diff --git a/artemis_sqlmap/Dbxref.xml b/artemis_sqlmap/Dbxref.xml
index b2da012b28745336f7f41c049a5619acc0f3a5a5..435a4d09b81c1d1ec7d187b9bb47bf3a7f3e6c2e 100644
--- a/artemis_sqlmap/Dbxref.xml
+++ b/artemis_sqlmap/Dbxref.xml
@@ -18,7 +18,7 @@
<resultMap id="select-feature-dbxref"
class="FeatureDbxref">
- <result property="feature_id" column="feature_id"/>
+ <result property="feature.id" column="feature_id"/>
<result property="dbxref.db.name" column="name"/>
<result property="dbxref.accession" column="accession"/>
<result property="dbxref.version" column="version"/>
@@ -66,14 +66,15 @@
WHERE dbxref_id=
(SELECT dbxref_id FROM dbxref WHERE accession=#dbxref.accession#
AND db_id=(SELECT db_id FROM db WHERE name=#dbxref.db.name#))
- AND feature_id=$feature_id$
+ AND feature_id=
+ (SELECT feature_id FROM feature WHERE uniquename=#feature.uniquename#)
</delete>
<insert id="insertFeatureDbxref" parameterClass="FeatureDbxref">
INSERT INTO feature_dbxref
(feature_id, dbxref_id, is_current)
VALUES
- ($feature_id$, $dbxref_id$, $current$)
+ ($feature.id$, $dbxref_id$, $current$)
</insert>
<insert id="insertDbxref" parameterClass="Dbxref">
diff --git a/artemis_sqlmap/Feature.xml b/artemis_sqlmap/Feature.xml
index 337577809e290d2955dd03231c94f6bc6c867bbe..0b01852f46b242341275c8deaa843dc4dd906771 100644
--- a/artemis_sqlmap/Feature.xml
+++ b/artemis_sqlmap/Feature.xml
@@ -9,9 +9,15 @@
<typeAlias alias="Feature"
type="uk.ac.sanger.artemis.chado.Feature"/>
+
+ <typeAlias alias="FeatureLoc"
+ type="uk.ac.sanger.artemis.chado.FeatureLoc"/>
+
+ <typeAlias alias="FeatureProp"
+ type="uk.ac.sanger.artemis.chado.FeatureProp"/>
- <typeAlias alias="ChadoTransaction"
- type="uk.ac.sanger.artemis.chado.ChadoTransaction"/>
+ <typeAlias alias="FeatureRelationship"
+ type="uk.ac.sanger.artemis.chado.FeatureRelationship"/>
<parameterMap id="schema-cvlist"
class="Feature">
@@ -23,7 +29,7 @@
class="Feature">
<result property="timelastmodified" column="timelastmodified"/>
<result property="id" column="id"/>
- <result property="feature_relationship.object_id" column="object_id"/>
+ <result property="feature_relationship.object.id" column="object_id"/>
<result property="feature_relationship.cvterm.cvtermId" column="relation_type_id"/>
<result property="feature_relationship.rank" column="rank"/>
<result property="featureloc.strand" column="strand" nullValue="0"/>
@@ -58,7 +64,7 @@
select="getFeatureRelationship" />
<result property="featureRelationshipsForSubjectId" column="{subject_id=id}"
select="getFeatureRelationship" />
- <result property="featureSynonymsForFeatureId" column="{uniquename=uniquename}"
+ <result property="featureSynonymsForFeatureId" column="{feature.uniquename=uniquename}"
select="getLazyFeatureSynonymsByUniquename" />
<result property="organism" column="organism_id" select="getOrganism" />
</resultMap>
@@ -74,23 +80,23 @@
</resultMap>
<resultMap id="select-featureprop"
- class="uk.ac.sanger.artemis.chado.FeatureProp">
+ class="FeatureProp">
<result property="value" column="value" />
<result property="rank" column="rank" />
<result property="cvterm" column="type_id" select="selectCvterm" />
</resultMap>
<resultMap id="select-relationship"
- class="uk.ac.sanger.artemis.chado.FeatureRelationship">
- <result property="subject_id" column="subject_id" />
- <result property="object_id" column="object_id" />
+ class="FeatureRelationship">
+ <result property="subject.id" column="subject_id" />
+ <result property="object.id" column="object_id" />
<result property="value" column="value" />
<result property="rank" column="rank" />
<result property="cvterm" column="type_id" select="selectCvterm" />
</resultMap>
<resultMap id="select-location"
- class="uk.ac.sanger.artemis.chado.FeatureLoc">
+ class="FeatureLoc">
<result property="srcfeature_id" column="srcfeature_id" nullValue="-999" />
<result property="fmin" column="fmin" nullValue="-999" />
<result property="fmax" column="fmax" nullValue="-999" />
@@ -134,30 +140,7 @@
</select>
- <!-- get feature id -->
- <select id="getFeatureID" parameterClass="ChadoTransaction"
- resultClass="Feature">
- SELECT feature_id AS id, uniquename FROM feature WHERE
- <dynamic>
- <isNotNull property="uniquename">
- <iterate property="uniquename" conjunction="OR">
- feature.uniquename='$uniquename[]$'
- </iterate>
- </isNotNull>
-
- <isNotNull property="parents">
- <iterate property="parents" conjunction="OR">
- feature.uniquename='$parents[]$'
- </iterate>
- </isNotNull>
-
- <isNotNull property="derives_from">
- <iterate property="derives_from" conjunction="OR">
- feature.uniquename='$derives_from[]$'
- </iterate>
- </isNotNull>
- </dynamic>
- </select>
+ <!-- get feature -->
<select id="getFeature" parameterClass="Feature"
resultMap="select-feature">
@@ -193,7 +176,7 @@
</select>
<select id="getLazyFeature" resultMap ="select-feature-lazy"
- parameterClass="Feature">
+ parameterClass="Feature">
SELECT
timelastmodified,
f.feature_id AS id,
@@ -212,18 +195,18 @@
<isNotNull property="uniquename">
<isNotNull property="featureSynonymsForFeatureId">
- <iterate property="featureSynonymsForFeatureId" conjunction="OR" open="(" close=" OR">
+ <iterate property="featureSynonymsForFeatureId" conjunction="OR" open="(" close=") OR">
f.feature_id=#featureSynonymsForFeatureId[].feature_id#
</iterate>
</isNotNull>
- uniquename LIKE #uniquename# OR name LIKE #uniquename# ) AND
+ uniquename LIKE #uniquename# OR name LIKE #uniquename# AND
</isNotNull>
<isGreaterThan property="cvterm.cvtermId" compareValue="0">
feature.type_id=$cvterm.cvtermId$ AND
</isGreaterThan>
</dynamic>
- f.feature_id > 0
+ f.feature_id > 0
</select>
<select id="getSchema" resultClass="java.lang.String">
@@ -270,62 +253,61 @@
</select>
- <!-- WRITE BACK METHODS -->
- <update id="updateAttributes"
- parameterClass="ChadoTransaction">
- UPDATE $chadoTable$
- SET
- <iterate property="properties" conjunction=",">
- $properties[]$
- </iterate>
-
- <isNotEqual property="chadoTable" compareValue="feature">
- FROM feature
- </isNotEqual>
-
- WHERE
- feature.feature_id=$chadoTable$.feature_id AND (
- <iterate property="uniquename" conjunction="OR">
- feature.uniquename='$uniquename[]$'
- </iterate>
- )
- <dynamic>
- <isNotNull property="constraint">
- <iterate prepend="AND" property="constraint" conjunction="AND">
- $constraint[]$
- </iterate>
- </isNotNull>
- </dynamic>
+ <!-- WRITE BACK METHODS -->
+
+ <!-- UPDATE -->
+ <update id="updateFeatureLoc"
+ parameterClass="FeatureLoc">
+ UPDATE featureloc
+ SET fmin=$fmin$, fmax=$fmax$, rank=$rank$, strand=$strand$, phase=$phase$
+ WHERE
+ <isNotNull property="feature.uniquename">
+ feature_id=(SELECT feature_id FROM feature WHERE uniquename=#feature.uniquename#)
+ </isNotNull>
</update>
-
- <insert id="insertAttributes"
- parameterClass="ChadoTransaction">
- INSERT INTO $chadoTable$
- (
- feature_id
- <iterate prepend="," property="propertiesName" conjunction="," >
- $propertiesName[]$
- </iterate>
- ) VALUES
- (
- $feature_id$
- <iterate prepend="," property="propertiesValue" conjunction="," >
- $propertiesValue[]$
- </iterate>
- )
+
+ <update id="updateFeature"
+ parameterClass="Feature">
+ UPDATE feature
+ SET uniquename=#uniquename#
+ <isNotNull property="cvterm.cvtermId">
+ , type_id=$cvterm.cvtermId$
+ </isNotNull>
+ <isNotNull property="timelastmodified">
+ , timelastmodified=#timelastmodified#
+ </isNotNull>
+ WHERE feature_id=$id$
+ </update>
+
+ <update id="updateFeatureProp"
+ parameterClass="FeatureProp">
+ UPDATE featureprop
+ SET value=#value#
+ WHERE rank=$rank$ AND type_id=$cvterm.cvtermId$ AND
+ feature_id=(SELECT feature_id FROM feature WHERE uniquename=#feature.uniquename#)
+ </update>
+
+ <update id="updateFeatureRelationshipsForSubjectId"
+ parameterClass="FeatureRelationship">
+ UPDATE feature_relationship
+ SET
+ rank=$rank$, type_id=$cvterm.cvtermId$
+ WHERE subject_id=
+ ( SELECT feature_id FROM feature WHERE uniquename=#subject.uniquename# )
+ AND object_id=
+ ( SELECT feature_id FROM feature WHERE uniquename=#object.uniquename# )
+ </update>
+
+ <!-- INSERT -->
+ <insert id="insertFeatureProp"
+ parameterClass="FeatureProp">
+ INSERT INTO featureprop
+ ( feature_id, type_id, value, rank )
+ VALUES
+ ( (SELECT feature_id FROM feature WHERE uniquename=#feature.uniquename#),
+ $cvterm.cvtermId$, #value#, $rank$ )
</insert>
- <delete id="deleteAttributes"
- parameterClass="ChadoTransaction">
- DELETE FROM $chadoTable$
- WHERE
- <iterate property="constraint" conjunction="AND">
- $constraint[]$
- </iterate>
- AND
- feature_id=$feature_id$
- </delete>
-
<insert id="insertFeature"
parameterClass="Feature">
INSERT INTO feature
@@ -352,32 +334,42 @@
$featureloc.phase$ )
</insert>
+ <insert id="insertFeatureRelationship"
+ parameterClass="FeatureRelationship">
+ INSERT INTO feature_relationship
+ ( subject_id, object_id, type_id )
+ VALUES
+ ( (SELECT feature_id FROM feature WHERE uniquename=#subject.uniquename#),
+ (SELECT feature_id FROM feature WHERE uniquename=#object.uniquename#),
+ $cvterm.cvtermId$ )
+ </insert>
+
+
+ <!-- DELETE -->
+
+ <delete id="deleteFeatureProp"
+ parameterClass="FeatureProp">
+ DELETE FROM featureprop
+ WHERE
+ <isNotNull property="feature.uniquename">
+ feature_id=
+ (SELECT feature_id FROM feature WHERE uniquename=#feature.uniquename#)
+ AND
+ </isNotNull>
+ <isGreaterThan property="rank" compareValue="-1">
+ rank=$rank$ AND
+ </isGreaterThan>
+ <isNotNull property="value">
+ value=#value# AND
+ </isNotNull>
+ type_id=$cvterm.cvtermId$
+ </delete>
+
<delete id="deleteFeature"
parameterClass="Feature">
DELETE FROM feature
WHERE uniquename=#uniquename#
</delete>
- <insert id="insertFeatureRelationship"
- parameterClass="Feature">
- INSERT INTO feature_relationship
- ( subject_id, object_id, type_id )
- VALUES
- ( $feature_relationship.subject_id$,
- $feature_relationship.object_id$,
- (SELECT cvterm_id FROM cvterm WHERE name=#feature_relationship.cvterm.name#) )
- </insert>
- <update id="updateFeatureRelationshipsForSubjectId"
- parameterClass="ChadoTransaction">
- UPDATE feature_relationship
- SET
- <iterate property="properties" conjunction=",">
- $properties[]$
- </iterate>
- WHERE feature_relationship.subject_id=
- ( SELECT feature_id FROM feature WHERE uniquename=#chadoFeature.uniquename# )
- AND feature_relationship.object_id=
- ( SELECT feature_id FROM feature WHERE uniquename=#parent_uniquename# )
- </update>
</sqlMap>
diff --git a/artemis_sqlmap/Synonym.xml b/artemis_sqlmap/Synonym.xml
index d993e7eca38cd87c6b97db7e43ecbb28cd5efd50..0d73c274588a359d36109deca7836a3b48f161fd 100644
--- a/artemis_sqlmap/Synonym.xml
+++ b/artemis_sqlmap/Synonym.xml
@@ -15,7 +15,7 @@
<resultMap id="select-alias"
class="FeatureSynonym">
- <result property="feature_id" column="feature_id"/>
+ <result property="feature.id" column="feature_id"/>
<result property="synonym_id" column="synonym_id"/>
<result property="pub_id" column="pub_id"/>
<result property="current" column="is_current"/>
@@ -28,7 +28,7 @@
<resultMap id="select-alias-part-lazy"
class="FeatureSynonym">
- <result property="feature_id" column="feature_id"/>
+ <result property="feature.id" column="feature_id"/>
<result property="synonym_id" column="synonym_id"/>
<result property="pub_id" column="pub_id"/>
<result property="current" column="is_current"/>
@@ -38,7 +38,7 @@
<resultMap id="select-alias-lazy"
class="FeatureSynonym">
- <result property="feature_id" column="feature_id"/>
+ <result property="feature.id" column="feature_id"/>
<result property="pub_id" column="pub_id"/>
<result property="current" column="is_current"/>
<result property="internal" column="is_internal"/>
@@ -72,8 +72,8 @@
SELECT fs.*
FROM feature_synonym fs
LEFT JOIN feature f ON f.feature_id=fs.feature_id
- <isNotNull property="uniquename">
- WHERE uniquename=#uniquename#
+ <isNotNull property="feature.uniquename">
+ WHERE uniquename=#feature.uniquename#
</isNotNull>
</select>
@@ -108,13 +108,13 @@
DELETE FROM feature_synonym WHERE
synonym_id=$synonym_id$ AND
feature_id=(SELECT feature_id FROM feature WHERE
- uniquename=#uniquename#)
+ uniquename=#feature.uniquename#)
</delete>
<insert id="insertFeatureAlias" parameterClass="FeatureSynonym">
INSERT INTO feature_synonym ( synonym_id, feature_id, pub_id )
VALUES ( $synonym_id$ ,
- (SELECT feature_id FROM feature WHERE uniquename=#uniquename#),
+ (SELECT feature_id FROM feature WHERE uniquename=#feature.uniquename#),
1)
</insert>
diff --git a/uk/ac/sanger/artemis/chado/ChadoDAO.java b/uk/ac/sanger/artemis/chado/ChadoDAO.java
index baa3fbf797ce78a578515d8b68c69a7b86777dbf..4fbe4b9d576e6c01588a5141cce65c09793c53e0 100644
--- a/uk/ac/sanger/artemis/chado/ChadoDAO.java
+++ b/uk/ac/sanger/artemis/chado/ChadoDAO.java
@@ -28,11 +28,9 @@ import java.sql.*;
import java.util.List;
/**
- *
* Data access object
* @see uk.ac.sanger.artemis.chado.JdbcDAO
* @see uk.ac.sanger.artemis.chado.IBatisDAO
- *
*/
public interface ChadoDAO
{
@@ -172,126 +170,32 @@ public interface ChadoDAO
//
// WRITE BACK
//
- /**
- * Update attributes defined by the <code>ChadoTransaction</code>.
