From ffab2217e81f0e49e04df3b9b6436d8fe2c6b331 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Tue, 16 May 2006 10:14:51 +0000
Subject: [PATCH] fixes for jdbc dao and docs added
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@4339 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../sanger/artemis/chado/ChadoFeatureLoc.java | 4 ++-
.../artemis/chado/ChadoFeatureProp.java | 17 +++++++++
.../chado/ChadoFeatureRelationship.java | 35 +++++++++++++++++++
uk/ac/sanger/artemis/chado/ChadoOrganism.java | 2 +-
uk/ac/sanger/artemis/chado/JdbcDAO.java | 19 ++++++++--
.../sanger/artemis/util/DatabaseDocument.java | 27 +++++++++-----
6 files changed, 92 insertions(+), 12 deletions(-)
diff --git a/uk/ac/sanger/artemis/chado/ChadoFeatureLoc.java b/uk/ac/sanger/artemis/chado/ChadoFeatureLoc.java
index 792e68028..d2ec985e0 100644
--- a/uk/ac/sanger/artemis/chado/ChadoFeatureLoc.java
+++ b/uk/ac/sanger/artemis/chado/ChadoFeatureLoc.java
@@ -24,11 +24,13 @@
package uk.ac.sanger.artemis.chado;
+/**
+ * Representation of featureloc table.
+ */
public class ChadoFeatureLoc
{
/** id of the parent feature */
private int srcfeature_id;
-
/** start position */
private int fmin;
/** end position */
diff --git a/uk/ac/sanger/artemis/chado/ChadoFeatureProp.java b/uk/ac/sanger/artemis/chado/ChadoFeatureProp.java
index de7b50775..6b998ad6c 100644
--- a/uk/ac/sanger/artemis/chado/ChadoFeatureProp.java
+++ b/uk/ac/sanger/artemis/chado/ChadoFeatureProp.java
@@ -24,6 +24,9 @@
package uk.ac.sanger.artemis.chado;
+/**
+ * Representation of featureprop table.
+ */
public class ChadoFeatureProp
{
@@ -67,11 +70,25 @@ public class ChadoFeatureProp
this.value = value;
}
+ /**
+ * Any feature can have multiple values for any particular property type -
+ * these are ordered in a list using rank, counting from zero. For
+ * properties that are single-valued rather than multi-valued, the
+ * default 0 value should be used.
+ * @return
+ */
public int getRank()
{
return rank;
}
+ /**
+ * Any feature can have multiple values for any particular property type -
+ * these are ordered in a list using rank, counting from zero. For
+ * properties that are single-valued rather than multi-valued, the
+ * default 0 value should be used.
+ * @param rank
+ */
public void setRank(int rank)
{
this.rank = rank;
diff --git a/uk/ac/sanger/artemis/chado/ChadoFeatureRelationship.java b/uk/ac/sanger/artemis/chado/ChadoFeatureRelationship.java
index 520ecb0c9..a532d8f5c 100644
--- a/uk/ac/sanger/artemis/chado/ChadoFeatureRelationship.java
+++ b/uk/ac/sanger/artemis/chado/ChadoFeatureRelationship.java
@@ -24,6 +24,9 @@
package uk.ac.sanger.artemis.chado;
+/**
+ * Representation of feature_relationship table.
+ */
public class ChadoFeatureRelationship
{
@@ -37,11 +40,21 @@ public class ChadoFeatureRelationship
/** ordering of subject features */
public int rank;
+ /**
+ * Get the cv term for the relationship type between
+ * subject and object (e.g. part_of).
+ * @return cvterm
+ */
public Cvterm getCvterm()
{
return cvterm;
}
+ /**
+ * Set the cv term for the relationship type between
+ * subject and object (e.g. part_of).
+ * @param cvterm
+ */
public void setCvterm(Cvterm cvterm)
{
this.cvterm = cvterm;
@@ -65,11 +78,25 @@ public class ChadoFeatureRelationship
this.object_id = object_id;
}
+ /**
+ * The ordering of subject features with respect to the object
+ * feature may be important (for example, exon ordering on a transcript
+ * - not always derivable if you take trans spliced genes into consideration).
+ * rank is used to order these; starts from zero.
+ * @return rank the rank
+ */
public int getRank()
{
return rank;
}
+ /**
+ * The ordering of subject features with respect to the object
+ * feature may be important (for example, exon ordering on a transcript
+ * - not always derivable if you take trans spliced genes into consideration).
+ * rank is used to order these; starts from zero.
