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Commit 5705be66 authored by tjc's avatar tjc
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ibatis added 

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@3805 ee4ac58c-ac51-4696-9907-e4b3aa274f04
parent abae7fe0
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uk/ac/sanger/artemis/util/DatabaseDocument.java
+ 271
− 36
View file @ 5705be66
......@@ -24,6 +24,8 @@
package uk.ac.sanger.artemis.util;
import com.ibatis.sqlmap.client.SqlMapClient;
import uk.ac.sanger.ibatis.*;
import uk.ac.sanger.artemis.io.GFFStreamFeature;
import uk.ac.sanger.artemis.chado.ChadoTransaction;
......@@ -33,6 +35,8 @@ import java.util.Hashtable;
import java.util.Vector;
import java.util.Enumeration;
import java.util.Date;
import java.util.List;
import java.util.Iterator;
import javax.swing.JOptionPane;
/**
......@@ -54,6 +58,7 @@ public class DatabaseDocument extends Document
private ByteBuffer gff_buff;
private String[] types = { "exon", "gene", "CDS", "transcript" };
private boolean splitGFFEntry;
private boolean iBatis = false;
/**
*
......@@ -65,6 +70,8 @@ public class DatabaseDocument extends Document
public DatabaseDocument(String location)
{
super(location);
if(System.getProperty("ibatis") != null)
iBatis = true;
}
/**
......@@ -79,6 +86,8 @@ public class DatabaseDocument extends Document
{
super(location);
this.feature_id = feature_id;
if(System.getProperty("ibatis") != null)
iBatis = true;
}
/**
......@@ -100,6 +109,8 @@ public class DatabaseDocument extends Document
this.feature_id = feature_id;
this.splitGFFEntry = splitGFFEntry;
this.progress_listener = progress_listener;
if(System.getProperty("ibatis") != null)
iBatis = true;
}
public DatabaseDocument(String location, String feature_id,
......@@ -109,6 +120,8 @@ public class DatabaseDocument extends Document
this.feature_id = feature_id;
this.gff_buff = gff_buff;
this.name = name;
if(System.getProperty("ibatis") != null)
iBatis = true;
}
/**
......@@ -140,22 +153,6 @@ public class DatabaseDocument extends Document
return name;
}
/**
*
* Return a Document with the last element stripped off.
*
**/
public String getFeatureName(String feature_id, Connection conn)
throws java.sql.SQLException
{
Statement st = conn.createStatement();
String sql = "SELECT name FROM feature WHERE feature_id= "+feature_id;
appendToLogFile(sql,sqlLog);
ResultSet rs = st.executeQuery(sql);
rs.next();
return rs.getString("name");
}
/**
*
......@@ -209,16 +206,25 @@ public class DatabaseDocument extends Document
try
{
Connection conn = getConnection();
System.out.println("Connected");
Connection conn = null;
gff_buffer = getGFF(conn,feature_id);
ByteBuffer entry = new ByteBuffer();
if(!iBatis)
conn = getConnection();
if(iBatis)
gff_buffer = getGFFiBatis(feature_id);
else
gff_buffer = getGFFJdbc(conn,feature_id);
ByteBuffer entry = new ByteBuffer();
if(splitGFFEntry)
{
if(gff_buffer[0].size() > 0)
entry.append(gff_buffer[0]);
if(iBatis)
getSequenceIbatis(entry);
else
getSequence(conn, entry);
}
else
......@@ -228,6 +234,10 @@ public class DatabaseDocument extends Document
if(gff_buffer[i].size() > 0)
entry.append(gff_buffer[i]);
}
if(iBatis)
getSequenceIbatis(entry);
else
getSequence(conn, entry);
}
......@@ -236,6 +246,7 @@ public class DatabaseDocument extends Document
instream = new ByteArrayInputStream(entry.getBytes());
if(conn != null)
conn.close();
return instream;
}
......@@ -284,13 +295,149 @@ public class DatabaseDocument extends Document
}
/**
*
* Return a feature name given the feature_id.
*
**/
private String getFeatureNameIbatis(String feature_id)
throws java.sql.SQLException
{
SqlMapClient sqlMap = DbSqlConfig.getSqlMapInstance();
return (String)sqlMap.queryForObject("getFeatureName",
feature_id);
}
/**
*
* Return a feature name given the feature_id.