- * @param tsn the <code>ChadoTransaction</code>
- * @return number of rows changed
- * @throws SQLException
- */
- public int updateAttributes
- (final ChadoTransaction tsn)
- throws SQLException;
-
- /**
- * Insert attributes defined by the <code>ChadoTransaction</code>.
- * @param tsn the <code>ChadoTransaction</code>
- * @throws SQLException
- */
- public void insertAttributes
- (final ChadoTransaction tsn)
- throws SQLException;
-
- /**
- * Delete attributes defined by the <code>ChadoTransaction</code>.
- * @param tsn the <code>ChadoTransaction</code>
- * @throws SQLException
- */
- public void deleteAttributes
- (final ChadoTransaction tsn)
- throws SQLException;
-
- /**
- * Insert a feature into the database defined by the <code>ChadoTransaction</code>.
- * @param tsn the <code>ChadoTransaction</code>
- * @parma srcfeature_id the parent feature identifier
- * @throws SQLException
- */
- public void insertFeature
- (final ChadoTransaction tsn,
- final String srcfeature_id)
- throws SQLException;
-
- /**
- * Delete a feature from the database defined by the <code>ChadoTransaction</code>.
- * @param tsn the <code>ChadoTransaction</code>
- * @return number of rows deleted
- * @throws SQLException
- */
- public int deleteFeature
- (final ChadoTransaction tsn)
- throws SQLException;
/**
- * Insert a dbxref for a feature.
- * @param tsn the <code>ChadoTransaction</code>
- * @return number of rows changed
- * @throws SQLException
+ * Merge (update) an already persistent object back to the database
+ * (at the end of the current transaction, or depending upon flush mode).
+ * This method is defined in all the DAOs. It's recommended to call it
+ * through an appropriate one eg SequenceDaoI for FeatureI
+ * @param o The object to merge
*/
- public int insertFeatureDbxref(final ChadoTransaction tsn)
- throws SQLException;
+ public void merge(Object o) throws SQLException;
/**
- * Delete a dbxref for a feature.
- * @param tsn the <code>ChadoTransaction</code>
- * @return number of rows changed
- * @throws SQLException
+ * Save the object to the database (at the end of the current transaction,
+ * or depending upon flush mode). This method is defined in all the DAOs.
+ * It's recommended to call it through an appropriate one eg SequenceDaoI
+ * for FeatureI
+ * @param o The object to store
*/
- public int deleteFeatureDbxref(final ChadoTransaction tsn)
- throws SQLException;
+ public void persist(Object o) throws SQLException;
/**
- * Insert a synonym for a feature.
- * @param tsn the <code>ChadoTransaction</code>
- * @return number of rows changed
- * @throws SQLException
+ * Remove the object from the database (at the end of the current transaction,
+ * or depending upon flush mode). This method is defined in all the DAOs.
+ * It's recommended to call it through an appropriate one eg SequenceDaoI for
+ * FeatureI
+ * @param o The object to delete
*/
- public int insertFeatureAlias(final ChadoTransaction tsn)
- throws SQLException;
-
- /**
- * Delete a synonym for a feature.
- * @param tsn the <code>ChadoTransaction</code>
- * @return number of rows changed
- * @throws SQLException
- */
- public int deleteFeatureAlias(final ChadoTransaction tsn)
- throws SQLException;
-
+ public void delete(Object o) throws SQLException;
- /**
- * Update feature_relationship for a feature.
- * @param tsn the <code>ChadoTransaction</code>
- * @return number of rows changed
- * @throws SQLException
- */
- public void updateFeatureRelationshipsForSubjectId(
- final ChadoTransaction tsn)
- throws SQLException;
- /**
- *
- * Write the time a feature was last modified
- * @param uniquename the unique name of the feature
- * @param timestamp the time stamp to use,
- * if NULL use CURRENT_TIMESTAMP
- * @return number of rows changed
- * @throws SQLException
- */
- public int writeTimeLastModified
- (final String uniquename,
- final Timestamp timestamp)
- throws SQLException;
-
- /**
- *
- * Write the time a feature was last accessed
- * @param uniquename the unique name of the feature
- * @param timestamp the time stamp to use,
- * if NULL use CURRENT_TIMESTAMP
- * @return number of rows changed
- * @throws SQLException
- */
- public int writeTimeAccessioned
- (final String uniquename,
- final Timestamp timestamp)
- throws SQLException;
}
diff --git a/uk/ac/sanger/artemis/chado/ChadoDemo.java b/uk/ac/sanger/artemis/chado/ChadoDemo.java
index f2ff149894cf447aa9b101f92e46c7a160c5156d..2dd5fe0a9b60290b49198342d08a3ec28a72276d 100644
--- a/uk/ac/sanger/artemis/chado/ChadoDemo.java
+++ b/uk/ac/sanger/artemis/chado/ChadoDemo.java
@@ -34,11 +34,8 @@ import java.awt.event.MouseEvent;
import java.awt.Dimension;
import java.net.ConnectException;
import java.sql.SQLException;
-import java.util.Iterator;
import java.util.List;
import java.util.Vector;
-import java.util.Hashtable;
-import java.util.Enumeration;
import javax.swing.JLabel;
import javax.swing.JOptionPane;
@@ -55,7 +52,6 @@ import javax.swing.JFrame;
import javax.swing.JMenu;
import javax.swing.JMenuBar;
import javax.swing.JMenuItem;
-import javax.swing.JSeparator;
import javax.swing.Box;
import javax.swing.event.ListSelectionListener;
import javax.swing.event.ListSelectionEvent;
diff --git a/uk/ac/sanger/artemis/chado/ChadoTransaction.java b/uk/ac/sanger/artemis/chado/ChadoTransaction.java
index ec4e78fcc038bd3661e5efa548bd2f96bf4b619b..2b1f8564db19d3d6d422e6dfa3a457415737c7e1 100644
--- a/uk/ac/sanger/artemis/chado/ChadoTransaction.java
+++ b/uk/ac/sanger/artemis/chado/ChadoTransaction.java
@@ -29,179 +29,56 @@ import java.util.Vector;
import java.util.StringTokenizer;
import java.sql.Timestamp;
+import uk.ac.sanger.artemis.io.GFFStreamFeature;
+
/**
-*
-* Store information about a SQL transaction <i>e.g</i> UPDATE, INSERT, DELETE
-* a feature or a feature attribute.
-*
-**/
+ * Store information about a SQL transaction <i>e.g</i> UPDATE, INSERT, DELETE
+ * a feature, featureloc, featureprop, feature_dbxref, feature_synonym.
+ **/
public class ChadoTransaction
{
//
- // ATTRIBUTE TRANSACTIONS
+ // FEATURE TRANSACTIONS
/** update statement */
public static final int UPDATE = 1;
/** insert statement */
public static final int INSERT = 2;
/** delete statement */
public static final int DELETE = 3;
-
- // FEATURE TRANSACTIONS
- /** insert feature statement */
- public static final int INSERT_FEATURE = 4;
- /** delete feature statement */
- public static final int DELETE_FEATURE = 5;
- // DBXREF TRANSACTIONS
- public static final int UPDATE_DBXREF = 6;
- public static final int INSERT_DBXREF = 7;
- public static final int DELETE_DBXREF = 8;
-
- // SYNONYM TRANSACTIONS
- public static final int INSERT_ALIAS = 9;
- public static final int DELETE_ALIAS = 10;
-
- // FEATURE RELATIONSHIPS
- public static final int UPDATE_FEATURE_RELATIONSHIP = 11;
-
- /** properties store <i>e.g.</i> value=<quote>product=hypothetical protein</quote> */
- private List properties;
- /** constraint store <i>e.g.</i> type_id=21078 */
- protected List constraint;
/** type of statement <i>e.g.</i> UPDATE, INSERT, DELETE, ... */
protected int type;
/** feature unique name */
- protected String uniquename;
- /** chado table for this transaction */
- protected String chadoTable;
- /** postgres schema */
- private String schema;
- /** feature id */
- private int feature_id;
+ protected String old_uniquename;
/** chado feature */
private Feature chadoFeature;
- /** feature dbxref */
- private FeatureDbxref dbxref;
- /** feature synonym */
- private FeatureSynonym alias;
/** last time feature was modified */
private Timestamp lastmodified;
/** the feature object */
private Object feature_obj;
- /** parent uniquenames */
- private List parents;
- /** derives_from uniquenames */
- private List derives_from;
- /** uniquename of the parent feature */
- private String parent_uniquename;
+
+ private GFFStreamFeature gff_feature;
+
/**
- * Used to construct a <code>ChadoTransaction</code> that can
- * be used to describe a SQL transaction.
- *
- * <i>e.g.</i> to DELETE a feature and where uniquename is a <code>String</code>:
- * <blockquote><pre>
- * ChadoTransaction tsn = new ChadoTransaction(ChadoTransaction.DELETE_FEATURE,
- * uniquename, "feature");
- * </pre></blockquote>
- *
- * Or to INSERT a feature property:
- * <blockquote><pre>
- * ChadoTransaction tsn = new ChadoTransaction(ChadoTransaction.INSERT,
- * feature_id, "featureprop");
- * tsn.addProperty("value", "'"+ qualifier_string +"'");
- * tsn.addProperty("type_id", "'"+cvterm_id+"'");
- * tsn.addProperty("rank", Integer.toString(value_index));
- * </pre></blockquote>
- *
- * @param type the transaction type
- * @param uniquename the unique name of feature
- * @param chadoTable the chado table used in transaction <i>e.g.</i>
- * feature, featureloc....
- */
- public ChadoTransaction(int type, String uniquename,
- String chadoTable,
- final Timestamp lastmodified,
- final Object feature_obj)
- {
- this.type = type;
- this.uniquename = uniquename;
- this.chadoTable = chadoTable;
- this.lastmodified = lastmodified;
- this.feature_obj = feature_obj;
- }
-
- /**
- * Used to construct a <code>ChadoTransaction</code> that can
- * be used to describe a SQL transaction.
- *
- * <i>e.g.</i> to INSERT a feature and where chado_feature is a
- * <code>Feature</code>:
- * <blockquote><pre>
- * ChadoTransaction tsn = new ChadoTransaction(ChadoTransaction.INSERT_FEATURE,
- * chado_feature);
- * </pre></blockquote>
- *
- * @param type the transaction type
- * @param chado_feature the <code>Feature</code> to be inserted
- * @param parents <code>Vector</code> of parent uniquenames
- * @param derives_from <code>Vector</code> of derives_from names
+ * Create a transaction to represent a single insert, delete or
+ * update.
+ * @param type the type of transcation, e.g. insert, delete, update.
+ * @param feature_obj the <code>Feature</code>, <code>FeatureLoc</code>,
+ * <code>FeatureProp</code>, <code>FeatureRelationship</code>, <code>FeatureDbxref</code>,
+ * or <code>FeatureSynonym</code>.
+ * @param lastmodified the last modified timestamp
+ * @param gff_feature the artemis GFF feature effected
*/
public ChadoTransaction(final int type,
- final Feature chadoFeature,
- final Vector parents,
- final Vector derives_from)
- {
- this.chadoFeature = chadoFeature;
- this.type = type;
- this.parents = parents;
- this.derives_from = derives_from;
- }
-
- /**
- * Used to construct a <code>ChadoTransaction</code> that can
- * be used to describe a SQL transaction.
- * @param type the transaction type
- * @param dbxref a feature dbxref
- */
- public ChadoTransaction(final int type,
- final String uniquename,
- final FeatureDbxref dbxref,
+ final Object feature_obj,
final Timestamp lastmodified,
- final Object feature_obj)
+ final GFFStreamFeature gff_feature)
{
- this.type = type;
- this.dbxref = dbxref;
- this.uniquename = uniquename;
+ this.type = type;
this.lastmodified = lastmodified;
this.feature_obj = feature_obj;
- }
-
- public ChadoTransaction(final int type,
- final FeatureSynonym alias,
- final Object feature_obj)
- {
- this.type = type;
- this.alias = alias;
- this.feature_obj = feature_obj;
- }
-
- public ChadoTransaction(final int type,
- final Feature chadoFeature,
- final String parent_uniquename)
- {
- this.type = type;
- this.chadoFeature = chadoFeature;
- this.parent_uniquename = parent_uniquename;
- }
-
- /**
- * The <code>Dbxref</code> used in a transaction.
