diff --git a/artemis_sqlmap/FeatureCvTerm.xml b/artemis_sqlmap/FeatureCvTerm.xml
index 29d98339a9f85c3cccf7704195dbe574e7d72ae4..85d460842add21578f8217599b03f2861ed35e86 100644
--- a/artemis_sqlmap/FeatureCvTerm.xml
+++ b/artemis_sqlmap/FeatureCvTerm.xml
@@ -22,6 +22,8 @@
<result property="pub.uniqueName" column="uniquename" />
<result property="cvTerm.dbXRef.accession" column="accession" />
<result property="cvTerm.dbXRef.db.name" column="name" />
+ <result property="featureCvTermDbXRefs" column="feature_cvterm_id"
+ select="getFeatureCvTermDbXRefByFeatureCvTerm" />
<!-- <result property="pub" column="pub_id" select="selectPub" /> -->
</resultMap>
@@ -56,4 +58,17 @@
ORDER BY fc.feature_cvterm_id, fc.rank, type_id, fcp.rank;
</select>
+ <delete id="deleteFeatureCvTerm" parameterClass="FeatureCvTerm">
+ DELETE FROM feature_cvterm WHERE
+ feature_cvterm_id=$featureCvTermId$
+ </delete>
+
+ <!-- UPDATE -->
+ <update id="updateFeatureCvTerm"
+ parameterClass="FeatureCvTerm">
+ UPDATE feature_cvterm
+ SET rank=$rank$
+ WHERE feature_cvterm_id=$featureCvTermId$
+ </update>
+
</sqlMap>
\ No newline at end of file
diff --git a/artemis_sqlmap/FeatureCvTermDbXRef.xml b/artemis_sqlmap/FeatureCvTermDbXRef.xml
index 459aa9a4b23bd5917a8de432a01e2559ed85faac..409f8451ee34292ce26bb6d3e95a69a5b2301700 100644
--- a/artemis_sqlmap/FeatureCvTermDbXRef.xml
+++ b/artemis_sqlmap/FeatureCvTermDbXRef.xml
@@ -7,6 +7,9 @@
<typeAlias alias="FeatureCvTermDbXRef"
type="org.gmod.schema.sequence.FeatureCvTermDbXRef"/>
+
+ <typeAlias alias="FeatureCvTerm"
+ type="org.gmod.schema.sequence.FeatureCvTerm"/>
<resultMap id="select-featurecvtermdbxref" class="FeatureCvTermDbXRef"
groupBy="featureCvTermId">
@@ -32,4 +35,12 @@
</dynamic>
</select>
+ <select id="getFeatureCvTermDbXRefByFeatureCvTerm" parameterClass="java.lang.Integer"
+ resultMap="select-featurecvtermdbxref">
+ SELECT fcd.feature_cvterm_id, dbx.*, db.name
+ FROM feature_cvterm_dbxref fcd
+ LEFT JOIN dbxref dbx ON dbx.dbxref_id=fcd.dbxref_id
+ LEFT JOIN db ON db.db_id=dbx.db_id
+ WHERE feature_cvterm_id=$feature_cvterm_id$
+ </select>
</sqlMap>
\ No newline at end of file
diff --git a/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java b/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java
index 0dfa0f5b5b4e42f60adf4eae2eac964ab854b843..4f20b63d11db0046754e0e1be1f4bd26422b588e 100644
--- a/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java
+++ b/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java
@@ -54,6 +54,7 @@ import java.util.List;
import java.util.Enumeration;
import javax.swing.JOptionPane;
+import org.gmod.schema.sequence.FeatureCvTermProp;
import org.gmod.schema.sequence.FeatureLoc;
import org.gmod.schema.sequence.FeatureProp;
import org.gmod.schema.sequence.FeatureDbXRef;
@@ -1113,7 +1114,8 @@ public class ChadoTransactionManager
tsn = new ChadoTransaction(ChadoTransaction.DELETE,
old_dbxref,
- feature.getLastModified(), feature);
+ feature.getLastModified(), feature);
+ sql.add(tsn);
}
else if(qualifier_name.equals("codon_start"))
{
@@ -1127,13 +1129,56 @@ public class ChadoTransactionManager
}
else if(isCvTag(qualifier_name))
{
+ /*Qualifier qual = feature.getQualifierByName(qualifier_name);
