diff --git a/artemis_sqlmap/Feature.xml b/artemis_sqlmap/Feature.xml
index 4a837149f034adf993b10e9f074501da7a674002..de00ed9bf1344b9874361600e50c1f6643628b43 100644
--- a/artemis_sqlmap/Feature.xml
+++ b/artemis_sqlmap/Feature.xml
@@ -72,7 +72,8 @@
select="getFeatureRelationship" />
<result property="featureSynonyms" column="{feature.uniqueName=uniqueName}"
select="getLazyFeatureSynonymsByUniquename" />
- <result property="organism" column="organism_id" select="getOrganism" />
+ <result property="organism" column="{organismId=organismId}"
+ select="getOrganism" />
</resultMap>
@@ -207,7 +208,7 @@
timelastmodified,
f.feature_id AS id,
uniquename,
- organism_id,
+ organism_id AS organismId,
name,
f.type_id,
seqlen AS length,
@@ -243,7 +244,7 @@
<select id="getResidueType" parameterClass="java.lang.String"
resultClass="java.lang.Long">
SELECT DISTINCT type_id
- FROM $value$.feature
+ FROM feature
WHERE residues notnull
</select>
@@ -256,8 +257,8 @@
uniquename,
feature_id,
type_id
- FROM organism, $schema$.feature WHERE
- organism.organism_id=$schema$.feature.organism_id AND
+ FROM organism, feature WHERE
+ organism.organism_id=feature.organism_id AND
residues notnull
<iterate prepend="AND" property="cvTermIds" conjunction="OR" open="(" close=")">
type_id=#cvTermIds[]#
diff --git a/artemis_sqlmap/Organism.xml b/artemis_sqlmap/Organism.xml
index 7aa505065d92994a2cf9c2b9c2cd0b27da1feca1..cc8c9d32d76acc3cc2d893b7674524fd4627c4f5 100644
--- a/artemis_sqlmap/Organism.xml
+++ b/artemis_sqlmap/Organism.xml
@@ -6,10 +6,19 @@
<sqlMap namespace="Organism">
- <select id="getOrganism" resultClass="org.gmod.schema.organism.Organism">
- SELECT organism_id AS organismId, abbreviation, genus, species, common_name, comment
+ <select id="getOrganism"
+ resultClass="org.gmod.schema.organism.Organism">
+ SELECT organism_id AS organismId, abbreviation, genus, species, common_name AS commonName, comment
FROM organism
- WHERE organism_id=#value#
+ <dynamic>
+ <isNotNull prepend="WHERE" property="organismId">
+ organism_id=#organismId#
+ </isNotNull>
+
+ <isNull prepend="ORDER BY" property="organismId">
+ commonName
+ </isNull>
+ </dynamic>
</select>
</sqlMap>
diff --git a/uk/ac/sanger/artemis/chado/ChadoDAO.java b/uk/ac/sanger/artemis/chado/ChadoDAO.java
index 881248c2fdb96f5791fe47223c38c10c98c1ccb4..af1c178e0f727a3abded3512fdcb34ddb805221d 100644
--- a/uk/ac/sanger/artemis/chado/ChadoDAO.java
+++ b/uk/ac/sanger/artemis/chado/ChadoDAO.java
@@ -164,6 +164,8 @@ public interface ChadoDAO
public FeatureCvTerm getFeatureCvTermByFeatureAndCvTerm(Feature feature,
CvTerm cvTerm, boolean not);
+ public List getOrganisms();
+
//
// WRITE BACK
//
diff --git a/uk/ac/sanger/artemis/chado/IBatisDAO.java b/uk/ac/sanger/artemis/chado/IBatisDAO.java
index 5f9b89370314fdd62e3f03adee3fbed2b79b97b3..017b335628bbedf1938116faa8585c797c355f8f 100644
--- a/uk/ac/sanger/artemis/chado/IBatisDAO.java
+++ b/uk/ac/sanger/artemis/chado/IBatisDAO.java
@@ -298,6 +298,11 @@ public class IBatisDAO implements ChadoDAO
return null;
}
+ public List getOrganisms()
+ {
+ return sqlMap.queryForList("getOrganism", null);
+ }
+
//
// WRITE BACK
//
diff --git a/uk/ac/sanger/artemis/chado/JdbcDAO.java b/uk/ac/sanger/artemis/chado/JdbcDAO.java
index 2aee5cf0223cf0366d973b2b70e2619203c4a5e9..aed3429db74b690a254e006cae691a3f42920c83 100644
--- a/uk/ac/sanger/artemis/chado/JdbcDAO.java
+++ b/uk/ac/sanger/artemis/chado/JdbcDAO.java