*
**/
private String getFeatureNameJdbc(String feature_id, Connection conn)
throws java.sql.SQLException
{
Statement st = conn.createStatement();
String sql = "SELECT name FROM feature WHERE feature_id= "+feature_id;
appendToLogFile(sql,sqlLog);
ResultSet rs = st.executeQuery(sql);
rs.next();
return rs.getString("name");
}
private ByteBuffer[] getGFFiBatis(String parentFeatureID)
throws java.sql.SQLException
{
SqlMapClient sqlMap = DbSqlConfig.getSqlMapInstance();
List featList = sqlMap.queryForList("getGffLine",
new Integer(feature_id));
ByteBuffer[] buffers = new ByteBuffer[types.length+1];
for(int i=0; i<buffers.length; i++)
buffers[i] = new ByteBuffer();
String parentFeature = getFeatureNameIbatis(parentFeatureID);
Hashtable hstore = new Hashtable();
ByteBuffer this_buff;
int feature_size = featList.size();
for(int i=0; i<feature_size; i++)
{
Feature feat = (Feature)featList.get(i);
int fmin = feat.getFmin()+1;
int fmax = feat.getFmax();
long type_id = feat.getType_id();
long prop_type_id = feat.getProp_type_id();
int strand = feat.getStrand();
String name = feat.getUniquename();
String typeName = getCvtermName(null,type_id);
String propTypeName = getCvtermName(null,prop_type_id);
String timelastmodified = feat.getTimelastmodified().toString();
String feature_id = Integer.toString(feat.getId());
hstore.put(feature_id, name);
String parent_id = feat.getObject_id();
if(parent_id != null && hstore.containsKey(parent_id))
parent_id = (String)hstore.get(parent_id);
// make gff format
// select buffer
this_buff = buffers[types.length];
for(int j=0; j<types.length; j++)
{
if(types[j].equals(typeName))
this_buff = buffers[j];
}
this_buff.append(parentFeature+"\t"); // seqid
this_buff.append("chado\t"); // source
this_buff.append(typeName+"\t"); // type
this_buff.append(fmin+"\t"); // start
this_buff.append(fmax+"\t"); // end
this_buff.append(".\t"); // score
if(strand == -1) // strand
this_buff.append("-\t");
else if(strand == 1)
this_buff.append("+\t");
else
this_buff.append(".\t");
this_buff.append(".\t"); // phase
this_buff.append("ID="+name+";");
if(parent_id != null)
this_buff.append("Parent="+parent_id+";");
this_buff.append("timelastmodified="+timelastmodified+";");
String value = "";
if(feat.getValue() != null)
value = GFFStreamFeature.encode(feat.getValue());
this_buff.append(propTypeName+"="+value); // attributes
// is the next line part of the same feature, if so merge
boolean rewind = false;
Feature featNext = null;
if(i < feature_size-1)
featNext = (Feature)featList.get(i+1);
// merge next line if part of the same feature
while(featNext != null &&
featNext.getUniquename().equals(name))
{
prop_type_id = feat.getProp_type_id();
propTypeName = getCvtermName(null,prop_type_id);
value = GFFStreamFeature.encode(feat.getValue());
this_buff.append(";"+propTypeName+"="+value);
i++;
if(i < feature_size-1)
featNext = (Feature)featList.get(i+1);
else
break;
}
this_buff.append("\n");
progress_listener.progressMade("Read from database: "+name);
}
return buffers;
}
/**
*
* Given a parent (chromosome, contig, supercontig) retrieve the features
* in the form of a GFF stream.
*
*/
private ByteBuffer[] getGFF(Connection conn, String parentFeatureID)
private ByteBuffer[] getGFFJdbc(Connection conn, String parentFeatureID)
throws java.sql.SQLException
{
Statement st = conn.createStatement(ResultSet.TYPE_SCROLL_INSENSITIVE, ResultSet.CONCUR_UPDATABLE);
......@@ -305,13 +452,6 @@ public class DatabaseDocument extends Document
" and (featureloc.rank=feature_relationship.rank OR feature_relationship.rank IS NULL)"+
" ORDER BY feature.type_id, uniquename";
// "SELECT timelastmodified, feature.feature_id, object_id, strand, fmin, fmax, uniquename, feature.type_id, "+
// " featureprop.type_id AS prop_type_id, featureprop.value FROM featureloc, featureprop, "+
// " feature LEFT JOIN feature_relationship ON feature_relationship.subject_id=feature.feature_id "+
// " WHERE srcfeature_id = "+parentFeatureID+" and featureloc.feature_id=featureprop.feature_id and "+
// " featureloc.feature_id=feature.feature_id ORDER BY feature.type_id, uniquename";
appendToLogFile(sql,sqlLog);
ResultSet rs = st.executeQuery(sql);
......@@ -319,7 +459,7 @@ public class DatabaseDocument extends Document
for(int i=0; i<buffers.length; i++)
buffers[i] = new ByteBuffer();
String parentFeature = getFeatureName(parentFeatureID,conn);
String parentFeature = getFeatureNameJdbc(parentFeatureID,conn);
Hashtable hstore = new Hashtable();
ByteBuffer this_buff;
......@@ -378,6 +518,7 @@ public class DatabaseDocument extends Document
this_buff.append(propTypeName+"="+value); // attributes
// is the next line part of the same feature, if so merge
boolean rewind = false;
while( (rewind = rs.next()) && rs.getString("uniquename").equals(name))
{
......@@ -414,11 +555,47 @@ public class DatabaseDocument extends Document
private String getCvtermName(Connection conn, long id)
{
if(cvterm == null)
{
if(iBatis)
getCvtermIbatis(null);
else
getCvterm(conn,null);
}
return (String)cvterm.get(new Long(id));
}
/**
*
* Look up cvterms names and id and return in a hashtable.
