diff --git a/artemis_sqlmap/Feature.xml b/artemis_sqlmap/Feature.xml
index b07917e695d2b01e2746cc64facc6f3a87985d71..e30fdf10413cc4cb06e8f7883f37ecfa2036dff7 100644
--- a/artemis_sqlmap/Feature.xml
+++ b/artemis_sqlmap/Feature.xml
@@ -25,7 +25,9 @@
<parameter property="featureCvTerms" javaType="java.util.List"/>
</parameterMap>
- <resultMap id="map-basicfeature" class="Feature">
+ <!-- resultMap templates below -->
+
+ <resultMap id="template-basicfeature" class="Feature">
<result property="timeLastModified" column="timelastmodified"/>
<result property="featureId" column="id"/>
<result property="uniqueName" column="uniquename"/>
@@ -33,9 +35,30 @@
<result property="seqLen" column="seqlen" nullValue="-1" />
<result property="obsolete" column="obsolete" />
</resultMap>
-
- <resultMap id="map-feature" class="Feature"
- groupBy="featureId" extends="map-basicfeature">
+
+ <resultMap id="template-basicfeature-all-lazy" class="Feature"
+ extends="template-basicfeature">
+ <result property="cvTerm" column="type_id" select="getCvtermByCvTermId" />
+ <result property="dbXRef" column="dbXRefId"
+ select="getDbXRefByDbXRefId" />
+ <result property="featureLocsForFeatureId" column="{id=id}"
+ select="getFeatureLoc" />
+ <result property="featureProps" column="{feature_id=id}"
+ select="getFeaturePropByFeatureId" />
+ <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="template-feature" class="Feature"
+ extends="template-basicfeature">
<result property="organism.organismId" column="organism_id"/>
<result property="dbXRef" resultMap="DbXRef.select-dbxref" />
<result property="featureProps" resultMap="FeatureProp.map-featureprop" />
@@ -51,42 +74,44 @@
select="getLazyFeatureSynonymsByUniquename" />
<result property="featureDbXRefs" column="{featureId=id}"
select="getFeatureDbXRef" />
- <result property="featureCvTerms" column="{{uniqueName=uniquename}}"
- select="getFeatureCvTermsByFeature"/>
<result property="featurePubs" column="{featureId=id}" select="getFeaturePubsByFeature"/>
</resultMap>
+
+ <!-- resultMap proper below -->
+
+ <resultMap id="map-feature" class="Feature"
+ groupBy="featureId" extends="template-feature">
+ <result property="featureCvTerms" column="{{uniqueName=uniquename}}"
+ select="getFeatureCvTermsByFeature"/>
+ </resultMap>
+
+ <resultMap id="map-feature-no-rank" class="Feature"
+ groupBy="featureId" extends="template-feature">
+ <result property="featureCvTerms" column="{{uniqueName=uniquename}}"
+ select="getFeatureCvTermsNoRankByFeature"/>
+ </resultMap>
+
- <!-- mapping for feature table and lazy loading of feature_dbxref, feature_relationship,
- featureprop, organism tables -->
-
- <resultMap id="map-feature-lazy-no-residues" class="Feature"
- extends="map-basicfeature">
- <result property="cvTerm" column="type_id" select="getCvtermByCvTermId" />
- <result property="dbXRef" column="dbXRefId"
- select="getDbXRefByDbXRefId" />
- <result property="featureLocsForFeatureId" column="{id=id}"
- select="getFeatureLoc" />
