diff --git a/uk/ac/sanger/artemis/chado/JdbcDAO.java b/uk/ac/sanger/artemis/chado/JdbcDAO.java
index 81aeb5131b55e6c4f031d97fa53526890fa72eba..7487a6778ce75458137df2893066232be946e2b3 100644
--- a/uk/ac/sanger/artemis/chado/JdbcDAO.java
+++ b/uk/ac/sanger/artemis/chado/JdbcDAO.java
@@ -33,6 +33,7 @@ import java.util.Vector;
import org.gmod.schema.sequence.Feature;
import org.gmod.schema.sequence.FeatureCvTerm;
+import org.gmod.schema.sequence.FeatureCvTermProp;
import org.gmod.schema.sequence.FeatureDbXRef;
import org.gmod.schema.sequence.FeatureProp;
import org.gmod.schema.sequence.Synonym;
@@ -42,6 +43,7 @@ import org.gmod.schema.sequence.FeatureSynonym;
import org.gmod.schema.general.DbXRef;
import org.gmod.schema.organism.Organism;
import org.gmod.schema.cv.CvTerm;
+import org.gmod.schema.cv.Cv;
import org.gmod.schema.general.Db;
import org.gmod.schema.pub.Pub;
@@ -186,7 +188,7 @@ public class JdbcDAO extends GmodDAO
String sql =
"SELECT feature_id, fc.feature_cvterm_id, is_not AS not, "+
"pub_id, fc.cvterm_id, fcp.type_id, fcp.value, fcp.rank, "+
- "db.name, dbxref.accession "+
+ "c.name AS cvterm_name, 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 c ON fc.cvterm_id=c.cvterm_id " +
@@ -197,6 +199,8 @@ public class JdbcDAO extends GmodDAO
sql = sql + " WHERE "+
"feature_id=(SELECT feature_id FROM feature WHERE uniquename=#uniqueName#)";
+ sql = sql + " ORDER BY fcp.feature_cvterm_id, fcp.rank";
+
appendToLogFile(sql, sqlLog);
try
@@ -220,6 +224,7 @@ public class JdbcDAO extends GmodDAO
CvTerm cvterm = new CvTerm();
cvterm.setCvTermId(rs.getInt("cvterm_id"));
+ cvterm.setName(rs.getString("cvterm_name"));
DbXRef dbxref = new DbXRef();
dbxref.setAccession(rs.getString("accession"));
@@ -235,28 +240,34 @@ public class JdbcDAO extends GmodDAO
List featureCvTermProps = new Vector();
int next_feature_cvterm_id = -1;
+ int rank;
+ int next_rank = -1;
+
int feature_cvterm_id = rs.getInt("feature_cvterm_id");
do
{
- FeatureProp featureProp = new FeatureProp();
+ rank = rs.getInt("rank");
+ FeatureCvTermProp featureProp = new FeatureCvTermProp();
CvTerm featurePropCvTerm = new CvTerm();
featurePropCvTerm.setCvTermId(rs.getInt("type_id"));
featureProp.setCvTerm(featurePropCvTerm);
featureProp.setValue(rs.getString("value"));
- featureProp.setRank(rs.getInt("rank"));
+ featureProp.setRank(rank);
featureCvTermProps.add(featureProp);
if(rs.next())
{
next_feature_cvterm_id = rs.getInt("feature_cvterm_id");
- if(feature_cvterm_id != next_feature_cvterm_id)
+ next_rank = rs.getInt("rank");
+ if(feature_cvterm_id != next_feature_cvterm_id ||
+ next_rank != rank)
rs.previous();
}
else
next_feature_cvterm_id = -1;
- } while(feature_cvterm_id == next_feature_cvterm_id);
+ } while(feature_cvterm_id == next_feature_cvterm_id && rank == next_rank);
feature_cvterm.setFeatureCvTermProps(featureCvTermProps);
featureCvTerms.add(feature_cvterm);
@@ -305,7 +316,8 @@ public class JdbcDAO extends GmodDAO
*/
public List getFeatureDbXRefsByFeatureUniquename(final String uniqueName)
{
- String sql = "SELECT db.name, dbx.accession, f.feature_id FROM "
+ String sql = "SELECT db.name, dbx.accession, dbx.version, dbx.description, "
+ + "dbx_f.feature_id, dbx_f.is_current FROM "
+ "feature_dbxref dbx_f "
+ "LEFT JOIN dbxref dbx ON dbx.dbxref_id=dbx_f.dbxref_id "
+ "LEFT JOIN db ON db.db_id=dbx.db_id "
@@ -314,6 +326,8 @@ public class JdbcDAO extends GmodDAO
if(uniqueName != null)
sql = sql + "WHERE f.uniquename='" + uniqueName + "'";
