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Commit 670a21b3 authored by tjc's avatar tjc
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change to how database manager is built 

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@9373 ee4ac58c-ac51-4696-9907-e4b3aa274f04
parent 75eac2fc
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uk/ac/sanger/artemis/util/DatabaseDocument.java
+ 41
− 199
View file @ 670a21b3
......@@ -67,7 +67,6 @@ import java.util.Collections;
import java.util.Comparator;
import java.util.HashSet;
import java.util.Hashtable;
import java.util.HashMap;
import java.util.Set;
import java.util.Vector;
import java.util.Enumeration;
......@@ -80,9 +79,7 @@ import javax.swing.JPasswordField;
/**
* Objects of this class are Documents created from a relational database.
*
*/
public class DatabaseDocument extends Document
{
private String name = null;
......@@ -148,6 +145,8 @@ public class DatabaseDocument extends Document
/** list of controlled_curation CV names */
private static Vector cvControledCuratioNames;
private static CvTermThread cvThread;
// controlled vocabulary
/** controlled_curation controlled vocabulary */
public static String CONTROLLED_CURATION_TAG_CVNAME =
......@@ -2269,62 +2268,51 @@ 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
* Get a list of the organisms with sequences
* @return
* @throws ConnectException
* @throws java.sql.SQLException
*/
public HashMap getDatabaseEntriesMultiSchema()
public List getOrganismsContainingSrcFeatures()
throws ConnectException, java.sql.SQLException
{
String schema = null;
HashMap db = null;
List list = null;
try
{
GmodDAO dao = getDAO();
schema_list = dao.getSchema();
cvThread = new CvTermThread(dao);
cvThread.start();
Iterator it = schema_list.iterator();
list = dao.getOrganismsContainingSrcFeatures();
while(it.hasNext())
Collections.sort(list, new Comparator()
{
schema = (String)it.next();
reset((String)getLocation(), schema);
try
public int compare(Object o1, Object o2)
{
dao = getDAO();
List list_residue_features = dao.getResidueFeatures();
Organism org1 = (Organism)o1;
Organism org2 = (Organism)o2;
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(), gene_builder);
String name1 = org1.getCommonName();
String name2 = org2.getCommonName();
if(db == null)
db = new HashMap();
db.put(schema + " - " + typeName + " - " + feature.getUniqueName(),
Integer.toString(feature.getFeatureId()));
}
}
catch(RuntimeException e){}
catch(java.sql.SQLException sqlExp){}
}
if(name1 == null)
name1 = org1.getGenus() + "." + org1.getSpecies();
if(name2 == null)
name2 = org2.getGenus() + "." + org2.getSpecies();
return name1.compareToIgnoreCase( name2 );
}
});
}
catch(RuntimeException sqlExp)
{
JOptionPane.showMessageDialog(null, "SQL Problems...\n"+
getLocation()+"\n"+
sqlExp.getMessage(),
"SQL Error",
JOptionPane.ERROR_MESSAGE);
logger4j.debug(sqlExp.getMessage());
//sqlExp.printStackTrace();
}
catch(ConnectException exp)
{
......@@ -2338,6 +2326,7 @@ public class DatabaseDocument extends Document
catch(java.sql.SQLException sqlExp)
{
JOptionPane.showMessageDialog(null, "SQL Problems....\n"+
getLocation()+"\n"+
sqlExp.getMessage(),
"SQL Error",
JOptionPane.ERROR_MESSAGE);
......@@ -2345,170 +2334,23 @@ public class DatabaseDocument extends Document
throw sqlExp;
}
return db;
}
/**
* 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 HashMap getDatabaseEntries()
throws ConnectException, java.sql.SQLException
{
HashMap db = null;
try
{
GmodDAO dao = getDAO();
CvTermThread cvThread = new CvTermThread(dao);
cvThread.start();
schema_list = dao.getOrganisms();