- * @return the feature dbxref
- */
- public FeatureDbxref getFeatureDbxref()
- {
- return dbxref;
+ this.gff_feature = gff_feature;
}
/**
@@ -213,23 +90,6 @@ public class ChadoTransaction
return chadoFeature;
}
- /**
- * Set the postgres schema.
- * @param the postgres schema
- */
- public void setSchema(final String schema)
- {
- this.schema = schema;
- }
-
- /**
- * Get the postgres schema.
- * @return the postgres schema
- */
- public String getSchema()
- {
- return schema;
- }
/**
* The type of SQL transaction
@@ -240,156 +100,31 @@ public class ChadoTransaction
return type;
}
- /**
- * Get the unique name for a feature.
- * @return the unique name for a feature.
- */
- public String getUniqueName()
- {
- return uniquename;
- }
-
/**
- * Get the chado table that is involved in the SQL command
- * @return the chado table
+ * Set the old uniquename, used when updating the uniquename
+ * @param uniquename
*/
- public String getChadoTable()
+ public void setOldUniquename(final String old_uniquename)
{
- return chadoTable;
- }
-
-
- /**
- * Add a property to this transaction that will be updated
- * or inserted.
- * @param name the property name
- * @param value the property value
- */
- public void addProperty(String name, String value)
- {
- if(properties == null)
- properties = new Vector();
-
- properties.add(name+"="+value);
- }
-
-
- /**
- * Set a constraint on this transaction.
- * @param name the constraint name
- * @param value the constraint value
- */
- public void setConstraint(String name, String value)
- {
- if(constraint == null)
- constraint = new Vector();
- constraint.add(name+"="+value);
- }
-
-
- /**
- * Get the properties for this transaction that will be changed.
- * @return the transaction properties used to INSERT/UPDATE
- */
- public List getProperties()
- {
- return properties;
- }
-
- /**
- * Set the properties for this transaction that will be changed.
- * @param properties the transaction properties used to INSERT/UPDATE
- */
- public void setProperties(List properties)
- {
- this.properties = properties;
- }
-
- /**
- * Get the names of the properties for this transaction that will
- * be changed.
- * @return the names of the properties to INSERT/UPDATE
- */
- public List getPropertiesName()
- {
- List propertiesName = new Vector();
- String property;
- int index;
- for(int i=0; i<properties.size();i++)
- {
- property = (String)properties.get(i);
- index = property.indexOf("=");
- propertiesName.add(property.substring(0,index));
- }
-
- return propertiesName;
- }
-
- /**
- * Get the values of the properties for this transaction that will
- * be changed..
- * @return the values of the properties to INSERT/UPDATE
- */
- public List getPropertiesValue()
- {
- List propertiesValue = new Vector();
- String property;
- int index;
- for(int i=0; i<properties.size();i++)
- {
- property = (String)properties.get(i);
- index = property.indexOf("=");
- propertiesValue.add(property.substring(index+1));
- }
-
- return propertiesValue;
- }
-
- /**
- * Get the constraints on this transaction.
- * @return the transaction constraints
- */
- public List getConstraint()
- {
- return constraint;
+ this.old_uniquename = old_uniquename;
}
/**
* Get the unique names of features to change.
*/
- public List getUniquename()
+ public String getOldUniquename()
{
- Vector names = new Vector();
-
- if(uniquename == null)
- return names;
-
- StringTokenizer tok = new StringTokenizer(uniquename,",");
- while(tok.hasMoreTokens())
- {
- names.add(tok.nextToken());
- }
-
- return names;
- }
-
- /**
- * Set the feature id
- * @param feature_id the feature identifier
- */
- public void setFeature_id(final int feature_id)
- {
- this.feature_id = feature_id;
+ return old_uniquename;
}
-
- /**
- * Get the feature id
- * @return the feature identifier
- */
- public int getFeature_id()
+
+ public String getUniquename()
{
- return feature_id;
+ if(getGff_feature() == null)
+ return null;
+
+ return (String)
+ getGff_feature().getQualifierByName("ID").getValues().get(0);
}
/**
@@ -406,44 +141,14 @@ public class ChadoTransaction
return feature_obj;
}
- public FeatureSynonym getAlias()
- {
- return alias;
- }
-
- public void setAlias(FeatureSynonym alias)
- {
- this.alias = alias;
- }
-
- public List getDerives_from()
- {
- return derives_from;
- }
-
- public void setDerives_from(Vector derives_from)
- {
- this.derives_from = derives_from;
- }
-
- public List getParents()
- {
- return parents;
- }
-
- public void setParents(Vector parents)
- {
- this.parents = parents;
- }
-
- public String getParent_uniquename()
+ public GFFStreamFeature getGff_feature()
{
- return parent_uniquename;
+ return gff_feature;
}
- public void setParent_uniquename(String parent_uniquename)
+ public void setGff_feature(GFFStreamFeature gff_feature)
{
- this.parent_uniquename = parent_uniquename;
+ this.gff_feature = gff_feature;
}
}
diff --git a/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java b/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java
index c834a9b0554d15245036a4116f60232798b459c7..b44abe55e7b7f0d488f5a49dd40ca283f997c725 100644
--- a/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java
+++ b/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java
@@ -219,7 +219,7 @@ public class ChadoTransactionManager
String segment_uniquename = feature.getSegmentID(range);
insertFeatureSegment(segment,segment_uniquename);
-// update feature_relationship.rank
+ // update feature_relationship.rank
updateFeatureRelationshipRank(feature, rv_new);
}
}
@@ -252,15 +252,6 @@ public class ChadoTransactionManager
{
ichanged = ((Integer)changes.elementAt(i)).intValue();
- /*
- Qualifier parent_qualifier = feature.getQualifierByName("Parent");
-
- String transcript = null;
- if(parent_qualifier != null)
- transcript =
- (String)parent_qualifier.getValues().get(0);
- */
-
Range range_new = (Range)rv_new.elementAt(ichanged);
Range range_old = (Range)rv_old.elementAt(ichanged);
String seg_id = feature.getSegmentID(range_new);
@@ -271,15 +262,11 @@ public class ChadoTransactionManager
if(feature.getSegmentRangeStore() != null)
feature.getSegmentRangeStore().put(seg_id, range_new);
- tsn = new ChadoTransaction(ChadoTransaction.UPDATE,
- seg_id, "featureloc",
- feature.getLastModified(),
- feature);
-
- if(range_new.getStart() != range_old.getStart())
- tsn.addProperty("fmin", Integer.toString(range_new.getStart()-1));
- if(range_new.getEnd() != range_old.getEnd())
- tsn.addProperty("fmax", Integer.toString(range_new.getEnd()));
+ FeatureLoc featureloc = getFeatureLoc(feature, seg_id, range_new);
+
+ tsn = new ChadoTransaction(ChadoTransaction.UPDATE,
+ featureloc,
+ feature.getLastModified(), feature);
sql.add(tsn);
}
@@ -381,28 +368,53 @@ public class ChadoTransactionManager
private void updateFeatureRelationshipRank(final GFFStreamFeature feature,
final RangeVector rv_new)
{
+
+
// update feature_relationship.rank
ChadoTransaction tsn;
Hashtable feature_relationship_rank_store = new Hashtable();
- String parent =
- (String)feature.getQualifierByName("Parent").getValues().get(0);
+ Qualifier qualifier_relation = feature.getQualifierByName("Parent");
- for(int i=0; i<rv_new.size(); i++)
+ for(int rank=0; rank<rv_new.size(); rank++)
{
- Range range = (Range)rv_new.elementAt(i);
+ Range range = (Range)rv_new.elementAt(rank);
String seq_id = feature.getSegmentID(range);
uk.ac.sanger.artemis.chado.Feature chado_feature =
new uk.ac.sanger.artemis.chado.Feature();
chado_feature.setUniquename(seq_id);
-
- tsn = new ChadoTransaction(
- ChadoTransaction.UPDATE_FEATURE_RELATIONSHIP,
- chado_feature,
- parent);
- tsn.addProperty("rank", "'"+ i +"'");
- sql.add(tsn);
- feature_relationship_rank_store.put(seq_id, new Integer(i));
+
+ List featureRelationshipsForSubjectId = null;
+ if(qualifier_relation != null)
+ {
+ StringVector parents = qualifier_relation.getValues();
+ if(parents.size() > 0)
+ featureRelationshipsForSubjectId = new Vector();
+
+ for(int i=0; i<parents.size(); i++)
+ {
+ uk.ac.sanger.artemis.chado.Feature parent =
+ new uk.ac.sanger.artemis.chado.Feature();
+ parent.setUniquename((String)parents.get(i));
+ FeatureRelationship feature_relationship =
+ new FeatureRelationship();
+ Cvterm cvterm = new Cvterm();
+ cvterm.setCvtermId(DatabaseDocument.getCvtermID("part_of").longValue());
+
+ feature_relationship.setObject(parent);
+ feature_relationship.setSubject(chado_feature);
+ feature_relationship.setCvterm(cvterm);
+ feature_relationship.setRank(rank);
+ featureRelationshipsForSubjectId.add(feature_relationship);
+
+ tsn = new ChadoTransaction(ChadoTransaction.UPDATE,
+ feature_relationship,
+ feature.getLastModified(), feature);
+ sql.add(tsn);
+ }
+ }
+
+ feature_relationship_rank_store.put(seq_id, new Integer(rank));
}
feature.setFeature_relationship_rank_store(feature_relationship_rank_store);
}
@@ -454,9 +466,6 @@ public class ChadoTransactionManager
featureloc.setStrand(1);
else
featureloc.setStrand(-1);
-
- Vector parent_features = null;
- Vector derives_features = null;
// codon_start attribute
try
@@ -476,29 +485,58 @@ public class ChadoTransactionManager
// relationship attributes
Qualifier qualifier_relation = feature.getQualifierByName("Parent");
+ List featureRelationshipsForSubjectId = null;
if(qualifier_relation != null)
{
StringVector parents = qualifier_relation.getValues();
if(parents.size() > 0)
- parent_features = new Vector();
+ featureRelationshipsForSubjectId = new Vector();
for(int i=0; i<parents.size(); i++)
- parent_features.add((String)parents.get(i));
+ {
+ uk.ac.sanger.artemis.chado.Feature parent =
+ new uk.ac.sanger.artemis.chado.Feature();
+ parent.setUniquename((String)parents.get(i));
+ FeatureRelationship feature_relationship =
+ new FeatureRelationship();
+ Cvterm cvterm = new Cvterm();
+ cvterm.setCvtermId(DatabaseDocument.getCvtermID("part_of").longValue());
+
+ feature_relationship.setObject(parent);
+ feature_relationship.setSubject(chado_feature);
+ feature_relationship.setCvterm(cvterm);
+ featureRelationshipsForSubjectId.add(feature_relationship);
+ }
}
qualifier_relation = feature.getQualifierByName("Derives_from");
if(qualifier_relation != null)
{
StringVector derives = qualifier_relation.getValues();
- if(derives.size() > 0)
- derives_features = new Vector();
+ if(derives.size() > 0 && featureRelationshipsForSubjectId == null)
+ featureRelationshipsForSubjectId = new Vector();
for(int i=0; i<derives.size(); i++)
- derives_features.add((String)derives.get(i));
+ {
+ uk.ac.sanger.artemis.chado.Feature parent =
+ new uk.ac.sanger.artemis.chado.Feature();
+ parent.setUniquename((String) derives.get(i));
+ FeatureRelationship feature_relationship = new FeatureRelationship();
+ Cvterm cvterm = new Cvterm();
+ cvterm.setCvtermId(DatabaseDocument.getCvtermID("derives_from")
+ .longValue());
+
+ feature_relationship.setObject(parent);
+ feature_relationship.setSubject(chado_feature);
+ feature_relationship.setCvterm(cvterm);
+ featureRelationshipsForSubjectId.add(feature_relationship);
+ }
}
+ chado_feature.setFeatureRelationshipsForSubjectId(
+ featureRelationshipsForSubjectId);
}
catch(InvalidRelationException ire){}
-
+
if(feature.isForwardFeature())
featureloc.setStrand(1);
else
@@ -517,10 +555,10 @@ public class ChadoTransactionManager
addQualifiers(feature.getQualifiers(), chado_feature);
// create transaction object
- ChadoTransaction tsn = new ChadoTransaction(ChadoTransaction.INSERT_FEATURE,
- chado_feature,
- parent_features,
- derives_features);
+
+ ChadoTransaction tsn = new ChadoTransaction(ChadoTransaction.INSERT,
+ chado_feature,
+ null, (GFFStreamFeature)null);
sql.add(tsn);
}
@@ -540,9 +578,6 @@ public class ChadoTransactionManager
featureloc.setStrand(1);
else
featureloc.setStrand(-1);
-
- Vector parent_features = null;
- Vector derives_features = null;
// codon_start attribute
Feature feature = segment.getFeature();
@@ -563,26 +598,55 @@ public class ChadoTransactionManager
// relationship attributes
Qualifier qualifier_relation = feature.getQualifierByName("Parent");
+ List featureRelationshipsForSubjectId = null;
if(qualifier_relation != null)
{
StringVector parents = qualifier_relation.getValues();
if(parents.size() > 0)
- parent_features = new Vector();
+ featureRelationshipsForSubjectId = new Vector();
for(int i=0; i<parents.size(); i++)
- parent_features.add((String)parents.get(i));
+ {
+ uk.ac.sanger.artemis.chado.Feature parent =
+ new uk.ac.sanger.artemis.chado.Feature();
+ parent.setUniquename((String)parents.get(i));
+ FeatureRelationship feature_relationship =
+ new FeatureRelationship();
+ Cvterm cvterm = new Cvterm();
+ cvterm.setCvtermId(DatabaseDocument.getCvtermID("part_of").longValue());
+
+ feature_relationship.setObject(parent);
+ feature_relationship.setSubject(chado_feature);
+ feature_relationship.setCvterm(cvterm);
+ featureRelationshipsForSubjectId.add(feature_relationship);
+ }
}
qualifier_relation = feature.getQualifierByName("Derives_from");
if(qualifier_relation != null)
{
StringVector derives = qualifier_relation.getValues();
- if(derives.size() > 0)
- derives_features = new Vector();
+ if(derives.size() > 0 && featureRelationshipsForSubjectId == null)
+ featureRelationshipsForSubjectId = new Vector();
for(int i=0; i<derives.size(); i++)
- derives_features.add((String)derives.get(i));
+ {
+ uk.ac.sanger.artemis.chado.Feature parent =
+ new uk.ac.sanger.artemis.chado.Feature();
+ parent.setUniquename((String) derives.get(i));
+ FeatureRelationship feature_relationship = new FeatureRelationship();
+ Cvterm cvterm = new Cvterm();
+ cvterm.setCvtermId(DatabaseDocument.getCvtermID("derives_from")
+ .longValue());
+
+ feature_relationship.setObject(parent);
+ feature_relationship.setSubject(chado_feature);
+ feature_relationship.setCvterm(cvterm);
+ featureRelationshipsForSubjectId.add(feature_relationship);
+ }
}
+ chado_feature.setFeatureRelationshipsForSubjectId(
+ featureRelationshipsForSubjectId);
}
catch(InvalidRelationException ire){}
@@ -599,22 +663,27 @@ public class ChadoTransactionManager
//addQualifiers(feature.getQualifiers(), chado_feature);
// create transaction object
- ChadoTransaction tsn = new ChadoTransaction(ChadoTransaction.INSERT_FEATURE,
- chado_feature,
- parent_features,
- derives_features);
+
+ ChadoTransaction tsn = new ChadoTransaction(ChadoTransaction.INSERT,
+ chado_feature,
+ null, (GFFStreamFeature)null);
+
sql.add(tsn);
}
/**
* Set the transaction for deleting a feature.