+ sql = sql + " ORDER BY f.type_id, uniquename";
+
appendToLogFile(sql, sqlLog);
try
@@ -329,11 +343,14 @@ public class JdbcDAO extends GmodDAO
Db db = new Db();
db.setName(rs.getString("name"));
dbxref.setAccession(rs.getString("accession"));
+ dbxref.setVersion(rs.getString("version"));
+ dbxref.setDescription(rs.getString("description"));
dbxref.setDb(db);
Feature feat = new Feature();
feat.setFeatureId(rs.getInt("feature_id"));
feature_dbxref.setDbXRef(dbxref);
feature_dbxref.setFeature(feat);
+ feature_dbxref.setCurrent(rs.getBoolean("is_current"));
dbxrefs.add(feature_dbxref);
}
@@ -586,33 +603,43 @@ public class JdbcDAO extends GmodDAO
do
{
// feature properties
- FeatureProp featureprop = new FeatureProp();
- CvTerm cvterm = new CvTerm();
- cvterm.setCvTermId(rs.getInt("prop_type_id"));
- featureprop.setCvTerm(cvterm);
- featureprop.setValue(rs.getString("value"));
+ int prop_type_id = rs.getInt("prop_type_id");
+
+ if(prop_type_id != 0)
+ {
+ FeatureProp featureprop = new FeatureProp();
+ CvTerm cvterm = new CvTerm();
+ cvterm.setCvTermId(prop_type_id);
+ featureprop.setCvTerm(cvterm);
+ featureprop.setValue(rs.getString("value"));
+
+ if(feature.getFeatureProps() == null
+ || feature.getFeatureProps().size() == 0)
+ feature.setFeatureProps(new Vector());
+ feature.addFeatureProp(featureprop);
+ }
- if(feature.getFeatureProps() == null ||
- feature.getFeatureProps().size() == 0)
- feature.setFeatureProps(new Vector());
- feature.addFeatureProp(featureprop);
-
// feature relationship
FeatureRelationship feature_relationship = new FeatureRelationship();
- cvterm = new CvTerm();
+ CvTerm cvterm = new CvTerm();
cvterm.setCvTermId(rs.getInt("relation_type_id"));
feature_relationship.setCvTerm(cvterm);
- Feature object = new Feature();
- object.setFeatureId(rs.getInt("object_id"));
- feature_relationship.setFeatureByObjectId(object);
+ int obj_id = rs.getInt("object_id");
- if(feature.getFeatureRelationshipsForSubjectId() == null ||
- feature.getFeatureRelationshipsForSubjectId().size() == 0)
- feature.setFeatureRelationshipsForSubjectId(new Vector());
+ if(obj_id != 0)
+ {
+ Feature object = new Feature();
+ object.setFeatureId(obj_id);
+ feature_relationship.setFeatureByObjectId(object);
+
+ if(feature.getFeatureRelationshipsForSubjectId() == null
+ || feature.getFeatureRelationshipsForSubjectId().size() == 0)
+ feature.setFeatureRelationshipsForSubjectId(new Vector());
+
+ feature.addFeatureRelationshipsForSubjectId(feature_relationship);
+ }
- feature.addFeatureRelationshipsForSubjectId(feature_relationship);
-
if(!rs.isLast())
{
rs.next();
@@ -787,7 +814,7 @@ public class JdbcDAO extends GmodDAO
*/
public List getCvTerms()
{
- String sql = "SELECT cvterm.cvterm_id, cvterm.name " +
+ String sql = "SELECT cvterm.cvterm_id, cvterm.name as cvterm_name, cv.NAME as cv_name " +
"FROM cvterm, cv WHERE cv.cv_id = cvterm.cv_id";
appendToLogFile(sql, sqlLog);
@@ -802,7 +829,10 @@ public class JdbcDAO extends GmodDAO
{
CvTerm cvterm = new CvTerm();
cvterm.setCvTermId(rs.getInt("cvterm_id"));
- cvterm.setName(rs.getString("name"));
+ cvterm.setName(rs.getString("cvterm_name"));
+ Cv cv = new Cv();
+ cv.setName(rs.getString("cv_name"));
+ cvterm.setCv(cv);
cvterms.add(cvterm);
}
return cvterms;
diff --git a/uk/ac/sanger/artemis/util/DatabaseDocument.java b/uk/ac/sanger/artemis/util/DatabaseDocument.java
index 388ebb867df114d5a625eb7af7e5aa707109c865..e5d60556c64c9b2e55e2d24af0ff1c7a8c168529 100644