- <result property="featureProps" column="{feature_id=id}"
- select="getFeaturePropByFeatureId" />
- <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" />
+ <!-- mapping for feature table and lazy loading -->
+ <resultMap id="map-feature-lazy-no-residues" class="Feature"
+ extends="template-basicfeature-all-lazy">
<result property="featureCvTerms" column="{{uniqueName=uniquename}}"
select="getFeatureCvTermsByFeature"/>
- <result property="organism" column="{organismId=organismId}"
- select="getOrganism" />
</resultMap>
<resultMap id="map-feature-lazy" class="Feature"
- extends="map-feature-lazy-no-residues">
+ extends="template-basicfeature-all-lazy">
+ <result property="featureCvTerms" column="{{uniqueName=uniquename}}"
+ select="getFeatureCvTermsByFeature"/>
+ <result property="residues" column="residues" />
+ </resultMap>
+
+ <resultMap id="map-feature-lazy-no-rank" class="Feature"
+ extends="template-basicfeature-all-lazy">
+ <result property="featureCvTerms" column="{{uniqueName=uniquename}}"
+ select="getFeatureCvTermsNoRankByFeature"/>
<result property="residues" column="residues" />
</resultMap>
-
<resultMap id="map-feature-name-lazy" class="Feature">
<result property="featureId" column="id"/>
@@ -94,11 +119,10 @@
<result property="cvTerm.name" column="name" />
<result property="featureRelationshipsForSubjectId" column="{subject_id=id}"
select="getParentFeatureRelationship" />
- </resultMap>
-
+ </resultMap>
<resultMap id="map-feature-withprop" class="Feature"
- groupBy="featureId" extends="map-basicfeature">
+ groupBy="featureId" extends="template-basicfeature">
<result property="cvTerm" column="type_id" select="getCvtermByCvTermId" />
<result property="featureProps" resultMap="FeatureProp.map-featureprop" />
<result property="featureDbXRefs" column="{featureId=id}"
@@ -117,7 +141,7 @@
<resultMap id="map-similaritymatch-lazy" class="Feature"
- groupBy="featureId" extends="map-basicfeature">
+ groupBy="featureId" extends="template-basicfeature">
<result property="cvTerm.cvTermId" column="type_id" />
<result property="featureLocsForFeatureId" column="{id=id}"
select="getFeatureLoc" />
@@ -157,10 +181,8 @@
<!-- SQL -->
<!-- get feature -->
-
- <select id="getFeature" parameterClass="Feature"
- resultMap="map-feature">
- SELECT
+ <sql id="sql-feature">
+ SELECT
timelastmodified,
f.feature_id AS id,
f.organism_id,
@@ -202,11 +224,20 @@
uniquename LIKE #uniqueName#
</isNotNull>
</dynamic>
+ </sql>
+
+ <select id="getFeature" parameterClass="Feature"
+ resultMap="map-feature">
+ <include refid="sql-feature"/>
+ </select>
+
+ <select id="getFeatureNoFeatureCvTermRank" parameterClass="Feature"
+ resultMap="map-feature-no-rank">
+ <include refid="sql-feature"/>
</select>
- <select id="getLazyFeature" resultMap ="map-feature-lazy"
- parameterClass="Feature">
- SELECT
+ <sql id="sql-lazy-feature">
+ SELECT
timelastmodified,
f.feature_id AS id,
uniquename,
@@ -246,6 +277,17 @@
cvterm.name=#cvTerm.name#
</isNotNull>
</dynamic>
+ </sql>
+