- * @param feature
*/
- private void deleteFeature(final String feature_uniquename)
+ private void deleteFeature(final String uniquename)
{
- ChadoTransaction tsn = new ChadoTransaction(ChadoTransaction.DELETE_FEATURE,
- feature_uniquename, "feature",
- null, null);
+ uk.ac.sanger.artemis.chado.Feature chado_feature =
+ new uk.ac.sanger.artemis.chado.Feature();
+ chado_feature.setUniquename(uniquename);
+
+ ChadoTransaction tsn = new ChadoTransaction(ChadoTransaction.DELETE,
+ chado_feature,
+ null, (GFFStreamFeature)null);
+
sql.add(tsn);
}
@@ -710,7 +779,7 @@ public class ChadoTransactionManager
final Key new_key,
final GFFStreamFeature feature)
{
- final String uniquename = (String)(feature.getQualifierByName("ID").getValues()).elementAt(0);
+ String uniquename = (String)(feature.getQualifierByName("ID").getValues()).elementAt(0);
ChadoTransaction tsn;
// updating the key
@@ -726,12 +795,19 @@ public class ChadoTransactionManager
JOptionPane.WARNING_MESSAGE);
}
else
- {
+ {
+ uk.ac.sanger.artemis.chado.Feature chado_feature =
+ new uk.ac.sanger.artemis.chado.Feature();
+ Cvterm cvterm = new Cvterm();
+ cvterm.setCvtermId( lcvterm_id.longValue() );
+
+ chado_feature.setCvterm(cvterm);
+ chado_feature.setUniquename(uniquename);
+
tsn = new ChadoTransaction(ChadoTransaction.UPDATE,
- uniquename, "feature",
- feature.getLastModified(),
- feature);
- tsn.addProperty("type_id", "'"+ lcvterm_id.toString() +"'");
+ chado_feature,
+ feature.getLastModified(), feature);
+
sql.add(tsn);
}
}
@@ -764,13 +840,32 @@ public class ChadoTransactionManager
continue;
}
- String cvterm_id = lcvterm_id.toString();
- tsn = new ChadoTransaction(ChadoTransaction.DELETE,
- uniquename, "featureprop",
- feature.getLastModified(),
- feature);
- tsn.setConstraint("type_id", cvterm_id);
- sql.add(tsn);
+
+ if(feature.getFeature_relationship_rank_store() != null)
+ {
+ Hashtable rank_hash = feature.getFeature_relationship_rank_store();
+ Enumeration id_keys= rank_hash.keys();
+ while(id_keys.hasMoreElements())
+ {
+ uniquename = (String)id_keys.nextElement();
+ FeatureProp featureprop = getFeatureProp(uniquename, null,
+ lcvterm_id, -1);
+ tsn = new ChadoTransaction(ChadoTransaction.DELETE,
+ featureprop,
+ feature.getLastModified(), feature);
+ sql.add(tsn);
+ }
+ }
+ else
+ {
+ FeatureProp featureprop = getFeatureProp(uniquename,
+ null, lcvterm_id, -1);
+
+ tsn = new ChadoTransaction(ChadoTransaction.DELETE,
+ featureprop,
+ feature.getLastModified(), feature);
+ sql.add(tsn);
+ }
}
}
@@ -817,10 +912,10 @@ public class ChadoTransactionManager
}
// get the cvterm_id for this featureprop/qualifier
- String cvterm_id = null;
+ Long lcvterm_id = null;
if(!name.equals("timelastmodified"))
{
- Long lcvterm_id = DatabaseDocument.getCvtermID(name);
+ lcvterm_id = DatabaseDocument.getCvtermID(name);
if(lcvterm_id == null) // chado doesn't recognise this
{
@@ -831,7 +926,6 @@ public class ChadoTransactionManager
JOptionPane.WARNING_MESSAGE);
continue;
}
- cvterm_id = lcvterm_id.toString();
}
if(old_index > -1 &&
@@ -842,22 +936,40 @@ public class ChadoTransactionManager
//
for(int rank = 0; rank < new_qualifier_strings.size();
++rank)
- {
+ {
String qualifier_string = (String)new_qualifier_strings.elementAt(rank);
int index = qualifier_string.indexOf("=");
if(index > -1)
qualifier_string = qualifier_string.substring(index+1);
- tsn = new ChadoTransaction(ChadoTransaction.UPDATE,
- uniquename, "featureprop",
- feature.getLastModified(),
- feature);
+ if(feature.getFeature_relationship_rank_store() != null)
+ {
+ Hashtable rank_hash = feature.getFeature_relationship_rank_store();
+ Enumeration id_keys= rank_hash.keys();
+ while(id_keys.hasMoreElements())
+ {
+ uniquename = (String)id_keys.nextElement();
+ FeatureProp featureprop = getFeatureProp(uniquename,
+ qualifier_string,
+ lcvterm_id, rank);
+ tsn = new ChadoTransaction(ChadoTransaction.UPDATE,
+ featureprop,
+ feature.getLastModified(), feature);
+ tsn.setGff_feature(feature);
+ sql.add(tsn);
+ }
+ }
+ else
+ {
+ FeatureProp featureprop = getFeatureProp(uniquename,
+ qualifier_string, lcvterm_id, rank);
- tsn.addProperty("value", "'"+ stripQuotes(qualifier_string) +"'");
- tsn.setConstraint("featureprop.type_id", "'"+cvterm_id+"'");
- tsn.setConstraint("rank", Integer.toString(rank));
- sql.add(tsn);
+ tsn = new ChadoTransaction(ChadoTransaction.UPDATE, featureprop,
+ feature.getLastModified(), feature);
+ tsn.setGff_feature(feature);
+ sql.add(tsn);
+ }
}
}
@@ -868,13 +980,34 @@ public class ChadoTransactionManager
//
if(old_index > -1)
{
- tsn = new ChadoTransaction(ChadoTransaction.DELETE,
- uniquename, "featureprop",
- feature.getLastModified(),
- feature);
+ if(feature.getFeature_relationship_rank_store() != null)
+ {
+ Hashtable rank_hash = feature.getFeature_relationship_rank_store();
+ Enumeration id_keys= rank_hash.keys();
+ while(id_keys.hasMoreElements())
+ {
+ uniquename = (String)id_keys.nextElement();
+ FeatureProp featureprop = getFeatureProp(uniquename, null,
+ lcvterm_id, -1);
+ tsn = new ChadoTransaction(ChadoTransaction.DELETE,
+ featureprop,
+ feature.getLastModified(), feature);
+ tsn.setGff_feature(feature);
+ sql.add(tsn);
+ }
+ }
+ else
+ {
+ FeatureProp featureprop = getFeatureProp(uniquename, null,
+ lcvterm_id, -1);
+
+ tsn = new ChadoTransaction(ChadoTransaction.DELETE,
+ featureprop,
+ feature.getLastModified(), feature);
- tsn.setConstraint("type_id", cvterm_id);
- sql.add(tsn);
+ tsn.setGff_feature(feature);
+ sql.add(tsn);
+ }
}
//
@@ -888,17 +1021,30 @@ public class ChadoTransactionManager
if(index > -1)
qualifier_string = qualifier_string.substring(index+1);
- tsn = new ChadoTransaction(ChadoTransaction.INSERT,
- uniquename, "featureprop",
- feature.getLastModified(),
- feature);
-
- tsn.addProperty("value", "'"+ stripQuotes(qualifier_string) +"'");
- tsn.addProperty("type_id", "'"+cvterm_id+"'");
- tsn.addProperty("rank", Integer.toString(rank));
-
- if(tsn !=null)
+ if(feature.getFeature_relationship_rank_store() != null)
+ {
+ Hashtable rank_hash = feature.getFeature_relationship_rank_store();
+ Enumeration id_keys= rank_hash.keys();
+ while(id_keys.hasMoreElements())
+ {
+ uniquename = (String)id_keys.nextElement();
+ FeatureProp featureprop = getFeatureProp(uniquename, qualifier_string,
+ lcvterm_id, rank);
+ tsn = new ChadoTransaction(ChadoTransaction.INSERT,
+ featureprop,
+ feature.getLastModified(), feature);
+ sql.add(tsn);
+ }
+ }
+ else
+ {
+ FeatureProp featureprop = getFeatureProp(uniquename, qualifier_string,
+ lcvterm_id, rank);
+ tsn = new ChadoTransaction(ChadoTransaction.INSERT,
+ featureprop,
+ feature.getLastModified(), feature);
sql.add(tsn);
+ }
}
}
@@ -944,14 +1090,16 @@ public class ChadoTransactionManager
if(new_qualifier.getValues() == null)
return;
- uniquename = (String) old_qualifier.getValues().get(0);
+ uk.ac.sanger.artemis.chado.Feature chado_feature =
+ new uk.ac.sanger.artemis.chado.Feature();
+
+ chado_feature.setUniquename((String)new_qualifier.getValues().get(0));
+
ChadoTransaction tsn = new ChadoTransaction(ChadoTransaction.UPDATE,
- uniquename, "feature",
- feature.getLastModified(),
- feature);
-
- tsn.addProperty("uniquename", "'" +
- stripQuotes((String) new_qualifier.getValues().get(0)) + "'");
+ chado_feature,
+ feature.getLastModified(), feature);
+ tsn.setOldUniquename( (String)old_qualifier.getValues().get(0) );
+
sql.add(tsn);
return;
}
@@ -976,17 +1124,20 @@ public class ChadoTransactionManager
qualifier_string.substring(0,index)+" acc="+qualifier_string.substring(index+1));
FeatureDbxref old_dbxref = new FeatureDbxref();
+ uk.ac.sanger.artemis.chado.Feature chado_feature =
+ new uk.ac.sanger.artemis.chado.Feature();
Dbxref dbxref = new Dbxref();
Db db = new Db();
db.setName(qualifier_string.substring(0,index));
dbxref.setAccession(qualifier_string.substring(index+1));
dbxref.setDb(db);
+ chado_feature.setUniquename(uniquename);
old_dbxref.setDbxref(dbxref);
-
- tsn = new ChadoTransaction(ChadoTransaction.DELETE_DBXREF,
- uniquename, old_dbxref,
- feature.getLastModified(),
- feature);
+ old_dbxref.setFeature(chado_feature);
+
+ tsn = new ChadoTransaction(ChadoTransaction.DELETE,
+ old_dbxref,
+ feature.getLastModified(), feature);
}
else if(isSynonymTag(qualifier_name))
{
@@ -994,15 +1145,18 @@ public class ChadoTransactionManager
qualifier_string);
FeatureSynonym alias = new FeatureSynonym();
+ uk.ac.sanger.artemis.chado.Feature chado_feature =
+ new uk.ac.sanger.artemis.chado.Feature();
+ chado_feature.setUniquename(uniquename);
+
Synonym synonym = new Synonym();
synonym.setName(qualifier_string);
alias.setSynonym(synonym);
- alias.setUniquename(uniquename);
+ alias.setFeature(chado_feature);
- tsn = new ChadoTransaction(ChadoTransaction.DELETE_ALIAS,
- alias,
- feature);
- //tsn.setConstraint("synonym.name", "'"+qualifier_string+"'");
+ tsn = new ChadoTransaction(ChadoTransaction.DELETE,
+ alias,
+ feature.getLastModified(), feature);
}
sql.add(tsn);
}
@@ -1033,11 +1187,14 @@ public class ChadoTransactionManager
dbxref.setDb(db);
dbxref.setAccession(qualifier_string.substring(index+1));
new_dbxref.setDbxref(dbxref);
-
- tsn = new ChadoTransaction(ChadoTransaction.INSERT_DBXREF,
- uniquename, new_dbxref,
- feature.getLastModified(),
- feature);
+ uk.ac.sanger.artemis.chado.Feature feat =
+ new uk.ac.sanger.artemis.chado.Feature();
+ feat.setUniquename(uniquename);
+ new_dbxref.setFeature(feat);
+
+ tsn = new ChadoTransaction(ChadoTransaction.INSERT,
+ new_dbxref,
+ feature.getLastModified(), feature);
}
else if(isSynonymTag(qualifier_name))
{
@@ -1045,6 +1202,10 @@ public class ChadoTransactionManager
qualifier_string);
Long lcvterm_id = DatabaseDocument.getCvtermID(qualifier_name);
FeatureSynonym alias = new FeatureSynonym();
+ uk.ac.sanger.artemis.chado.Feature chado_feature =
+ new uk.ac.sanger.artemis.chado.Feature();
+ chado_feature.setUniquename(uniquename);
+
Synonym synonym = new Synonym();
Cvterm cvterm = new Cvterm();
cvterm.setCvtermId(lcvterm_id.longValue());
@@ -1052,14 +1213,11 @@ public class ChadoTransactionManager
synonym.setCvterm(cvterm);
alias.setSynonym(synonym);
- alias.setUniquename(uniquename);
+ alias.setFeature(chado_feature);
-
- tsn = new ChadoTransaction(ChadoTransaction.INSERT_ALIAS,
- alias,
- feature);
- //tsn.setConstraint("synonym.name", "'"+qualifier_string+"'");
- //tsn.addProperty("type_id", lcvterm_id.toString());
+ tsn = new ChadoTransaction(ChadoTransaction.INSERT,
+ alias,
+ feature.getLastModified(), feature);
}
sql.add(tsn);
}
@@ -1075,13 +1233,88 @@ public class ChadoTransactionManager
*/
private String stripQuotes(String s)
{
+ if(s == null)
+ return null;
+
if(s.startsWith("\"") && s.endsWith("\""))
s = s.substring(1,s.length()-1);
return s;
}
+ /**
+ * Get the FeatureLoc object
+ * @param feature
+ * @param seg_id
+ * @param range_new
+ * @return
+ */
+ private FeatureLoc getFeatureLoc(GFFStreamFeature feature,
+ String seg_id, Range range_new)
+ {
+ FeatureLoc featureloc = new FeatureLoc();
+ uk.ac.sanger.artemis.chado.Feature chado_feature =
+ new uk.ac.sanger.artemis.chado.Feature();
+ chado_feature.setUniquename(seg_id);
+
+ featureloc.setFeature(chado_feature);
+ featureloc.setFmax(range_new.getEnd());
+ featureloc.setFmin(range_new.getStart()-1);
+
+ if(feature.getFeature_relationship_rank_store() != null)
+ {
+ Hashtable rank_hash = feature.getFeature_relationship_rank_store();
+ if(rank_hash.containsKey(seg_id))
+ {
+ Integer rank = (Integer)rank_hash.get(seg_id);
+ featureloc.setRank(rank.intValue());
+ }
+ else
+ featureloc.setRank(0);
+ }
+ else
+ featureloc.setRank(0);
+
+ boolean is_complement = feature.getLocation().isComplement();
+ if(is_complement)
+ featureloc.setStrand(-1);
+ else
+ featureloc.setStrand(1);
+
+ Qualifier qualifier_phase = feature.getQualifierByName("codon_start");
+ if(qualifier_phase != null)
+ {
+ String phase = (String)(qualifier_phase.getValues()).elementAt(0);
+ if(phase.equals ("1"))
+ featureloc.setPhase(0);
+ else if(phase.equals("2"))
+ featureloc.setPhase(1);
+ else if(phase.equals("3"))
+ featureloc.setPhase(2);
+ }
+
+ return featureloc;
+ }
+
+ private FeatureProp getFeatureProp(final String uniquename,
+ final String qualifier_string,
+ final Long lcvterm_id,
+ final int rank)
+ {
+ FeatureProp featureprop = new FeatureProp();
+ uk.ac.sanger.artemis.chado.Feature chado_feature =
+ new uk.ac.sanger.artemis.chado.Feature();
+ chado_feature.setUniquename(uniquename);
+ Cvterm cvterm = new Cvterm();
+ cvterm.setCvtermId(lcvterm_id.longValue());
+ featureprop.setValue(stripQuotes(qualifier_string));
+ featureprop.setRank(rank);
+ featureprop.setCvterm(cvterm);
+ featureprop.setFeature(chado_feature);
+ return featureprop;
+ }
+
/**
* Invoked when a deletion or insertion occurs in a Bases object.