+ StringVector values = qual.getValues();
+ int beginIndex = qualifier_string.indexOf("term=")+5;
+ int endIndex = qualifier_string.indexOf(";",beginIndex);
+ final String thisTerm;
+ if(endIndex > -1)
+ thisTerm = qualifier_string.substring(beginIndex, endIndex);
+ else
+ thisTerm = qualifier_string.substring(beginIndex);*/
+
Splash.logger4j.debug(uniquename+" in handleReservedTags() DELETE "+
qualifier_name+" "+qualifier_string);
+
FeatureCvTerm feature_cvterm = getFeatureCvTerm(qualifier_name, qualifier_string,
uniquename);
+ /*Vector rankables = null;
+ int rank = 0;
+ for(int j=0; j<values.size(); j++)
+ {
+ String val = (String)values.get(j);
+ if(val.indexOf(thisTerm) > -1 &&
+ !val.equals(qualifier_string))
+ {
+ if(rankables == null)
+ rankables = new Vector();
+
+ FeatureCvTerm fc = getFeatureCvTerm(qualifier_name, val,
+ uniquename);
+ fc.setRank(rank);
+ rankables.add(fc);
+ rank++;
+ System.out.println("UPDATE ------> "+values.get(j));
+ }
+ }*/
+
tsn = new ChadoTransaction(ChadoTransaction.DELETE,
feature_cvterm,
- feature.getLastModified(), feature);
+ feature.getLastModified(), feature);
+ sql.add(tsn);
+
+ /*if(rankables != null)
+ {
+ for(int j=0; j<rankables.size(); j++)
+ {
+ feature_cvterm = (FeatureCvTerm)rankables.get(j);
+ tsn = new ChadoTransaction(ChadoTransaction.UPDATE,
+ feature_cvterm,
+ feature.getLastModified(), feature);
+ }
+ }*/
}
else if(isSynonymTag(qualifier_name))
{
@@ -1145,9 +1190,10 @@ public class ChadoTransactionManager
tsn = new ChadoTransaction(ChadoTransaction.DELETE,
feature_synonym,
- feature.getLastModified(), feature);
+ feature.getLastModified(), feature);
+ sql.add(tsn);
}
- sql.add(tsn);
+
}
}
@@ -1404,6 +1450,7 @@ public class ChadoTransactionManager
return feature_cvterm;
}
+ List featureCvTermProps = new Vector();
StringVector strings = StringVector.getStrings(qualifier_string, ";");
for(int i=0; i<strings.size(); i++)
{
@@ -1452,8 +1499,19 @@ public class ChadoTransactionManager
// feature_cvterm_prop's
+ if(this_qualifier_part.toLowerCase().startsWith("evidence="))
+ {
+ String evidence = this_qualifier_part.substring(9);
+ FeatureCvTermProp featureCvTermProp = new FeatureCvTermProp();
+ featureCvTermProp.setValue(evidence);
+ featureCvTermProps.add(featureCvTermProp);
+
+ continue;
+ }
}
+ feature_cvterm.setFeatureCvTermProps(featureCvTermProps);
+
Splash.logger4j.debug("Finished building FeatureCvTerm for "+uniqueName);
return feature_cvterm;
}
diff --git a/uk/ac/sanger/artemis/chado/IBatisDAO.java b/uk/ac/sanger/artemis/chado/IBatisDAO.java
index 742ac5edf1a2dc20de29a8d3063da4d5ad06d40f..5f4097df5370e18cc8d485d4db413715daa7af2b 100644
--- a/uk/ac/sanger/artemis/chado/IBatisDAO.java
+++ b/uk/ac/sanger/artemis/chado/IBatisDAO.java
@@ -31,6 +31,7 @@ import java.sql.*;
import org.gmod.schema.sequence.Feature;
import org.gmod.schema.sequence.FeatureCvTerm;
+import org.gmod.schema.sequence.FeatureCvTermDbXRef;
import org.gmod.schema.sequence.FeatureDbXRef;
import org.gmod.schema.sequence.FeatureProp;
import org.gmod.schema.sequence.Synonym;
@@ -450,6 +451,9 @@ public class IBatisDAO extends GmodDAO
sqlMap.update("updateFeatureProp", o);
else if(o instanceof FeatureRelationship)