--- a/uk/ac/sanger/artemis/util/DatabaseDocument.java
+++ b/uk/ac/sanger/artemis/util/DatabaseDocument.java
@@ -40,6 +40,7 @@ import org.gmod.schema.sequence.FeatureLoc;
import org.gmod.schema.sequence.FeatureRelationship;
import org.gmod.schema.sequence.FeatureSynonym;
import org.gmod.schema.sequence.FeatureCvTerm;
+import org.gmod.schema.sequence.FeatureCvTermProp;
import org.gmod.schema.cv.CvTerm;
import org.gmod.schema.general.DbXRef;
import org.gmod.schema.organism.Organism;
@@ -797,7 +798,8 @@ public class DatabaseDocument extends Document
//this_buff.append("feature_id="+feature_id+";");
// attributes
- if(feat.getFeatureProps() != null)
+ if(feat.getFeatureProps() != null &&
+ feat.getFeatureProps().size() > 0)
{
List featureprops = (List)feat.getFeatureProps();
for(int j=0; j<featureprops.size(); j++)
@@ -853,12 +855,49 @@ public class DatabaseDocument extends Document
{
feature_cvterm = (FeatureCvTerm)v_feature_cvterms.get(j);
+ CvTerm cvterm = getCvTerm( feature_cvterm.getCvTerm().getCvTermId(), dao);
DbXRef dbXRef = feature_cvterm.getCvTerm().getDbXRef();
-
- this_buff.append("GO=");
- if(feature_cvterm.isNot())
- this_buff.append("qualifier=NOT;");
- this_buff.append(dbXRef.getDb().getName()+":"+dbXRef.getAccession()+";");
+
+ if(cvterm.getCv().getName().equals("genedb_controlledcuration"))
+ {
+ int cvtermId = feature_cvterm.getCvTerm().getCvTermId();
+ String cvName = getCvTerm(cvtermId, dao).getCv().getName();
+
+ this_buff.append("controlled_curation=");
+ this_buff.append("cv="+cvName+"%3B");
+ this_buff.append("term="+feature_cvterm.getCvTerm().getName()+"%3B");
+ this_buff.append("db_xref="+dbXRef.getDb().getName() + ":"
+ + dbXRef.getAccession() + "%3B");
+
+ List feature_cvtermprops = (List)feature_cvterm.getFeatureCvTermProps();
+ for(int i=0; i<feature_cvtermprops.size(); i++)
+ {
+ FeatureCvTermProp feature_cvtermprop = (FeatureCvTermProp)feature_cvtermprops.get(i);
+ this_buff.append(getCvtermName(feature_cvtermprop.getCvTerm().getCvTermId(), dao));
+ this_buff.append("=");
+ this_buff.append(feature_cvtermprop.getValue());
+ if(i<feature_cvtermprops.size())
+ this_buff.append("%3B");
+ }
+ this_buff.append(";");
+ }
+ else
+ {
+ this_buff.append("GO=");
+
+ if(cvterm.getCv().getName().equals("molecular_function"))
+ this_buff.append("aspect=F%3B");
+ else if(cvterm.getCv().getName().equals("cellular_component"))
+ this_buff.append("aspect=C%3B");
+ else if(cvterm.getCv().getName().equals("biological_process"))
+ this_buff.append("aspect=P%3B");
+
+ if(feature_cvterm.isNot())
+ this_buff.append("qualifier=NOT%3B");
+
+ this_buff.append("GOid="+dbXRef.getDb().getName() + ":"
+ + dbXRef.getAccession() + ";");
+ }
}
//System.out.println(new String(this_buff.getBytes()));
}
@@ -890,11 +929,16 @@ public class DatabaseDocument extends Document
* @return the cvterm name
*/
private static String getCvtermName(long id, GmodDAO dao)
+ {
+ return getCvTerm(id, dao).getName();
+ }
+
+ private static CvTerm getCvTerm(long id, GmodDAO dao)
{
if(cvterms == null)
- getCvterm(dao);
+ getCvterms(dao);
- return ((CvTerm)cvterms.get(new Long(id))).getName();
+ return (CvTerm)cvterms.get(new Long(id));
}
/**
@@ -902,7 +946,7 @@ public class DatabaseDocument extends Document
* @param dao the data access object
* @return the cvterm <code>Hashtable</code>
*/
- private static Hashtable getCvterm(GmodDAO dao)
+ private static Hashtable getCvterms(GmodDAO dao)
{
cvterms = new Hashtable();