**/
diff --git a/uk/ac/sanger/artemis/chado/FeatureDbxref.java b/uk/ac/sanger/artemis/chado/FeatureDbxref.java
index bc4ecd83f8f4fc6c65a128aa07d6bb18eae4843a..54b5576dd9957b815b6d27ebf02ec248c8199090 100644
--- a/uk/ac/sanger/artemis/chado/FeatureDbxref.java
+++ b/uk/ac/sanger/artemis/chado/FeatureDbxref.java
@@ -28,23 +28,21 @@ package uk.ac.sanger.artemis.chado;
* Representation of the chado feature_dbxref.
*/
public class FeatureDbxref
-{
- private String schema;
-
+{
/** feature_dbxref */
- private int feature_id;
+ private Feature feature;
private int dbxref_id;
private boolean current = true;
private Dbxref dbxref;
- public int getFeature_id()
+ public Feature getFeature()
{
- return feature_id;
+ return feature;
}
- public void setFeature_id(int feature_id)
+ public void setFeature(Feature feature)
{
- this.feature_id = feature_id;
+ this.feature = feature;
}
public boolean isCurrent()
@@ -57,15 +55,6 @@ public class FeatureDbxref
this.current = current;
}
- public String getSchema()
- {
- return schema;
- }
-
- public void setSchema(String schema)
- {
- this.schema = schema;
- }
public int getDbxref_id()
{
diff --git a/uk/ac/sanger/artemis/chado/FeatureLoc.java b/uk/ac/sanger/artemis/chado/FeatureLoc.java
index c329b5b3ca475e7f1f37c3cf90e12add922d5223..ae6dca0215e5fbac7fae9f21a1eff61280d4d7c2 100644
--- a/uk/ac/sanger/artemis/chado/FeatureLoc.java
+++ b/uk/ac/sanger/artemis/chado/FeatureLoc.java
@@ -29,6 +29,8 @@ package uk.ac.sanger.artemis.chado;
*/
public class FeatureLoc
{
+ /** CHADO feature */
+ private Feature feature;
/** id of the parent feature */
private int srcfeature_id = 0;
/** start position */
@@ -45,6 +47,10 @@ public class FeatureLoc
private int locgroup;
/** Used when a feature has >1 location */
private int rank;
+
+ private boolean minPartial;
+
+ private boolean maxPartial;
/**
* Get the strand. The orientation/directionality of the location.
@@ -203,4 +209,34 @@ public class FeatureLoc
this.residue_info = residue_info;
}
+ public Feature getFeature()
+ {
+ return feature;
+ }
+
+ public void setFeature(Feature feature)
+ {
+ this.feature = feature;
+ }
+
+ public boolean isMaxPartial()
+ {
+ return maxPartial;
+ }
+
+ public void setMaxPartial(boolean maxPartial)
+ {
+ this.maxPartial = maxPartial;
+ }
+
+ public boolean isMinPartial()
+ {
+ return minPartial;
+ }
+
+ public void setMinPartial(boolean minPartial)
+ {
+ this.minPartial = minPartial;
+ }
+
}
\ No newline at end of file
diff --git a/uk/ac/sanger/artemis/chado/FeatureProp.java b/uk/ac/sanger/artemis/chado/FeatureProp.java
index 857aea56743be57a54a2c5539c7794c4be71cc60..121787a98cee7772b98767f43511cd8e7e30e69e 100644
--- a/uk/ac/sanger/artemis/chado/FeatureProp.java
+++ b/uk/ac/sanger/artemis/chado/FeatureProp.java
@@ -29,7 +29,7 @@ package uk.ac.sanger.artemis.chado;
*/
public class FeatureProp
{
-
+ public Feature feature;
public Cvterm cvterm;
public String value;
public int rank;
@@ -93,4 +93,14 @@ public class FeatureProp
{
this.rank = rank;
}
+
+ public Feature getFeature()
+ {
+ return feature;
+ }
+
+ public void setFeature(Feature feature)
+ {
+ this.feature = feature;
+ }
}
\ No newline at end of file
diff --git a/uk/ac/sanger/artemis/chado/FeatureRelationship.java b/uk/ac/sanger/artemis/chado/FeatureRelationship.java
index 73952055ca7faa1d8a5be293129cfea3715a4b84..47c86993dd25cb6b4faa1382be97d31bcf12f75b 100644
--- a/uk/ac/sanger/artemis/chado/FeatureRelationship.java
+++ b/uk/ac/sanger/artemis/chado/FeatureRelationship.java
@@ -30,9 +30,9 @@ package uk.ac.sanger.artemis.chado;
public class FeatureRelationship
{
- public int subject_id;
+ public Feature subject;
/** id of the parent feature */
- public int object_id;
+ public Feature object;
/** cv term of feature relationship (e.g. part_of) */
public Cvterm cvterm;
/** Additional notes/comments */
@@ -64,18 +64,18 @@ public class FeatureRelationship
* Get the parent feature_id.
* @return the parent feature_id
*/
- public int getObject_id()
+ public Feature getObject()
{
- return object_id;
+ return object;
}
/**
* Set the parent feature_id.
* @param object_id the parent feature_id
*/
- public void setObject_id(int object_id)
+ public void setObject(Feature object)
{
- this.object_id = object_id;
+ this.object = object;
}
/**
@@ -102,14 +102,14 @@ public class FeatureRelationship
this.rank = rank;
}
- public int getSubject_id()
+ public Feature getSubject()
{
- return subject_id;
+ return subject;
}
- public void setSubject_id(int subject_id)
+ public void setSubject(Feature subject)
{
- this.subject_id = subject_id;
+ this.subject = subject;
}
/**
diff --git a/uk/ac/sanger/artemis/chado/FeatureSynonym.java b/uk/ac/sanger/artemis/chado/FeatureSynonym.java
index 4020a3dd8bd57a50092feb8341e4eee0db1f5405..97b9d3d4044159de51756397171e410164cc1dfe 100644
--- a/uk/ac/sanger/artemis/chado/FeatureSynonym.java
+++ b/uk/ac/sanger/artemis/chado/FeatureSynonym.java
@@ -29,12 +29,9 @@ package uk.ac.sanger.artemis.chado;
* linked to feature via feature_synonym table.
*/
public class FeatureSynonym
-{
- private String schema;
- private String uniquename;
-
+{
// feature_synonym
- private Integer feature_id;
+ private Feature feature;
private Integer synonym_id;
private Integer pub_id;
private boolean current;
@@ -42,34 +39,15 @@ public class FeatureSynonym
private Synonym synonym;
- public String getSchema()
- {
- return schema;
- }
-
- public void setSchema(String schema)
- {
- this.schema = schema;
- }
-
- public String getUniquename()
- {
- return uniquename;
- }
-
- public void setUniquename(String uniquename)
- {
- this.uniquename = uniquename;
- }
- public Integer getFeature_id()
+ public Feature getFeature()
{
- return feature_id;
+ return feature;
}
- public void setFeature_id(Integer feature_id)
+ public void setFeature(Feature feature)
{
- this.feature_id = feature_id;
+ this.feature = feature;
}
public Integer getSynonym_id()
diff --git a/uk/ac/sanger/artemis/chado/IBatisDAO.java b/uk/ac/sanger/artemis/chado/IBatisDAO.java
index 166f39908b47e53781322604afffd39c52ead7ac..dd6ac98c3773e0d0bd45b2c881139e6c91d57e95 100644
--- a/uk/ac/sanger/artemis/chado/IBatisDAO.java
+++ b/uk/ac/sanger/artemis/chado/IBatisDAO.java
@@ -296,85 +296,87 @@ public class IBatisDAO implements ChadoDAO
//
// WRITE BACK
//
+
/**
- *
- * Update attributes defined by the <code>Transaction</code>.
- * @param tsn the <code>Transaction</code>
- * @return number of rows changed
- * @throws SQLException
+ * Merge (update) an already persistent object back to the database (at the end of
+ * the current transaction, or depending upon flush mode). This method is defined in
+ * all the DAOs. It's recommended to call it through an appropriate one eg SequenceDaoI
+ * for FeatureI
+ *
+ * @param o The object to merge
+ * @throws SQLException
*/
- public int updateAttributes
- (final ChadoTransaction tsn)
- throws SQLException
- {
- return sqlMap.update("updateAttributes", tsn);
+ public void merge(Object o) throws SQLException
+ {
+ if(o instanceof FeatureLoc)
+ sqlMap.update("updateFeatureLoc", o);
+ else if(o instanceof Feature)
+ sqlMap.update("updateFeature", o);
+ else if(o instanceof FeatureProp)
+ sqlMap.update("updateFeatureProp", o);
+ else if(o instanceof FeatureRelationship)
+ sqlMap.update("updateFeatureRelationshipsForSubjectId", o);
}
-
+
+
/**
- * Insert attributes defined by the <code>Transaction</code>.
- * @param tsn the <code>Transaction</code>
- * @throws SQLException
+ * Save the object to the database (at the end of the current transaction,
+ * or depending upon flush mode). This method is defined in all the DAOs.
+ * It's recommended to call it through an appropriate one eg SequenceDaoI
+ * for FeatureI
+ * @param o The object to store
+ * @throws SQLException
*/
- public void insertAttributes
- (final ChadoTransaction tsn)
- throws SQLException
+ public void persist(Object o) throws SQLException
{
- // get the feature id's
- List feature_ids = sqlMap.queryForList("getFeatureID", tsn);
-
- for(int i=0; i<feature_ids.size(); i++)
- {
- tsn.setFeature_id( ((Feature)feature_ids.get(i)).getId() );
- sqlMap.insert("insertAttributes", tsn);
- }
+ if(o instanceof FeatureProp)
+ sqlMap.insert("insertFeatureProp", o);
+ else if(o instanceof Feature)
+ insertFeature((Feature)o);
+ else if(o instanceof FeatureDbxref)
+ insertFeatureDbxref((FeatureDbxref)o);
+ else if(o instanceof FeatureSynonym)
+ insertFeatureAlias((FeatureSynonym)o);
}
-
+
+
/**
- * Delete attributes defined by the <code>Transaction</code>.
