR f.name LIKE #uniqueName# ESCAPE '/') AND              
          </isNotNull>
          
          <isGreaterThan property="cvTerm.cvTermId" compareValue="0"> 
            f.type_id=$cvTerm.cvTermId$ AND
          </isGreaterThan>
          
         <isNotNull property="cvTerm.name"> 
            cvterm.name=#cvTerm.name# AND
          </isNotNull>
       </dynamic>
         f.feature_id > 0 
    </select>

    <select id="getLazyFeatureById" resultMap ="select-feature-lazy" >
	 SELECT
	    timelastmodified,
	 	f.feature_id AS id,
	 	uniquename,
	 	organism_id AS organismId,
		f.name,
	 	f.type_id,
	 	f.dbxref_id AS dbXRefId,
		seqlen AS length,
		residues
	 FROM feature f
	 WHERE f.feature_id=$featureId$
    </select>
    
    <!-- Returns matches for all features on a given srcfeature -->
     <select id="getLazySimilarityMatches" parameterClass="java.lang.Integer" 
                             resultMap="select-similaritymatch">
        SELECT 
         timelastmodified, 
         f.feature_id AS id, 
         f.uniquename, 
         f.type_id,
         f.name,
	 	 f.seqlen AS length,
	 	 f.residues,
         srcfeature_id, fmin, fmax, strand, phase, residue_info, locgroup, rank
       FROM feature f 
       LEFT JOIN featureloc fl ON f.feature_id=fl.feature_id 
       WHERE  f.feature_id IN 
         (   SELECT feature_id FROM featureloc WHERE srcfeature_id IN 
           ( SELECT feature_id  FROM featureloc WHERE srcfeature_id=$value$) ) 
       ORDER BY f.feature_id
     </select>

     <!-- Returns matches for a list of feature_id's -->
     <select id="getLazySimilarityMatchesByFeatureIds" parameterClass="java.util.List" 
                             resultMap="select-similaritymatch">
        SELECT 
         timelastmodified, 
         f.feature_id AS id, 
         f.uniquename, 
         f.type_id,
         f.name,
	 	 f.seqlen AS length,
	 	 f.residues,
         srcfeature_id, fmin, fmax, strand, phase, residue_info, locgroup, rank
       FROM feature f 
       LEFT JOIN featureloc fl ON f.feature_id=fl.feature_id 
       WHERE  f.feature_id IN 
         (   SELECT feature_id FROM featureloc WHERE srcfeature_id IN
           <iterate open="(" close=")" conjunction=",">
            #[]#
           </iterate>
         ) 
       ORDER BY f.feature_id
     </select>


    <select id="getSchema" resultClass="java.lang.String">
       SELECT schema_name FROM information_schema.schemata WHERE schema_name=schema_owner
         ORDER BY schema_name
    </select>

    <select id="getResidueType" parameterClass="java.lang.String" 
            resultClass="java.lang.Long">
       SELECT DISTINCT type_id 
       FROM feature 
       WHERE residues notnull
    </select>


    <select id="getResidueFeatures" parameterClass="java.util.Map"
            resultMap="select-feature-with-residues-result">
       SELECT
         name,
         uniquename,
         feature_id,
         type_id
       FROM feature WHERE residues notnull AND residues NOT LIKE ''
       <!--
         <iterate prepend="AND" property="cvTermIds" conjunction="OR" open="(" close=")">
           type_id=#cvTermIds[]#
         </iterate>
       ORDER BY abbreviation, type_id 
       -->
    </select>

    
    <select id="currval" resultClass="java.lang.Integer" 
            parameterClass="java.lang.String">
      SELECT currval('$value$')
    </select>


    <!--  WRITE BACK METHODS  -->
    
    <!--  UPDATE  -->
    <update id="updateFeature"
            parameterClass="Feature">
      UPDATE feature
      SET uniquename=#uniqueName#
      <isNotNull property="cvTerm.cvTermId">
        , type_id=$cvTerm.cvTermId$
      </isNotNull>
      <isNotNull property="timeLastModified">
        , timelastmodified=#timeLastModified#
      </isNotNull>
      WHERE feature_id=$featureId$
    </update>
   
    <update id="updateFeatureResidues"
            parameterClass="uk.ac.sanger.artemis.chado.FeatureForUpdatingResidues">
            UPDATE feature SET 
            residues=substring(residues from 1 for $startBase$) || 
                     <dynamic>
                     <isNotNull property="newSubSequence">
                       #newSubSequence# ||
                     </isNotNull>
                     </dynamic>
                     substring(residues from $endBase$ for $basesToEnd$),
            seqlen=$seqLen$
            WHERE feature_id=$featureId$
    </update>
    
    <!--  INSERT  -->
    <insert id="insertFeature" 
            parameterClass="Feature">
      INSERT INTO feature 
        ( feature_id, organism_id, name, uniquename, type_id
          <isGreaterThan property="seqLen" compareValue="0"> , seqlen </isGreaterThan>
          <isNotNull property="dbXRef.dbXRefId"> , dbxref_id </isNotNull> )
      VALUES
        ( nextval('feature_feature_id_seq'),
          $organism.organismId$,
          #name#,
          #uniqueName#,
          $cvTerm.cvTermId$
          <isGreaterThan property="seqLen" compareValue="0"> , $seqLen$ </isGreaterThan>
          <isNotNull property="dbXRef.dbXRefId"> , $dbXRef.dbXRefId$ </isNotNull> )
    </insert>
   
   <!--
   <update id="updateRegionSequence"
            parameterClass="Feature">
            UPDATE feature SET 
            residues=substring(residues from 1 for $featureLoc.fmin$) || 
                     #residues,jdbcType=text# ||
                     substring(residues from $featureLoc.fmin$ for 
                               (seqLen + $seqLen$)),
            seqlen=(seqLen+$seqLen$)
            WHERE feature_id=$featureLoc.featureBySrcFeatureId.featureId$
   </update>
   -->
   
   <!--  DELETE  -->
   <delete id="deleteFeature" 
           parameterClass="Feature">
      DELETE FROM feature
      WHERE uniquename=#uniqueName# AND type_id=$cvTerm.cvTermId$
   </delete>
   
   <delete id="deleteFeatureById" 
           parameterClass="Feature">
      DELETE FROM feature
      WHERE feature_id=$featureId$
   </delete>
</sqlMap>