@@ -283,8 +283,12 @@ public class JdbcDAO
final String schema)
{
String sql = new String(
- "SELECT abbreviation, uniquename, name, feature_id, type_id FROM organism, "+
- schema + ".feature WHERE (");
+ "SELECT abbreviation, uniquename, name, feature_id, type_id FROM organism, ");
+
+ if(schema != null || !schema.equals(""))
+ sql = sql + schema +"." ;
+
+ sql = sql + "feature WHERE (";
for(int j = 0; j < cvTermIds.size(); j++)
{
@@ -293,8 +297,12 @@ public class JdbcDAO
sql = sql + " OR ";
}
- sql = sql + ") and organism.organism_id=" + schema
- + ".feature.organism_id " + "and residues notnull "
+ sql = sql + ") and organism.organism_id=";
+
+ if(schema != null || !schema.equals(""))
+ sql = sql + schema +"." ;
+
+ sql = sql + "feature.organism_id " + "and residues notnull "
+ "ORDER BY abbreviation";
appendToLogFile(sql, sqlLog);
@@ -336,8 +344,11 @@ public class JdbcDAO
*/
public List getResidueType(final String schema)
{
- String sql = "SELECT DISTINCT type_id FROM " +schema+
- ".feature WHERE residues notnull";
+ String sql = "SELECT DISTINCT type_id FROM ";
+
+ if(schema != null || !schema.equals(""))
+ sql = sql + schema +"." ;
+ sql = sql + "feature WHERE residues notnull";
appendToLogFile(sql, sqlLog);
List cvterm_ids = new Vector();
@@ -552,6 +563,40 @@ public class JdbcDAO
}
+ public List getOrganisms()
+ {
+ String sql = "SELECT organism_id AS organismId, abbreviation, "+
+ "genus, species, common_name AS commonName, comment "+
+ "FROM organism ORDER BY commonName";
+
+ appendToLogFile(sql, sqlLog);
+ List organisms = new Vector();
+
+ try
+ {
+ Statement st = conn.createStatement();
+ ResultSet rs = st.executeQuery(sql);
+
+ while(rs.next())
+ {
+ Organism organism = new Organism();
+ organism.setOrganismId(rs.getInt("organismId"));
+ organism.setAbbreviation(rs.getString("abbreviation"));
+ organism.setGenus(rs.getString("genus"));
+ organism.setSpecies(rs.getString("species"));
+ organism.setCommonName(rs.getString("commonName"));
+ organism.setComment(rs.getString("comment"));
+ organisms.add(organism);
+ }
+ }
+ catch(SQLException sqle)
+ {
+ throw new RuntimeException(sqle);
+ }
+ return organisms;
+ }
+
+
//
// WRITE
//
diff --git a/uk/ac/sanger/artemis/components/DatabaseEntrySource.java b/uk/ac/sanger/artemis/components/DatabaseEntrySource.java
index bac513adc6a431af702f85b82a955fd019503fdd..4c05e1b14475f398bea6b33484ff444f35e3ae3e 100644
--- a/uk/ac/sanger/artemis/components/DatabaseEntrySource.java
+++ b/uk/ac/sanger/artemis/components/DatabaseEntrySource.java
@@ -34,6 +34,8 @@ import java.io.*;
import java.util.*;
import java.net.ConnectException;
+import org.gmod.schema.organism.Organism;
+
import uk.ac.sanger.artemis.util.*;
import uk.ac.sanger.artemis.*;
import uk.ac.sanger.artemis.sequence.*;
@@ -304,14 +306,19 @@ public class DatabaseEntrySource implements EntrySource
final Object v_organism[] = entries.keySet().toArray();
final int v_organism_size = v_organism.length;
- Arrays.sort(v_organism);
-
+ Arrays.sort(v_organism);
+
for(int i=0; i<schema.size(); i++)
{
- String name = (String)schema.get(i);
+ int nchild = 0;
+ String name;
+
+ if(schema.get(i) instanceof String)
+ name = (String)schema.get(i);
+ else
+ name = ((Organism)schema.get(i)).getCommonName();
+
schema_node = new DefaultMutableTreeNode(name);
- top.add(schema_node);
-
Hashtable seq_type_node = new Hashtable();