- * @param tsn the <code>Transaction</code>
- * @throws SQLException
+ * Remove the object from the database (at the end of the current transaction,
+ * or depending upon flush mode). This method is defined in all the DAOs.
+ * It's recommended to call it through an appropriate one eg SequenceDaoI for
+ * FeatureI
+ * @param o The object to delete
*/
- public void deleteAttributes
- (final ChadoTransaction tsn)
- throws SQLException
+ public void delete(Object o) throws SQLException
{
- // get the feature id's
- List feature_ids = sqlMap.queryForList("getFeatureID", tsn);
-
- for(int i=0; i<feature_ids.size(); i++)
- {
- tsn.setFeature_id( ((Feature)feature_ids.get(i)).getId() );
- sqlMap.delete("deleteAttributes", tsn);
- }
+ if(o instanceof Feature)
+ sqlMap.delete("deleteFeature", o);
+ else if(o instanceof FeatureProp)
+ sqlMap.delete("deleteFeatureProp", o);
+ else if(o instanceof FeatureDbxref)
+ sqlMap.delete("deleteFeatureDbxref", o);
+ else if(o instanceof FeatureSynonym)
+ deleteFeatureSynonym((FeatureSynonym)o);
}
+
/**
- * Insert a feature into the database defined by the <code>Transaction</code>.
- * @param tsn the <code>Transaction</code>
- * @parma srcfeature_id the parent feature identifier
+ * Insert a feature into the database defined by the <code>Feature</code>.
+ * @param feature the feature to insert
* @throws SQLException
*/
- public void insertFeature
- (final ChadoTransaction tsn,
- final String srcfeature_id)
+ private void insertFeature
+ (final Feature feature)
throws SQLException
{
- // get the organism id from the srcfeature_id
- Feature feature = new Feature();
- FeatureLoc featureloc = new FeatureLoc();
- feature.setFeatureloc(featureloc);
-
- featureloc.setSrcfeature_id(Integer.parseInt(srcfeature_id));
-
Integer organism_id = (Integer)sqlMap.queryForObject("getOrganismID", feature);
//
// insert feature into feature table
- Feature chadoFeature = tsn.getChadoFeature();
Organism organism = new Organism();
organism.setId(organism_id.intValue());
- chadoFeature.setOrganism(organism);
- sqlMap.insert("insertFeature", chadoFeature);
+ feature.setOrganism(organism);
+ sqlMap.insert("insertFeature", feature);
//
// get the current feature_id sequence value
@@ -383,229 +385,114 @@ public class IBatisDAO implements ChadoDAO
//
// insert feature location into featureloc
- chadoFeature.getFeatureloc().setSrcfeature_id(Integer.parseInt(srcfeature_id));
- chadoFeature.setId(feature_id);
- sqlMap.insert("insertFeatureLoc", chadoFeature);
+ feature.setId(feature_id);
+ sqlMap.insert("insertFeatureLoc", feature);
- // insert feature relationship
- if(tsn.getParents() != null ||
- tsn.getDerives_from() != null)
+ // insert feature relationships
+ if(feature.getFeatureRelationshipsForSubjectId() != null)
{
- List feature_ids = sqlMap.queryForList("getFeatureID", tsn);
+ List parents = feature.getFeatureRelationshipsForSubjectId();
- for(int i=0; i<feature_ids.size(); i++)
+ for(int i=0; i<parents.size(); i++)
{
FeatureRelationship feature_relationship =
- new FeatureRelationship();
- feature_relationship.setObject_id( ((Feature)feature_ids.get(i)).getId() );
- feature_relationship.setSubject_id(feature_id);
-
- Cvterm cvterm = new Cvterm();
- if(tsn.getParents().contains(
- ((Feature)feature_ids.get(i)).getUniquename() ))
- cvterm.setName("part_of");
- else
- cvterm.setName("derives_from");
-
- feature_relationship.setCvterm(cvterm);
- chadoFeature.setFeature_relationship(feature_relationship);
- sqlMap.insert("insertFeatureRelationship", chadoFeature);
+ (FeatureRelationship)parents.get(i);
+ sqlMap.insert("insertFeatureRelationship", feature_relationship);
}
-
}
}
-
/**
- * Delete a feature from the database defined by the <code>Transaction</code>.
- * @param tsn the <code>Transaction</code>
- * @return number of rows deleted
+ * Insert a feature_dbxref for a feature.
+ * @param feature_dbxref the <code>FeatureDbxref</code>
* @throws SQLException
*/
- public int deleteFeature
- (final ChadoTransaction tsn)
+ private void insertFeatureDbxref(final FeatureDbxref feature_dbxref)
throws SQLException
{
- Feature chadoFeature = new Feature();
- chadoFeature.setUniquename(tsn.getUniqueName());
-
- return sqlMap.delete("deleteFeature", chadoFeature);
- }
+ Integer db_id = (Integer)sqlMap.queryForObject("getDbId",
+ feature_dbxref.getDbxref().getDb());
+
+ System.out.print(db_id.intValue());
- /**
- * Insert a dbxref for a feature.
- * @param tsn the <code>Transaction</code>
- * @return number of rows changed
- * @throws SQLException
- */
- public int insertFeatureDbxref(final ChadoTransaction tsn)
- throws SQLException
- {
- FeatureDbxref dbxref = tsn.getFeatureDbxref();
- Integer db_id = (Integer)sqlMap.queryForObject("getDbId",
- dbxref.getDbxref().getDb());
if(db_id == null)
throw new SQLException("No database called "+
- dbxref.getDbxref().getDb().getName()+" found (for "+
- tsn.getUniqueName()+
- ") check the spelling!");
+ feature_dbxref.getDbxref().getDb().getName()+" found (for "+
+ feature_dbxref.getFeature().getUniquename()+
+ ") check the spelling!");
- dbxref.getDbxref().setDb_id(db_id.intValue());
+ feature_dbxref.getDbxref().setDb_id(db_id.intValue());
- Integer dbxref_id = (Integer)sqlMap.queryForObject("getDbxrefId", dbxref.getDbxref());
+ Integer dbxref_id =
+ (Integer)sqlMap.queryForObject("getDbxrefId", feature_dbxref.getDbxref());
if(dbxref_id == null)
{
// create a new accession entry in dbxref
- sqlMap.insert("insertDbxref", dbxref.getDbxref());
+ sqlMap.insert("insertDbxref", feature_dbxref.getDbxref());
// now get the new dbxref_id
- dbxref_id = (Integer)sqlMap.queryForObject("getDbxrefId", dbxref.getDbxref());
+ dbxref_id = (Integer)sqlMap.queryForObject("getDbxrefId",
+ feature_dbxref.getDbxref());
}
- dbxref.setDbxref_id(dbxref_id.intValue());
-
- // get the feature id's
- List feature_ids = sqlMap.queryForList("getFeatureID", tsn);
- dbxref.setFeature_id( ((Feature)feature_ids.get(0)).getId() );
+ feature_dbxref.setDbxref_id(dbxref_id.intValue());
- sqlMap.insert("insertFeatureDbxref", dbxref);
+ // get the feature id's
+ Feature feature = getFeatureByUniqueName(
+ feature_dbxref.getFeature().getUniquename());
+ feature_dbxref.getFeature().setId( feature.getId() );
- return 1;
+ sqlMap.insert("insertFeatureDbxref", feature_dbxref);
}
- /**
- * Delete a dbxref for a feature.
- * @param tsn the <code>Transaction</code>
- * @return number of rows changed
- * @throws SQLException
- */
- public int deleteFeatureDbxref(final ChadoTransaction tsn)
- throws SQLException
- {
- FeatureDbxref dbxref = tsn.getFeatureDbxref();
-
- // get the feature id's
- List feature_ids = sqlMap.queryForList("getFeatureID", tsn);
-
- dbxref.setFeature_id( ((Feature)feature_ids.get(0)).getId() );
- return sqlMap.delete("deleteFeatureDbxref", dbxref);
- }
/**
- * Insert a synonym for a feature.
- * @param tsn the <code>Transaction</code>
- * @return number of rows changed
+ * Insert a feature_synonym for a feature.
+ * @param feature_synonym the <code>FeatureSynonym</code>
* @throws SQLException
*/
- public int insertFeatureAlias(final ChadoTransaction tsn)
+ private void insertFeatureAlias(final FeatureSynonym feature_synonym)
throws SQLException
{
- final FeatureSynonym alias = tsn.getAlias();
-
Synonym synonym =
(Synonym)sqlMap.queryForObject("getSynonymByNameAndType",
- alias.getSynonym());
+ feature_synonym.getSynonym());
if(synonym == null)
{
// create a new synonym name
- sqlMap.insert("insertAlias", alias);
+ sqlMap.insert("insertAlias", feature_synonym);
synonym =
(Synonym)sqlMap.queryForObject("getSynonymByNameAndType",
- alias.getSynonym());
+ feature_synonym.getSynonym());
}
- alias.setSynonym_id(synonym.getSynonym_id());
- sqlMap.insert("insertFeatureAlias", alias);
- return 1;
+ feature_synonym.setSynonym_id(synonym.getSynonym_id());
+ sqlMap.insert("insertFeatureAlias", feature_synonym);
}
/**
- * Delete a synonym for a feature.
- * @param tsn the <code>Transaction</code>
- * @return number of rows changed
+ * Delete a feature_synonym for a feature.
+ * @param feature_synonym the <code>FeatureSynonym</code>
* @throws SQLException
*/
- public int deleteFeatureAlias(final ChadoTransaction tsn)
+ private int deleteFeatureSynonym(final FeatureSynonym feature_synonym)
throws SQLException
{
- final FeatureSynonym alias = tsn.getAlias();
-
List feature_synonym_list =
- sqlMap.queryForList("getFeatureSynonymsByName", alias.getSynonym());
+ sqlMap.queryForList("getFeatureSynonymsByName", feature_synonym.getSynonym());
final FeatureSynonym synonym =
(FeatureSynonym)feature_synonym_list.get(0);
- alias.setSynonym_id(synonym.getSynonym().getSynonym_id());
+ feature_synonym.setSynonym_id(synonym.getSynonym().getSynonym_id());
// check this name is not used some where else,
// i.e. in more than one row
if(feature_synonym_list.size() > 1)
- return sqlMap.delete("deleteFeatureAlias", alias);
- else
- return sqlMap.delete("deleteAlias", alias);
- }
-
- /**
- * Update feature_relationship for a feature.
- * @param tsn the <code>Transaction</code>
- * @return number of rows changed
- * @throws SQLException
- */
- public void updateFeatureRelationshipsForSubjectId(
- final ChadoTransaction tsn)
- throws SQLException
- {
- sqlMap.update("updateFeatureRelationshipsForSubjectId", tsn);
- }
-
- /**
- * Write the time a feature was last modified
- * @param uniquename the unique name of the feature
- * @param timestamp the time stamp to use,
- * if NULL use CURRENT_TIMESTAMP
- * @return number of rows changed
- * @throws SQLException
- */
- public int writeTimeLastModified
- (final String uniquename,
- final Timestamp timestamp)
- throws SQLException
- {
- ChadoTransaction tsn = new ChadoTransaction(ChadoTransaction.UPDATE,
- uniquename, "feature",
- null, null);
- if(timestamp == null)
- tsn.addProperty("timelastmodified", "CURRENT_TIMESTAMP");
+ return sqlMap.delete("deleteFeatureAlias", feature_synonym);
else
- tsn.addProperty("timelastmodified", "'"+ timestamp.toString() + "'");
-
- return updateAttributes(tsn);
- }
-
- /**
- * Write the time a feature was last accessed
- * @param uniquename the unique name of the feature
- * @param timestamp the time stamp to use,
- * if NULL use CURRENT_TIMESTAMP
- * @return number of rows changed
- * @throws SQLException
- */
- public int writeTimeAccessioned
- (final String uniquename,
- final Timestamp timestamp)
- throws SQLException
- {
- ChadoTransaction tsn = new ChadoTransaction(ChadoTransaction.UPDATE,
- uniquename, "feature",
- null, null);
- if(timestamp == null)
- tsn.addProperty("timelastmodified", "CURRENT_TIMESTAMP");
- else
- tsn.addProperty("timelastmodified", "'"+ timestamp.toString() + "'");
-
- return updateAttributes(tsn);
+ return sqlMap.delete("deleteAlias", feature_synonym);
}
public void startTransaction() throws SQLException
@@ -647,7 +534,9 @@ public class IBatisDAO implements ChadoDAO
if(i < feature_size - 1)
featNext = (Feature)list.get(i + 1);
-
+ else
+ featNext = null;
+
// merge next line if part of the same feature
while(featNext != null && featNext.getUniquename().equals(name))
{
@@ -679,7 +568,7 @@ public class IBatisDAO implements ChadoDAO
for(int i = 0; i < list.size(); i++)
{
FeatureDbxref dbxref = (FeatureDbxref)list.get(i);
- Integer feature_id = new Integer(dbxref.getFeature_id());
+ Integer feature_id = new Integer(dbxref.getFeature().getId());
String value = dbxref.getDbxref().getDb().getName() + ":" +
dbxref.getDbxref().getAccession();
if(dbxrefHash.containsKey(feature_id))
@@ -698,7 +587,4 @@ public class IBatisDAO implements ChadoDAO
return dbxrefHash;
}
-
-
}
-
diff --git a/uk/ac/sanger/artemis/chado/JdbcDAO.java b/uk/ac/sanger/artemis/chado/JdbcDAO.java
index 6758a870a76bd62816e6fa35a5ebcfd19ee3836c..52d5519a57266e2aca722fa523c89da00854c28a 100644
--- a/uk/ac/sanger/artemis/chado/JdbcDAO.java
+++ b/uk/ac/sanger/artemis/chado/JdbcDAO.java
@@ -238,7 +238,10 @@ public class JdbcDAO
cvterm = new Cvterm();
cvterm.setCvtermId(rs.getLong("relation_type_id"));
feature_relationship.setCvterm(cvterm);
- feature_relationship.setObject_id( rs.getInt("object_id") );
+
+ Feature object = new Feature();
+ object.setId( rs.getInt("object_id") );
+ feature_relationship.setObject( object );
feature.setFeature_relationship(feature_relationship);
// feature organism
@@ -419,8 +422,10 @@ public class JdbcDAO
db.setName( rs.getString("name") );
dbxref.setAccession( rs.getString("accession") );
dbxref.setDb(db);
+ Feature feat = new Feature();
+ feat.setId( rs.getInt("feature_id") );
feature_dbxref.setDbxref(dbxref);
- feature_dbxref.setFeature_id( rs.getInt("feature_id") );
+ feature_dbxref.setFeature(feat);
dbxrefs.add(feature_dbxref);
}
@@ -459,9 +464,11 @@ public class JdbcDAO
Synonym syn = new Synonym();
syn.setName(rs.getString("name"));
syn.setCvterm(cvterm);
-
+ Feature feat = new Feature();
+ feat.setId(rs.getInt("feature_id"));
+
alias.setSynonym(syn);
- alias.setFeature_id(new Integer(rs.getInt("feature_id")));
+ alias.setFeature(feat);
alias.setPub_id(new Integer(rs.getInt("pub_id")));
alias.setInternal(rs.getBoolean("is_internal"));
alias.setCurrent(rs.getBoolean("is_current"));
@@ -487,176 +494,231 @@ public class JdbcDAO
//
// WRITE
//
+
+
/**
- * Update attributes defined by the <code>ChadoTransaction</code>.