sqlMap.update("updateFeatureRelationshipsForSubjectId", o);
+ else if(o instanceof FeatureCvTerm)
+ sqlMap.update("updateFeatureCvTerm", o);
+
}
@@ -490,6 +494,8 @@ public class IBatisDAO extends GmodDAO
sqlMap.delete("deleteFeatureDbXRef", o);
else if(o instanceof FeatureSynonym)
deleteFeatureSynonym((FeatureSynonym)o);
+ else if(o instanceof FeatureCvTerm)
+ deleteFeatureCvTerm((FeatureCvTerm)o);
}
@@ -627,6 +633,97 @@ public class IBatisDAO extends GmodDAO
return sqlMap.delete("deleteAlias", feature_synonym);
}
+ /**
+ * Delete featureCvTerm and update associated feature_cvterm.rank's
+ * if appropriate
+ * @param featureCvTerm
+ */
+ private void deleteFeatureCvTerm(FeatureCvTerm featureCvTerm)
+ {
+ List featureCvTerms = getFeatureCvTermsByFeature(featureCvTerm.getFeature());
+
+ List featureCvTermDbXRefs = new Vector();;
+
+ if(featureCvTerm.getFeatureCvTermDbXRefs() != null &&
+ featureCvTerm.getFeatureCvTermDbXRefs().size() > 0)
+ featureCvTermDbXRefs = (List)featureCvTerm.getFeatureCvTermDbXRefs();
+
+ // delete feature_cvterm and update ranks if asppropriate
+ FeatureCvTerm deleteme = null;
+ Vector rankable = null;
+
+ for(int i=0; i<featureCvTerms.size(); i++)
+ {
+ FeatureCvTerm this_feature_cvterm = (FeatureCvTerm)featureCvTerms.get(i);
+ if(this_feature_cvterm.getCvTerm().getName().equals(
+ featureCvTerm.getCvTerm().getName() ))
+ {
+ List this_featureCvTermDbXRefs = (List)this_feature_cvterm.getFeatureCvTermDbXRefs();
+
+ if(this_featureCvTermDbXRefs == null)
+ this_featureCvTermDbXRefs = new Vector();
+
+ if(this_featureCvTermDbXRefs.size() != featureCvTermDbXRefs.size())
+ {
+ if(rankable == null)
+ rankable = new Vector();
+
+ rankable.add(this_feature_cvterm);
+ continue;
+ }
+
+ boolean found = true;
+ for(int j=0; j<this_featureCvTermDbXRefs.size(); j++)
+ {
+ FeatureCvTermDbXRef fcd = (FeatureCvTermDbXRef)this_featureCvTermDbXRefs.get(j);
+ if(!containsFeatureCvTermDbXRef(fcd, featureCvTermDbXRefs))
+ {
+ found = false;
+ break;
+ }
+ }
+ if(!found)
+ {
+ if(rankable == null)
+ rankable = new Vector();
+
+ rankable.add(this_feature_cvterm);
+ continue;
+ }
+ deleteme = this_feature_cvterm;
+ }
+ }
+ sqlMap.delete("deleteFeatureCvTerm", deleteme);
+
+ if(rankable != null)
+ {
+
+ // feature_cvterm.rank needs updating for those stored here
+ System.out.println( "********> "+ deleteme.getCvTerm().getCv().getName() + " rank = " +
+ deleteme.getRank());
+ for(int i=0; i<rankable.size(); i++)
+ {
+ FeatureCvTerm fc = (FeatureCvTerm)rankable.get(i);
+ System.out.println( "********> "+ fc.getCvTerm().getCv().getName() + " rank = " +
+ fc.getRank());
+ fc.setRank(i);
+ sqlMap.delete("updateFeatureCvTerm", fc);
+ }
+ }
+ }
+
+ private boolean containsFeatureCvTermDbXRef(FeatureCvTermDbXRef fcd, List featureCvTermDbXRefs)
+ {
+ for(int i=0; i<featureCvTermDbXRefs.size(); i++)
+ {
+ FeatureCvTermDbXRef this_fcd = (FeatureCvTermDbXRef)featureCvTermDbXRefs.get(i);
+ if( this_fcd.getDbXRef().getAccession().equals( fcd.getDbXRef().getAccession() ) &&
+ this_fcd.getDbXRef().getDb().getName().equals( fcd.getDbXRef().getDb().getName() ))
+ return true;
+ }
+ return false;
+ }
+
public void startTransaction() throws SQLException
{
sqlMap.startTransaction();