+ * @param rank
+ */
public void setRank(int rank)
{
this.rank = rank;
@@ -85,11 +112,19 @@ public class ChadoFeatureRelationship
this.subject_id = subject_id;
}
+ /**
+ * Additional notes/comments
+ * @return
+ */
public String getValue()
{
return value;
}
+ /**
+ * Additional notes/comments
+ * @param value
+ */
public void setValue(String value)
{
this.value = value;
diff --git a/uk/ac/sanger/artemis/chado/ChadoOrganism.java b/uk/ac/sanger/artemis/chado/ChadoOrganism.java
index aeb13d9f5..328d245d3 100644
--- a/uk/ac/sanger/artemis/chado/ChadoOrganism.java
+++ b/uk/ac/sanger/artemis/chado/ChadoOrganism.java
@@ -95,7 +95,7 @@ public class ChadoOrganism
return comment;
}
- public void setComment()
+ public void setComment(String comment)
{
this.comment = comment;
}
diff --git a/uk/ac/sanger/artemis/chado/JdbcDAO.java b/uk/ac/sanger/artemis/chado/JdbcDAO.java
index bb48bab2b..516008823 100644
--- a/uk/ac/sanger/artemis/chado/JdbcDAO.java
+++ b/uk/ac/sanger/artemis/chado/JdbcDAO.java
@@ -171,7 +171,8 @@ public class JdbcDAO
String sql = "SELECT timelastmodified, f.feature_id, object_id,"
+ " fl.strand, fmin, fmax, uniquename, f.type_id,"
- + " fp.type_id AS prop_type_id, fp.value, fl.phase"
+ + " fp.type_id AS prop_type_id, fp.value, fl.phase,"
+ + " f.organism_id, abbreviation, genus, species, common_name, comment"
+ " FROM " + schema + ".feature f"
+ " LEFT JOIN " + schema + ".feature_relationship fr ON "
+ "fr.subject_id=" + "f.feature_id"
@@ -179,8 +180,10 @@ public class JdbcDAO
+ "fp.feature_id=" + "f.feature_id"
+ " LEFT JOIN " + schema + ".featureloc fl ON "
+ "f.feature_id=" + "fl.feature_id"
+ + " LEFT JOIN organism ON organism.organism_id=f.organism_id"
+ " WHERE ";
+
if(uniquename != null)
sql = sql + "uniquename LIKE '" + uniquename +"'";
@@ -213,6 +216,7 @@ public class JdbcDAO
feature.setCvterm(new Cvterm());
feature.getCvterm().setId( rs.getLong("type_id") );
+ // feature properties
ChadoFeatureProp featureprop = new ChadoFeatureProp();
Cvterm cvterm = new Cvterm();
cvterm.setId(rs.getLong("prop_type_id"));
@@ -226,10 +230,21 @@ public class JdbcDAO
feature.setTimelastmodified( rs.getTimestamp("timelastmodified") );
feature.setId( rs.getInt("feature_id") );
+ // feature relationship
ChadoFeatureRelationship feature_relationship = new ChadoFeatureRelationship();
feature_relationship.setObject_id( rs.getInt("object_id") );
feature.setFeature_relationship(feature_relationship);
+ // feature organism
+ ChadoOrganism organism = new ChadoOrganism();
+ organism.setAbbreviation(rs.getString("abbreviation"));
+ organism.setComment(rs.getString("comment"));
+ organism.setCommon_name(rs.getString("common_name"));
+ organism.setGenus(rs.getString("genus"));
+ organism.setId(rs.getInt("organism_id"));
+ organism.setSpecies(rs.getString("species"));
+ feature.setOrganism(organism);
+
list.add(feature);
}
// merge same features in the list
@@ -494,7 +509,7 @@ public class JdbcDAO
"LEFT JOIN cvterm ON s.type_id=cvterm_id";
if(uniquename != null)
- sql = sql + "WHERE uniquename='"+uniquename+"'";
+ sql = sql + " WHERE uniquename='"+uniquename+"'";
appendToLogFile(sql, sqlLog);
Statement st = conn.createStatement();
diff --git a/uk/ac/sanger/artemis/util/DatabaseDocument.java b/uk/ac/sanger/artemis/util/DatabaseDocument.java
index dd3de5b68..cb7fa71ca 100644
--- a/uk/ac/sanger/artemis/util/DatabaseDocument.java
+++ b/uk/ac/sanger/artemis/util/DatabaseDocument.java
@@ -27,6 +27,7 @@ package uk.ac.sanger.artemis.util;
import com.ibatis.sqlmap.client.SqlMapClient;
import uk.ac.sanger.artemis.io.GFFStreamFeature;
import uk.ac.sanger.artemis.chado.*;
+import uk.ac.sanger.artemis.components.DatabaseEntrySource;
import java.sql.*;
@@ -916,14 +917,19 @@ public class DatabaseDocument extends Document
{
try
{
- DbSqlConfig.init(new JPasswordField());
- SqlMapClient sqlMap = DbSqlConfig.getSqlMapInstance();
-
- ChadoFeature feature = new ChadoFeature();
- feature.setUniquename(args[0]);
- feature.setSchema(args[1]);
-
- List featureList = sqlMap.queryForList("getFeature", feature);
+ ChadoDAO dao;
+ DatabaseEntrySource src = new DatabaseEntrySource();
+ src.setLocation(true);
+
+ if(System.getProperty("ibatis") == null)
+ dao = new JdbcDAO(src.getLocation(), src.getPfield());
+ else
+ dao = new IBatisDAO(src.getPfield());
+
+ ChadoFeature feature;
+ List schemas = new Vector();
+ schemas.add(args[1]);
+ List featureList = dao.getFeature(args[0], schemas);
System.out.println("FINISHED getFeature()");
for(int i = 0; i < featureList.size(); i++)
{
@@ -947,5 +953,10 @@ public class DatabaseDocument extends Document
{
sqle.printStackTrace();
}
+ catch(ConnectException e)
+ {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
}
}
--
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