- * @param tsn the <code>ChadoTransaction</code>
- * @return number of rows changed
+ * Merge (update) an already persistent object back to the database
+ * (at the end of the current transaction, or depending upon flush mode).
+ * This method is defined in all the DAOs. It's recommended to call it
+ * through an appropriate one eg SequenceDaoI for FeatureI
+ * @param o The object to merge
+ */
+ public void merge(Object o) throws SQLException
+ {
+ if(o instanceof FeatureLoc)
+ updateFeatureLoc((FeatureLoc)o);
+ else if(o instanceof Feature)
+ updateFeature((Feature)o);
+ else if(o instanceof FeatureProp)
+ updateFeatureProp((FeatureProp)o);
+ else if(o instanceof FeatureRelationship)
+ updateFeatureRelationship((FeatureRelationship)o);
+ }
+
+ /**
+ * Save the object to the database (at the end of the current transaction,
+ * or depending upon flush mode). This method is defined in all the DAOs.
+ * It's recommended to call it through an appropriate one eg SequenceDaoI
+ * for FeatureI
+ * @param o The object to store
+ */
+ public void persist(Object o) throws SQLException
+ {
+ if(o instanceof FeatureProp)
+ insertFeatureProp((FeatureProp)o);
+ else if(o instanceof Feature)
+ insertFeature((Feature)o);
+ else if(o instanceof FeatureDbxref)
+ insertFeatureDbxref((FeatureDbxref)o);
+ else if(o instanceof FeatureSynonym)
+ insertFeatureAlias((FeatureSynonym)o);
+ }
+
+ /**
+ * Remove the object from the database (at the end of the current transaction,
+ * or depending upon flush mode). This method is defined in all the DAOs.
+ * It's recommended to call it through an appropriate one eg SequenceDaoI for
+ * FeatureI
+ * @param o The object to delete
+ */
+ public void delete(Object o) throws SQLException
+ {
+ if(o instanceof Feature)
+ deleteFeature((Feature)o);
+ else if(o instanceof FeatureProp)
+ deleteFeatureProp((FeatureProp)o);
+ else if(o instanceof FeatureDbxref)
+ deleteFeatureDbxref((FeatureDbxref)o);
+ else if(o instanceof FeatureSynonym)
+ deleteFeatureSynonym((FeatureSynonym)o);
+ }
+
+
+ /**
+ * Update a feature location with the give <code>FeatureLoc</code>
+ * object.
+ * @param featureloc the new <code>FeatureLoc</code> object.
* @throws SQLException
*/
- public int updateAttributes
- (final ChadoTransaction tsn)
- throws SQLException
+ private void updateFeatureLoc(FeatureLoc featureloc)
+ throws SQLException
{
- List uniquename = tsn.getUniquename();
-
- StringBuffer sqlBuff = new StringBuffer();
- String chadoTable = tsn.getChadoTable();
- sqlBuff.append("UPDATE "+chadoTable);
- sqlBuff.append(" SET ");
-
- List properties = tsn.getProperties();
- for(int i=0; i<properties.size(); i++)
- {
- sqlBuff.append((String)properties.get(i));
- if(i < properties.size()-1)
- sqlBuff.append(" , ");
- }
+ final String sql = "UPDATE featureloc SET fmin=?, fmax=?, rank=?, strand=?, phase=? "+
+ "WHERE feature_id=(SELECT feature_id FROM feature WHERE uniquename=?)";
- sqlBuff.append(" FROM feature");
- sqlBuff.append(" WHERE feature.feature_id="+
- chadoTable+".feature_id AND (");
+ PreparedStatement pstmt = conn.prepareStatement(sql);
+ pstmt.setInt(1, featureloc.getFmin());
+ pstmt.setInt(2, featureloc.getFmax());
+ pstmt.setInt(3, featureloc.getRank());
+ pstmt.setInt(4, featureloc.getStrand());
+ pstmt.setInt(5, featureloc.getPhase());
+ pstmt.setString(6, featureloc.getFeature().getUniquename());
+ appendToLogFile(sql, sqlLog);
+
+ pstmt.executeUpdate();
+ }
+
+ /**
+ * Update a feature with a given <code>Feature</code> object.
+ * @param feature the new <code>Feature</code> object.
+ * @throws SQLException
+ */
+ private void updateFeature(Feature feature)
+ throws SQLException
+ {
+ String sql = "UPDATE feature SET uniquename=?";
+ if(feature.getCvterm() != null)
+ sql = sql+", type_id=?";
+
+ if(feature.getTimelastmodified() != null)
+ sql = sql+", timelastmodified=?";
- for(int i=0; i<uniquename.size(); i++)
+ sql = sql+"WHERE feature_id=?";
+
+ PreparedStatement pstmt = conn.prepareStatement(sql);
+ pstmt.setString(1, feature.getUniquename());
+ int param = 2;
+ if(feature.getCvterm() != null)
{
- sqlBuff.append(" feature.uniquename='" +
- (String)uniquename.get(i) +"' ");
- if(i < uniquename.size()-1)
- sqlBuff.append("OR");
+ pstmt.setLong(param, feature.getCvterm().getCvtermId());
+ param++;
}
-
- sqlBuff.append(")");
-
- List constraints = tsn.getConstraint();
- if(constraints != null)
+
+ if(feature.getTimelastmodified() != null)
{
- for(int i=0; i<constraints.size(); i++)
- {
- sqlBuff.append(" AND ");
- // looks like specifying table, so include schema
- String constraint = (String)constraints.get(i);
- /*
- int index;
- if( (index = constraint.indexOf(".")) > -1 &&
- constraint.indexOf("=") > index)
- sqlBuff.append(schema+".");
- */
- sqlBuff.append(constraint);
- }
+ pstmt.setTimestamp(param,
+ feature.getTimelastmodified());
+ param++;
}
+
+ pstmt.setInt(param, feature.getId());
+ appendToLogFile(sql, sqlLog);
+ pstmt.executeUpdate();
+ }
+
+ /**
+ * Update a feature property with a given <code>FeatureProp</code>
+ * object.
+ * @param featureprop the new <code>FeatureProp</code> object.
+ * @throws SQLException
+ */
+ private void updateFeatureProp(FeatureProp featureprop)
+ throws SQLException
+ {
+ String sql = "UPDATE featureprop SET value=? "+
+ "WHERE rank=? AND type_id=? AND "+
+ "feature_id=(SELECT feature_id FROM feature WHERE uniquename=?)";
- String sql = sqlBuff.toString();
-
+ PreparedStatement pstmt = conn.prepareStatement(sql);
+ pstmt.setString(1,featureprop.getValue());
+ pstmt.setInt(2,featureprop.getRank());
+ pstmt.setLong(3, featureprop.getCvterm().getCvtermId());
+ pstmt.setString(4, featureprop.getFeature().getUniquename());
+
appendToLogFile(sql, sqlLog);
- Statement st = conn.createStatement();
- return st.executeUpdate(sql);
+ pstmt.executeUpdate();
}
+
/**
- * Insert attributes defined by the <code>ChadoTransaction</code>.
- * @param tsn the <code>ChadoTransaction</code>
+ * Insert attributes defined by the <code>FeatureProp</code>.
+ * @param featureprop the new <code>FeatureProp</code>
* @throws SQLException
*/
- public void insertAttributes
- (final ChadoTransaction tsn)
+ private void insertFeatureProp
+ (final FeatureProp featureprop)
throws SQLException
{
- StringBuffer sqlBuff;
-
- List uniquename = tsn.getUniquename();
- String chadoTable = tsn.getChadoTable();
- for(int i=0; i<uniquename.size(); i++)
- {
- sqlBuff = new StringBuffer();
- sqlBuff.append("INSERT INTO "+chadoTable);
- StringBuffer sqlKeys = new StringBuffer();
- StringBuffer sqlValues = new StringBuffer();
-
- sqlKeys.append("feature_id , ");
- sqlValues.append("(SELECT feature_id FROM feature WHERE uniquename='"+
- (String)uniquename.get(i)+"') , ");
-
- String name;
+ StringBuffer sqlBuff = new StringBuffer();
- List propertiesName = tsn.getPropertiesName();
- List propertiesValue = tsn.getPropertiesValue();
- for(int j=0; j<propertiesName.size(); j++)
- {
- name = (String)propertiesName.get(j);
- sqlKeys.append(name);
- sqlValues.append((String)propertiesValue.get(j));
- if(j < propertiesName.size()-1)
- {
- sqlKeys.append(" , ");
- sqlValues.append(" , ");
- }
- }
-
- sqlBuff.append(" ( "+sqlKeys.toString()+" ) ");
- sqlBuff.append(" values ");
- sqlBuff.append(" ( "+sqlValues.toString()+" )");
+ sqlBuff.append("INSERT INTO featureprop");
+ sqlBuff.append(" ( feature_id, type_id, value, rank ) ");
+ sqlBuff.append("VALUES ");
+
+ sqlBuff.append("((SELECT feature_id FROM feature WHERE uniquename=");
+ sqlBuff.append("'"+ featureprop.getFeature().getUniquename()+"')," );
+ sqlBuff.append(featureprop.getCvterm().getCvtermId()+", ");
+ sqlBuff.append(featureprop.getValue()+",");
+ sqlBuff.append(featureprop.getRank());
- appendToLogFile(new String(sqlBuff), sqlLog);
+ appendToLogFile(new String(sqlBuff), sqlLog);
- Statement st = conn.createStatement();
- int rowCount = st.executeUpdate(new String(sqlBuff));
- System.out.println(rowCount+" row(s) inserted");
- }
+ Statement st = conn.createStatement();
+ int rowCount = st.executeUpdate(new String(sqlBuff));
+ System.out.println(rowCount + " row(s) inserted");
}
/**
- * Delete attributes defined by the <code>ChadoTransaction</code>.
- * @param tsn the <code>ChadoTransaction</code>
+ * Delete attributes defined by the <code>FeatureProp</code>.
+ * @param featureprop the new <code>FeatureProp</code>
* @throws SQLException
*/
- public void deleteAttributes
- (final ChadoTransaction tsn)
+ private void deleteFeatureProp
+ (final FeatureProp featureprop)
throws SQLException
{
- StringBuffer sqlBuff;
-
- List uniquename = tsn.getUniquename();
- String chadoTable = tsn.getChadoTable();
- for(int i=0; i<uniquename.size(); i++)
- {
- sqlBuff = new StringBuffer();
+ StringBuffer sqlBuff = new StringBuffer();
+ String uniquename = featureprop.getFeature().getUniquename();
- sqlBuff.append("DELETE FROM "+chadoTable+" WHERE ");
+ sqlBuff.append("DELETE FROM featureprop WHERE ");
- List constraints = tsn.getConstraint();
- for(int j=0; j<constraints.size(); j++)
- sqlBuff.append((String)constraints.get(j)+" AND ");
+ if(uniquename != null)
+ sqlBuff.append("feature_id="+
+ "(SELECT feature_id FROM feature WHERE uniquename='"+
+ uniquename+"') AND ");
+
+ if(featureprop.getRank() > -1)
+ sqlBuff.append("rank="+featureprop.getRank()+" AND ");
+
+ if(featureprop.getValue() != null)
+ sqlBuff.append("value="+featureprop.getValue()+" AND ");
+
+ sqlBuff.append("type_id="+featureprop.getCvterm().getCvtermId());
- sqlBuff.append("feature_id=(SELECT feature_id FROM "+
- "feature WHERE uniquename='"+
- (String)uniquename.get(i)+"')");
-
- System.out.println(sqlBuff.toString());
- appendToLogFile(new String(sqlBuff), sqlLog);
+ appendToLogFile(new String(sqlBuff), sqlLog);
- Statement st = conn.createStatement();
- int rowCount = st.executeUpdate(new String(sqlBuff));
- System.out.println(rowCount+" row(s) deleted");
- }
+ Statement st = conn.createStatement();
+ int rowCount = st.executeUpdate(new String(sqlBuff));
+ System.out.println(rowCount+" row(s) deleted");
}
/**
- * Insert a feature into the database defined by the <code>ChadoTransaction</code>.
- * @param tsn the <code>ChadoTransaction</code>
- * @parma srcfeature_id the parent feature identifier
+ * Insert a feature into the database defined by the <code>Feature</code>.
