handle schema without feature_cvterm.rank column

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@5178 ee4ac58c-ac51-4696-9907-e4b3aa274f04

artemis_sqlmap/FeatureCvTerm.xml

@@ -8,7 +8,8 @@
       <typeAlias alias="FeatureCvTerm"
         type="org.gmod.schema.sequence.FeatureCvTerm"/>
         
-     <resultMap id="select-featurecvterm" class="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" />
@@ -16,7 +17,7 @@
         <result property="cvTerm.name"       column="cvterm_name" />
         <result property="cvTerm.cv.name"    column="cv_name" />
         <result property="not"               column="is_not" />
-        <result property="rank"              column="fc_rank" />
+
         <result property="featureCvTermProps" resultMap="FeatureCvTermProp.feature_cvtermprop"  />
         <result property="pub.pubId"         column="pub_id" />
         <result property="pub.uniqueName"    column="uniquename" />
@@ -27,17 +28,49 @@
         <!-- <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 -->
      <select id="getFeatureCvTermsByFeature" parameterClass="Feature"
              resultMap="select-featurecvterm">
+        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
+        <dynamic>
+          <isNotNull property="uniqueName" prepend="WHERE">
+            feature_id=(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">
         SELECT
           fc.feature_id,
           fc.feature_cvterm_id,
           fc.cvterm_id, 
-          fc.rank AS fc_rank, 
           fc.is_not, 
-          fcp.type_id, fcp.value, fcp.rank,
+          fcp.type_id, fcp.value, fcp.rank AS fcp_rank,
           cvterm.name AS cvterm_name,
           cv.name AS cv_name,
           pub.pub_id, 
@@ -56,9 +89,23 @@
             feature_id=(SELECT feature_id FROM feature WHERE uniquename=#uniqueName#)
           </isNotNull>
         </dynamic>
-        ORDER BY fc.feature_cvterm_id, fc.rank, type_id, fcp.rank;
+        ORDER BY fc.feature_cvterm_id, type_id, fcp.rank;
+     </select>
+     
+     
+     
+     <select id="getFeatureCvTermColumnsForASchema" parameterClass="java.lang.String"
+             resultClass="java.lang.String">
+       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=$featureCvTermId$

artemis_sqlmap/FeatureCvTermProp.xml

@@ -11,7 +11,7 @@
      <resultMap id="feature_cvtermprop" class="FeatureCvTermProp">
         <result property="cvTerm.cvTermId" column="type_id" />
         <result property="value" column="value" />
-        <result property="rank" column="rank" />
+        <result property="rank" column="fcp_rank" />
      </resultMap>
      
     <!-- INSERT -->