+ <select id="getLazyFeature" resultMap ="map-feature-lazy"
+ parameterClass="Feature">
+ <include refid="sql-lazy-feature"/>
+ </select>
+
+ <select id="getLazyFeatureNoFeatureCvTermRank"
+ resultMap ="map-feature-lazy-no-rank"
+ parameterClass="Feature">
+ <include refid="sql-lazy-feature"/>
</select>
@@ -264,52 +306,6 @@
FROM feature f
WHERE f.feature_id=$featureId$
</select>
-
- <select id="getLazyFeatureById" resultMap ="map-feature-lazy" >
- SELECT
- timelastmodified,
- f.feature_id AS id,
- uniquename,
- organism_id AS organismId,
- f.is_obsolete AS obsolete,
- f.name AS feature_name,
- f.type_id,
- f.dbxref_id AS dbXRefId,
- f.seqlen,
- residues
- FROM feature f
- WHERE f.feature_id=$featureId$
- </select>
-
- <select id="getLazyFeatureNameAndTypeById" resultMap ="map-feature-name-lazy" >
- SELECT
- uniquename, cvTerm.name, feature_id AS id
- FROM feature f
- LEFT JOIN cvterm ON cvterm.cvterm_id=type_id
- WHERE f.feature_id=$featureId$
- </select>
-
-
- <select id="getFeatureById" resultMap ="map-feature-withprop"
- cacheModel="feature-cache">
- SELECT
- timelastmodified,
- f.feature_id AS id,
- uniquename,
- organism_id AS organismId,
- f.is_obsolete AS obsolete,
- f.name AS feature_name,
- f.type_id,
- f.dbxref_id,
- f.seqlen,
- fp.type_id AS prop_type_id, fp.rank AS prop_rank, fp.value, fp.featureprop_id,
- dbxref.*, db.*
- FROM feature f
- LEFT JOIN featureprop fp ON fp.feature_id=f.feature_id
- LEFT JOIN dbxref ON f.dbxref_id=dbxref.dbxref_id
- LEFT JOIN db ON dbxref.db_id=db.db_id
- WHERE f.feature_id=$featureId$
- </select>
<select id="getFeaturesByListOfIds" resultMap ="map-feature-withprop">
SELECT
@@ -407,36 +403,6 @@
</select>
- <!--
- <select id="getResidueFeatures" parameterClass="java.lang.Integer"
- resultMap="map-feature-with-residues-result">
- SELECT feature.name, uniquename, feature_id, type_id,
- feature.organism_id, abbreviation, genus, species, common_name,
- cvterm.name AS cvterm_name
- FROM feature
- LEFT JOIN organism ON organism.organism_id=feature.organism_id
- LEFT JOIN cvterm ON cvterm.cvterm_id=feature.type_id
- WHERE <isNotNull> feature.organism_id=$value$ AND </isNotNull>
- cvterm.name!='mRNA' AND cvterm.name!='pseudogenic_transcript' AND
- cvterm.name!='polypeptide' AND
- residues notnull AND residues NOT LIKE '' ORDER BY common_name
- </select>
-
- <select id="getResidueFeaturesByOrganismCommonName" parameterClass="java.lang.String"
- resultMap="map-feature-with-residues-result">
- SELECT feature.name, uniquename, feature_id, type_id,
- feature.organism_id, abbreviation, genus, species, common_name,
- cvterm.name AS cvterm_name
- FROM feature
- LEFT JOIN organism ON organism.organism_id=feature.organism_id
- LEFT JOIN cvterm ON cvterm.cvterm_id=feature.type_id
- WHERE <isNotNull> organism.common_name=#value# AND </isNotNull>
- cvterm.name!='mRNA' AND cvterm.name!='pseudogenic_transcript' AND
- cvterm.name!='polypeptide' AND
- residues notnull AND residues NOT LIKE '' ORDER BY common_name
- </select>
- -->