*
*/
private Hashtable getCvtermIbatis(String cv_name)
{
cvterm = new Hashtable();
try
{
SqlMapClient sqlMap = DbSqlConfig.getSqlMapInstance();
List cvtem_list = sqlMap.queryForList("getCvterm", null);
Iterator it = cvtem_list.iterator();
while(it.hasNext())
{
Cvterm cv = (Cvterm)it.next();
cvterm.put(new Long(cv.getId()), cv.getName());
}
}
catch (SQLException sqle)
{
System.err.println(this.getClass() + ": SQLException retrieving CvTerms");
System.err.println(sqle);
}
return cvterm;
}
/**
*
* Look up cvterms names and id and return in a hashtable.
......@@ -463,6 +640,17 @@ public class DatabaseDocument extends Document
}
public ByteBuffer getSequenceIbatis(ByteBuffer buff) throws java.sql.SQLException
{
SqlMapClient sqlMap = DbSqlConfig.getSqlMapInstance();
Feature feat = (Feature)sqlMap.queryForObject("getSequence", new Integer(feature_id));
buff.append("##FASTA\n>");
buff.append(feat.getName());
buff.append("\n");
buff.append(feat.getResidues());
return buff;
}
public ByteBuffer getSequence(Connection conn, ByteBuffer buff) throws java.sql.SQLException
{
Statement st = conn.createStatement();
......@@ -485,12 +673,20 @@ public class DatabaseDocument extends Document
}
public Hashtable getDatabaseEntries()
{
if(iBatis)
return getDatabaseEntriesIbatis();
else
return getDatabaseEntriesJdbc();
}
/**
*
* Create a hashtable of the available entries.
*
**/
public Hashtable getDatabaseEntries()
private Hashtable getDatabaseEntriesJdbc()
{
db = new Hashtable();
organism = new Vector();
......@@ -519,7 +715,8 @@ public class DatabaseDocument extends Document
sql = sql + " OR ";
}
sql = sql + ") " + " and organism.organism_id=feature.organism_id "+
sql = sql + ") and organism.organism_id=feature.organism_id "+
"and residues notnull "+
"ORDER BY abbreviation";
appendToLogFile(sql,sqlLog);
......@@ -555,6 +752,44 @@ public class DatabaseDocument extends Document
return db;
}
/**
*
* Create a hashtable of the available entries.
*
**/
private Hashtable getDatabaseEntriesIbatis()
{
db = new Hashtable();
organism = new Vector();
try
{
SqlMapClient sqlMap = DbSqlConfig.getSqlMapInstance();
List list = sqlMap.queryForList("getResidueType", null);
List list_residue_features = sqlMap.queryForList("getResidueFeatures", list);
Iterator it = list_residue_features.iterator();
while(it.hasNext())
{
Feature feat = (Feature)it.next();
String org = feat.getAbbreviation();
String typeName = getCvtermName(null,feat.getType_id());
db.put(org+" - "+typeName+" - "+feat.getName(),
Integer.toString(feat.getId()));
if(!organism.contains(org))
organism.add(org);
}
}
catch(java.sql.SQLException sqlExp)
{
JOptionPane.showMessageDialog(null, "SQL Problems...",
"SQL Error",
JOptionPane.ERROR_MESSAGE);
sqlExp.printStackTrace();
}
return db;
}
public Vector getOrganism()
{
return organism;
......
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