for(int j = 0; j < v_organism_size; j++)
@@ -336,8 +343,11 @@ public class DatabaseEntrySource implements EntrySource
seq_node = new DefaultMutableTreeNode(seq_name);
typ_node.add(seq_node);
+ nchild++;
}
}
+ if(nchild > 0)
+ top.add(schema_node);
}
}
diff --git a/uk/ac/sanger/artemis/util/DatabaseDocument.java b/uk/ac/sanger/artemis/util/DatabaseDocument.java
index 9a9ecded3d72f7344d2c07afb8a87c4427c8646b..792934376836cff178694737f49de04b7dfc39aa 100644
--- a/uk/ac/sanger/artemis/util/DatabaseDocument.java
+++ b/uk/ac/sanger/artemis/util/DatabaseDocument.java
@@ -39,6 +39,7 @@ import org.gmod.schema.sequence.FeatureLoc;
import org.gmod.schema.sequence.FeatureRelationship;
import org.gmod.schema.sequence.FeatureSynonym;
import org.gmod.schema.cv.CvTerm;
+import org.gmod.schema.organism.Organism;
import java.sql.*;
import java.text.SimpleDateFormat;
@@ -232,6 +233,7 @@ public class DatabaseDocument extends Document
private void reset(String location, String schema)
{
this.schema = schema;
+
if(!location.endsWith("="+schema))
{
int index = location.lastIndexOf('=');
@@ -976,6 +978,91 @@ public class DatabaseDocument extends Document
}
+ /**
+ * Create a hashtable of the available entries with residues.
+ * @return a <code>Hashtable</code> of the <code>String</code>
+ * representation (schema-type-feature_name) and the
+ * corresponding feature_id
+ * @throws ConnectException
+ * @throws java.sql.SQLException
+ */
+ public Hashtable getDatabaseEntries2()
+ throws ConnectException, java.sql.SQLException
+ {
+ db = new Hashtable();
+ String schema = null;
+
+ try
+ {
+ ChadoDAO dao = null;
+ dao = getDAO();
+ schema_list = dao.getOrganisms();
+ Iterator it = schema_list.iterator();
+
+ while(it.hasNext())
+ {
+ Organism organism = (Organism)it.next();
+ schema = organism.getCommonName();
+
+ reset((String)getLocation(), schema);
+
+ try
+ {
+ dao = getDAO();
+ List list = dao.getResidueType(schema);
+
+ if(list.size() == 0) // no residues for this organism
+ continue;
+
+ List list_residue_features = dao.getResidueFeatures(list, schema);
+ Iterator it_residue_features = list_residue_features.iterator();
+ while(it_residue_features.hasNext())
+ {
+ Feature feature = (Feature)it_residue_features.next();
+ String typeName = getCvtermName(feature.getCvTerm().getCvTermId(), getDAO());
+
+ db.put(schema + " - " + typeName + " - " + feature.getUniqueName(),
+ Integer.toString(feature.getFeatureId()));
+ }
+ }
+ catch(RuntimeException e)
+ {
+ }
+ catch(java.sql.SQLException sqlExp)
+ {
+ }
+ }
+
+ }
+ catch(RuntimeException sqlExp)
+ {
+ JOptionPane.showMessageDialog(null, "SQL Problems...\n"+
+ sqlExp.getMessage(),
+ "SQL Error",
+ JOptionPane.ERROR_MESSAGE);
+ sqlExp.printStackTrace();
+ }
+ catch(ConnectException exp)
+ {
+ JOptionPane.showMessageDialog(null, "Connection Problems...\n"+
+ exp.getMessage(),
+ "Connection Error",
+ JOptionPane.ERROR_MESSAGE);
+ throw exp;
+ }
+ catch(java.sql.SQLException sqlExp)
+ {
+ JOptionPane.showMessageDialog(null, "SQL Problems....\n"+
+ sqlExp.getMessage(),
+ "SQL Error",
+ JOptionPane.ERROR_MESSAGE);
+ throw sqlExp;
+ }
+
+ return db;
+ }
+
+
/**
* Get the data access object (DAO).
* @return data access object
@@ -992,7 +1079,10 @@ public class DatabaseDocument extends Document
else
{
if(connIB == null)
+ {
+ System.setProperty("chado", (String)getLocation());
connIB = new IBatisDAO(pfield);
+ }
return connIB;
}
}