/*Organism org = new Organism();
org.setCommonName("web");
schema_list.add(org);*/
final List pg_schemas = dao.getSchema();
// build a lookup hash of residue features in the
// main schema
Hashtable residueFeaturesLookup = new Hashtable();
List list_residue_features = dao.getResidueFeatures();
for(int i=0; i<list_residue_features.size(); i++)
{
Feature feature = (Feature)list_residue_features.get(i);
Integer organismId = new Integer(feature.getOrganism().getOrganismId());
List features;
if(residueFeaturesLookup.containsKey(organismId))
features= (List)residueFeaturesLookup.get(organismId);
else
features = new Vector();
features.add(feature);
residueFeaturesLookup.put(organismId, features);
}
// loop over organisms to identify those with features
// containing residues
Iterator it = schema_list.iterator();
while(it.hasNext())
{
final Organism organism = (Organism)it.next();
String orgName = organism.getCommonName();
if(orgName == null || orgName.equals(""))
{
orgName = organism.getGenus() + "." + organism.getSpecies();
organism.setCommonName(orgName);
}
// search to see if this is in its own schema
Iterator schemasIt = pg_schemas.iterator();
while(schemasIt.hasNext())
{
schema = (String)schemasIt.next();
if( schema.equalsIgnoreCase(organism.getCommonName()) )
{
reset((String)getLocation(), schema);
dao = getDAO();
orgName = schema;
singleSchema = false;
break;
}
return list;
}
try
public static boolean isCvThreadAlive()
{
if(organism.getOrganismId() > 0)
{
Integer organismId = new Integer(organism.getOrganismId());
if(cvThread == null)
return false;
if(residueFeaturesLookup.containsKey(organismId))
list_residue_features = (List)residueFeaturesLookup.get(organismId);
else if(singleSchema && residueFeaturesLookup.size()>0)
continue;
else
list_residue_features = dao.getResidueFeatures(organismId);
}
if(cvThread.isAlive())
return true;
else
list_residue_features =
dao.getResidueFeaturesByOrganismCommonName(organism.getCommonName());
Iterator it_residue_features = list_residue_features.iterator();
while(it_residue_features.hasNext())
{
final Feature feature = (Feature)it_residue_features.next();
final String typeName = feature.getCvTerm().getName();
if(db == null)
db = new HashMap();
if(organismNames == null)
organismNames = new Vector();
if(!organismNames.contains(orgName))
organismNames.add(orgName);
db.put(orgName + " - " + typeName + " - " + feature.getUniqueName(),
Integer.toString(feature.getFeatureId()));
}
}
catch(RuntimeException e)
{
e.printStackTrace();
}
return false;
}
residueFeaturesLookup.clear();
list_residue_features.clear();
// now wait for cvterm to be loaded
while(cvThread.isAlive())
Thread.sleep(10);
}
catch(RuntimeException sqlExp)
public List getResidueFeatures(Integer organismId)
{
JOptionPane.showMessageDialog(null, "SQL Problems...\n"+
getLocation()+"\n"+
sqlExp.getMessage(),
"SQL Error",
JOptionPane.ERROR_MESSAGE);
logger4j.debug(sqlExp.getMessage());
//sqlExp.printStackTrace();
}
catch(ConnectException exp)
{
JOptionPane.showMessageDialog(null, "Connection Problems...\n"+
exp.getMessage(),
"Connection Error",
JOptionPane.ERROR_MESSAGE);
logger4j.debug(exp.getMessage());
throw exp;
}
catch(java.sql.SQLException sqlExp)
{
JOptionPane.showMessageDialog(null, "SQL Problems....\n"+
getLocation()+"\n"+
sqlExp.getMessage(),
"SQL Error",
JOptionPane.ERROR_MESSAGE);
logger4j.debug(sqlExp.getMessage());
throw sqlExp;
}
catch(InterruptedException e)
{
// TODO Auto-generated catch block
e.printStackTrace();
}
return db;
return getDAOOnly().getResidueFeatures(organismId);
}
/**
......
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