-
<sql id="source_feature_cvterm_names">
cvterm.name LIKE '%chromosome%' OR cvterm.name LIKE '%sequence%' OR
cvterm.name IN ('supercontig', 'ultra_scaffold', 'golden_path_region', 'contig')
diff --git a/artemis_sqlmap/FeatureCvTerm.xml b/artemis_sqlmap/FeatureCvTerm.xml
index 3abdec1dfc49df8dfcab35c290950a6e11e3a5bb..6ef8cd98e14b5e55f38f4bc3f6ad849d2a4d46b1 100644
--- a/artemis_sqlmap/FeatureCvTerm.xml
+++ b/artemis_sqlmap/FeatureCvTerm.xml
@@ -5,16 +5,14 @@
<sqlMap namespace="FeatureCvTerm">
- <cacheModel id="featurecvterm-rank-cache" type ="LRU" readOnly="true">
+ <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" />
@@ -41,10 +39,8 @@
<!-- select feature_cvterm -->
-
- <select id="getFeatureCvTermsBySrcFeature" parameterClass="org.gmod.schema.sequence.Feature"
- resultMap="select-featurecvterm">
- SELECT
+ <sql id="sql_select_feature_cvterm">
+ SELECT
fc.*,
fcp.type_id, fcp.value, fcp.rank AS fcp_rank,
cvterm.name AS cvterm_name,
@@ -60,6 +56,11 @@
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">
@@ -71,22 +72,7 @@
<select id="getFeatureCvTermsNoRankBySrcFeature" parameterClass="org.gmod.schema.sequence.Feature"
resultMap="select-featurecvterm-no-rank">
- 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
+ <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">
@@ -98,22 +84,7 @@
<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
+ <include refid="sql_select_feature_cvterm"/>
<dynamic>
<isNotNull property="uniqueName" prepend="WHERE">
feature_id IN (SELECT feature_id FROM feature WHERE uniquename=#uniqueName#)
@@ -121,30 +92,12 @@
</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.is_not,
- 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
+ <include refid="sql_select_feature_cvterm"/>
<dynamic>
<isNotNull property="uniqueName" prepend="WHERE">
feature_id=(SELECT feature_id FROM feature WHERE uniquename=#uniqueName#)
@@ -154,7 +107,6 @@
</select>
-
<select id="getFeatureCvTermColumnsForASchema" parameterClass="java.lang.String"
resultClass="java.lang.String" cacheModel="featurecvterm-rank-cache">
SELECT pg_attribute.attname
diff --git a/uk/ac/sanger/artemis/chado/IBatisDAO.java b/uk/ac/sanger/artemis/chado/IBatisDAO.java
index 83dabe75396d3809e43941182a3dbbb2f4ecd7f7..47ac96692a522a06b1200cde18d8a3851f979e06 100644
--- a/uk/ac/sanger/artemis/chado/IBatisDAO.java
+++ b/uk/ac/sanger/artemis/chado/IBatisDAO.java
@@ -64,6 +64,8 @@ public class IBatisDAO extends GmodDAO
private static org.apache.log4j.Logger logger4j =
org.apache.log4j.Logger.getLogger(IBatisDAO.class);
private SqlMapClientWrapper sqlMap;
+ private boolean featureCvTermRank = true;
+ private boolean featureCvTermRankChecked = false;
/**
* Define a iBatis data access object. This uses <code>DbSqlConfig</code>
@@ -87,6 +89,33 @@ public class IBatisDAO extends GmodDAO
sqlMap.close();
}
+ /**
+ * Test to see if this is an old chado database version
+ * without the feature_cvterm.rank column.
+ * @return true if the feature_cvterm.rank column exists.
+ */
+ private boolean isFeatureCvTermRank()
+ {
+ if(featureCvTermRankChecked)
+ return featureCvTermRank;
+
+ String schema = ArtemisUtils.getCurrentSchema();
+ // check column names
+ List list = sqlMap.queryForList("getFeatureCvTermColumnsForASchema", schema);
+ featureCvTermRank = false;
+ for(int i=0; i<list.size(); i++)
+ {
+ if( ((String)list.get(i)).equals("rank") )
+ {
+ featureCvTermRank = true;
+ break;
+ }
+ }
+
+ featureCvTermRankChecked = true;
+ return featureCvTermRank;
+ }
+
//////
////// GeneralDaoI
//////
@@ -143,23 +172,7 @@ public class IBatisDAO extends GmodDAO
public List getFeatureCvTermsBySrcFeature(Feature srcFeature)
{
-// find whether current schema has a feature_cvterm.rank column
- String schema = ArtemisUtils.getCurrentSchema();
-
- // check column names
- List list = sqlMap.queryForList("getFeatureCvTermColumnsForASchema", schema);
-
- boolean rank_exists = false;
- for(int i=0; i<list.size(); i++)
- {
- if( ((String)list.get(i)).equals("rank") )
- {
- rank_exists = true;
- break;
- }
- }
-
- if(rank_exists)
+ if(isFeatureCvTermRank())
{
logger4j.debug("USE getFeatureCvTermsBySrcFeature()");
return sqlMap.queryForList("getFeatureCvTermsBySrcFeature",
@@ -223,7 +236,11 @@ public class IBatisDAO extends GmodDAO
org.gmod.schema.sequence.Feature feature =
new org.gmod.schema.sequence.Feature();
feature.setFeatureId(id);
- return (Feature)sqlMap.queryForObject("getLazyFeature", feature);
+
+ if(isFeatureCvTermRank())
+ return (Feature)sqlMap.queryForObject("getLazyFeature", feature);
+ else
+ return (Feature)sqlMap.queryForObject("getLazyFeatureNoFeatureCvTermRank", feature);
}
public List getFeaturesByListOfIds(final List featureIds)
@@ -236,7 +253,11 @@ public class IBatisDAO extends GmodDAO
org.gmod.schema.sequence.Feature feature =
new org.gmod.schema.sequence.Feature();
feature.setUniqueName(uniquename);
- return sqlMap.queryForList("getLazyFeature", feature);
+
+ if(isFeatureCvTermRank())
+ return sqlMap.queryForList("getLazyFeature", feature);
+ else
+ return sqlMap.queryForList("getLazyFeatureNoFeatureCvTermRank", feature);
}
public Feature getFeatureByUniqueName(String uniquename, String featureType)
@@ -249,7 +270,10 @@ public class IBatisDAO extends GmodDAO
cvTerm.setName(featureType);
feature.setCvTerm(cvTerm);
- return (Feature)sqlMap.queryForObject("getLazyFeature", feature);
+ if(isFeatureCvTermRank())
+ return (Feature)sqlMap.queryForObject("getLazyFeature", feature);
+ else
+ return (Feature)sqlMap.queryForObject("getLazyFeatureNoFeatureCvTermRank", feature);
}
@@ -270,10 +294,10 @@ public class IBatisDAO extends GmodDAO
feature.setUniqueName(name);
feature.setFeatureSynonyms(feature_synonym_list);
- List features = sqlMap.queryForList("getLazyFeature", feature);
-
- return features;
-
+ if(isFeatureCvTermRank())
+ return sqlMap.queryForList("getLazyFeature", feature);
+ else
+ return sqlMap.queryForList("getLazyFeatureNoFeatureCvTermRank", feature);
}
/**
@@ -318,11 +342,10 @@ public class IBatisDAO extends GmodDAO
*/
public List getFeaturesByLocatedOnFeature(final Feature feature)
{
- List feature_list = sqlMap.queryForList("getFeature", feature);
-
- // merge same features in the list
- //return mergeList(feature_list);
- return feature_list;
+ if(isFeatureCvTermRank())
+ return sqlMap.queryForList("getFeature", feature);
+ else
+ return sqlMap.queryForList("getFeatureNoFeatureCvTermRank", feature);
}
/**
@@ -349,23 +372,7 @@ public class IBatisDAO extends GmodDAO
*/
public List getFeatureCvTermsByFeature(Feature feature)
{
- // find whether current schema has a feature_cvterm.rank column
- String schema = ArtemisUtils.getCurrentSchema();
-
- // check column names
- List list = sqlMap.queryForList("getFeatureCvTermColumnsForASchema", schema);
-
- boolean rank_exists = false;
- for(int i=0; i<list.size(); i++)
- {
- if( ((String)list.get(i)).equals("rank") )
- {
- rank_exists = true;
- break;
- }
- }
-
- if(rank_exists)
+ if(isFeatureCvTermRank())
return
sqlMap.queryForList("getFeatureCvTermsByFeature", feature);
else