+ * @param feature the new <code>Feature</code>
* @throws SQLException
*/
- public void insertFeature
- (final ChadoTransaction tsn,
- final String srcfeature_id)
+ private void insertFeature
+ (final Feature feature)
throws SQLException
{
//
// get the organism_id
Statement st = conn.createStatement();
String sql = "SELECT organism_id from " +
- "feature where feature_id = '" + srcfeature_id + "'";
+ "feature where feature_id = '" +
+ feature.getFeatureloc().getSrcfeature_id() + "'";
appendToLogFile(sql, sqlLog);
ResultSet rs = st.executeQuery(sql);
@@ -664,7 +726,6 @@ public class JdbcDAO
final int organism_id = rs.getInt("organism_id");
- Feature chadoFeature = tsn.getChadoFeature();
// insert new feature into feature table
StringBuffer sql_buff = new StringBuffer();
sql_buff.append("INSERT INTO feature (");
@@ -676,9 +737,9 @@ public class JdbcDAO
sql_buff.append(" ) VALUES ( ");
sql_buff.append("nextval('feature_feature_id_seq') , ");
sql_buff.append(organism_id+" , ");
- sql_buff.append("'"+chadoFeature.getName()+"'"+" , ");
- sql_buff.append("'"+chadoFeature.getUniquename()+"'"+" , ");
- sql_buff.append(Long.toString(chadoFeature.getCvterm().getCvtermId()));
+ sql_buff.append("'"+feature.getName()+"'"+" , ");
+ sql_buff.append("'"+feature.getUniquename()+"'"+" , ");
+ sql_buff.append(Long.toString(feature.getCvterm().getCvtermId()));
sql_buff.append(" )");
sql = new String(sql_buff);
@@ -709,32 +770,61 @@ public class JdbcDAO
sql_buff.append(" ) VALUES ( ");
sql_buff.append("nextval('featureloc_featureloc_id_seq') , ");
sql_buff.append(feature_id+" , ");
- sql_buff.append(srcfeature_id+" , ");
- sql_buff.append(chadoFeature.getFeatureloc().getFmin()+" , ");
- sql_buff.append(chadoFeature.getFeatureloc().getFmax()+" , ");
- sql_buff.append(chadoFeature.getFeatureloc().getStrand()+" , ");
- sql_buff.append(chadoFeature.getFeatureloc().getPhase());
+ sql_buff.append(feature.getFeatureloc().getSrcfeature_id()+" , ");
+ sql_buff.append(feature.getFeatureloc().getFmin()+" , ");
+ sql_buff.append(feature.getFeatureloc().getFmax()+" , ");
+ sql_buff.append(feature.getFeatureloc().getStrand()+" , ");
+ sql_buff.append(feature.getFeatureloc().getPhase());
sql_buff.append(" )");
sql = new String(sql_buff);
appendToLogFile(sql, sqlLog);
st = conn.createStatement();
rowCount = st.executeUpdate(sql);
+
+
+// insert feature relationships
+ if(feature.getFeatureRelationshipsForSubjectId() != null)
+ {
+ List parents = feature.getFeatureRelationshipsForSubjectId();
+ for(int i=0; i<parents.size(); i++)
+ {
+ // insert feature_relationship
+ FeatureRelationship feature_relationship =
+ (FeatureRelationship)parents.get(i);
+
+ sql_buff = new StringBuffer();
+ sql_buff.append("INSERT INTO feature_relationship ");
+ sql_buff.append("( subject_id, object_id, type_id ) ");
+ sql_buff.append("VALUES ");
+ sql_buff.append("( (SELECT feature_id FROM feature WHERE uniquename='");
+ sql_buff.append(feature_relationship.getSubject().getUniquename()+"'), ");
+ sql_buff.append("(SELECT feature_id FROM feature WHERE uniquename='");
+ sql_buff.append(feature_relationship.getObject().getUniquename()+"'), ");
+ sql_buff.append(feature_relationship.getCvterm().getCvtermId()+")");
+
+ sql = new String(sql_buff);
+ appendToLogFile(sql, sqlLog);
+ st = conn.createStatement();
+ rowCount = st.executeUpdate(sql);
+
+ }
+ }
+
}
/**
* Delete a feature from the database defined by the
- * <code>ChadoTransaction</code>.
- * @param tsn the <code>ChadoTransaction</code>
- * @return number of rows deleted
+ * <code>Feature</code>.
+ * @param feature the new <code>Feature</code>
* @throws SQLException
*/
- public int deleteFeature
- (final ChadoTransaction tsn)
+ private int deleteFeature
+ (final Feature feature)
throws SQLException
{
String sql = "DELETE FROM feature WHERE uniquename='"+
- tsn.getUniqueName()+"'";
+ feature.getUniquename()+"'";
appendToLogFile(sql, sqlLog);
Statement st = conn.createStatement();
@@ -742,20 +832,16 @@ public class JdbcDAO
}
/**
- * Insert a dbxref for a feature.
- * @param tsn the <code>ChadoTransaction</code>
- * @return number of rows changed
+ * Insert a feature_dbxref for a feature.
+ * @param feature_dbxref the new <code>FeatureDbxref</code>
* @throws SQLException
*/
- public int insertFeatureDbxref(final ChadoTransaction tsn)
+ private void insertFeatureDbxref(final FeatureDbxref feature_dbxref)
throws SQLException
- {
- final FeatureDbxref dbxref = tsn.getFeatureDbxref();
- final String uniquename = tsn.getUniqueName();
-
+ {
// find database id
String sql = "SELECT db_id FROM db WHERE name='"+
- dbxref.getDbxref().getDb().getName()+"'";
+ feature_dbxref.getDbxref().getDb().getName()+"'";
Statement st = conn.createStatement();
ResultSet rs = st.executeQuery(sql);
@@ -763,14 +849,14 @@ public class JdbcDAO
if(!exists)
throw new SQLException("No database called "+
- dbxref.getDbxref().getDb().getName()+
- " found (for "+uniquename+
- ") check the spelling!");
+ feature_dbxref.getDbxref().getDb().getName()+
+ " found (for "+feature_dbxref.getFeature().getUniquename()+
+ ") check the spelling!");
final int db_id = rs.getInt("db_id");
// find if accession exists already
String sqlDbxrefId = "SELECT dbxref_id FROM dbxref WHERE accession='"+
- dbxref.getDbxref().getAccession()+"' AND db_id="+db_id;
+ feature_dbxref.getDbxref().getAccession()+"' AND db_id="+db_id;
appendToLogFile(sqlDbxrefId, sqlLog);
rs = st.executeQuery(sqlDbxrefId);
@@ -780,7 +866,7 @@ public class JdbcDAO
{
// create a new accession entry in dbxref
sql = "INSERT INTO dbxref ( db_id, accession ) "+
- "VALUES ("+db_id+", '"+dbxref.getDbxref().getAccession()+"' )";
+ "VALUES ("+db_id+", '"+feature_dbxref.getDbxref().getAccession()+"' )";
appendToLogFile(sql, sqlLog);
int rowCount = st.executeUpdate(new String(sql));
@@ -796,49 +882,47 @@ public class JdbcDAO
"(feature_id, dbxref_id, is_current)"+
" VALUES "+
"( (SELECT feature_id FROM "+
- "feature WHERE uniquename='"+uniquename+"'), "+
- dbxref_id+", "+ Boolean.toString(dbxref.isCurrent())+")";
+ "feature WHERE uniquename='"+feature_dbxref.getFeature().getUniquename()+"'), "+
+ dbxref_id+", "+ Boolean.toString(feature_dbxref.isCurrent())+")";
System.out.println(sql);
appendToLogFile(sql, sqlLog);
- return st.executeUpdate(new String(sql));
+ st.executeUpdate(new String(sql));
}
/**
- * Delete a dbxref for a feature.
- * @param tsn the <code>ChadoTransaction</code>
- * @return number of rows changed
+ * Delete a feature_dbxref for a feature.
+ * @param feature_dbxref the new <code>FeatureDbxref</code>
* @throws SQLException
*/
- public int deleteFeatureDbxref(final ChadoTransaction tsn)
+ private void deleteFeatureDbxref(final FeatureDbxref feature_dbxref)
throws SQLException
{
- final FeatureDbxref dbxref = tsn.getFeatureDbxref();
- final String uniquename = tsn.getUniqueName();
+ final String uniquename = feature_dbxref.getFeature().getUniquename();
final String sql =
"DELETE FROM feature_dbxref "+
"WHERE dbxref_id="+
- "(SELECT dbxref_id FROM dbxref WHERE accession='"+dbxref.getDbxref().getAccession()+"' "+
- "AND db_id=(SELECT db_id FROM db WHERE name='"+dbxref.getDbxref().getDb().getName()+"'))"+
+ "(SELECT dbxref_id FROM dbxref WHERE accession='"+
+ feature_dbxref.getDbxref().getAccession()+"' "+
+ "AND db_id=(SELECT db_id FROM db WHERE name='"+
+ feature_dbxref.getDbxref().getDb().getName()+"'))"+
"AND feature_id=(SELECT feature_id FROM "+
"feature WHERE uniquename='"+uniquename+"')";
Statement st = conn.createStatement();
- return st.executeUpdate(sql);
+ st.executeUpdate(sql);
}
/**
- * Insert a synonym for a feature.
- * @param tsn the <code>ChadoTransaction</code>
- * @return number of rows changed
+ * Insert a feature_synonym for a feature.
+ * @param feature_synonym the new <code>FeatureSynonym</code>
* @throws SQLException
*/
- public int insertFeatureAlias(final ChadoTransaction tsn)
+ private void insertFeatureAlias(final FeatureSynonym feature_synonym)
throws SQLException
{
- final FeatureSynonym alias = tsn.getAlias();
- final String uniquename = alias.getUniquename();
- final String synonym_name = alias.getSynonym().getName();
+ final String uniquename = feature_synonym.getFeature().getUniquename();
+ final String synonym_name = feature_synonym.getSynonym().getName();
String sql;
@@ -854,7 +938,8 @@ public class JdbcDAO
if(!exists)
{
// create a new synonym name
- String type_id = Long.toString(alias.getSynonym().getCvterm().getCvtermId());
+ String type_id =
+ Long.toString(feature_synonym.getSynonym().getCvterm().getCvtermId());
sql = "INSERT INTO "+
"synonym (name, type_id, synonym_sgml) values ( '"+
@@ -877,21 +962,20 @@ public class JdbcDAO
" 1)";
appendToLogFile(sql, sqlLog);
- return st.executeUpdate(sql);
+ st.executeUpdate(sql);
}
/**
- * Delete a synonym for a feature.
- * @param tsn the <code>ChadoTransaction</code>
+ * Delete a feature_synonym for a feature.
+ * @param feature_synonym the new <code>FeatureSynonym</code>
* @return number of rows changed
* @throws SQLException
*/
- public int deleteFeatureAlias(final ChadoTransaction tsn)
+ private void deleteFeatureSynonym(final FeatureSynonym feature_synonym)
throws SQLException
{
- final FeatureSynonym alias = tsn.getAlias();
- final String uniquename = alias.getUniquename();
- final String synonym_name = alias.getSynonym().getName();
+ final String uniquename = feature_synonym.getFeature().getUniquename();
+ final String synonym_name = feature_synonym.getSynonym().getName();
String sql = "SELECT synonym_id FROM synonym WHERE "+
"synonym.name='"+synonym_name+"'";
@@ -916,41 +1000,31 @@ public class JdbcDAO
sql = "DELETE FROM synonym WHERE synonym_id="+synonym_id;
st = conn.createStatement();
- return st.executeUpdate(sql);
+ st.executeUpdate(sql);
}
/**
* Update feature_relationship for a feature.
- * @param tsn the <code>ChadoTransaction</code>
- * @return number of rows changed
+ * @param feature_relationship the <code>FeatureRelationship</code>
* @throws SQLException
*/
- public void updateFeatureRelationshipsForSubjectId(
- final ChadoTransaction tsn)
+ private void updateFeatureRelationship(
+ final FeatureRelationship feature_relationship)
throws SQLException
- {
- final Feature chado_feature = tsn.getChadoFeature();
- final String parent = tsn.getParent_uniquename();
-
-
+ {
StringBuffer sqlBuff = new StringBuffer();
sqlBuff.append("UPDATE feature_relationship ");
sqlBuff.append(" SET ");
-
- List properties = tsn.getProperties();
- for(int i=0; i<properties.size(); i++)
- {
- sqlBuff.append((String)properties.get(i));
- if(i < properties.size()-1)
- sqlBuff.append(" , ");
- }
-
- sqlBuff.append(" WHERE feature_relationship.subject_id="+
- "(SELECT feature_id FROM feature WHERE uniquename='"+
- chado_feature.getUniquename()+"') AND "+
- "feature_relationship.object_id="+
- "(SELECT feature_id FROM feature WHERE uniquename='"+
- parent+"')");
+ sqlBuff.append(" rank="+feature_relationship.getRank()+", ");
+ sqlBuff.append(" type_id="+feature_relationship.getCvterm().getCvtermId());
+ sqlBuff.append(" WHERE ");
+ sqlBuff.append("subject_id=");
+ sqlBuff.append("( SELECT feature_id FROM feature WHERE uniquename='");
+ sqlBuff.append(feature_relationship.getSubject().getUniquename()+"' ) ");
+ sqlBuff.append("AND ");
+ sqlBuff.append("object_id=");
+ sqlBuff.append("( SELECT feature_id FROM feature WHERE uniquename='");
+ sqlBuff.append(feature_relationship.getObject().getUniquename()+"' ) ");
String sql = sqlBuff.toString();
@@ -960,79 +1034,7 @@ public class JdbcDAO
st.executeUpdate(sql);
}
- /**
- * Write the time a feature was last modified
- * @param uniquename the unique name of the feature
- * @param timestamp the time stamp to use,
- * if NULL use CURRENT_TIMESTAMP
- * @return number of rows changed
- * @throws SQLException
- */
- public int writeTimeLastModified
- (final String uniquename,
- final Timestamp timestamp)
- throws SQLException
- {
- String sql = "UPDATE "+
- "feature SET timelastmodified=";
-
- if(timestamp == null)
- sql = sql +"CURRENT_TIMESTAMP";
- else
- sql = sql +"?";
-
- sql = sql + " WHERE uniquename= ?";
-
- PreparedStatement pstmt = conn.prepareStatement(sql);
-
- int param = 1;
- if(timestamp != null)
- {
- pstmt.setTimestamp(param, timestamp);
- param++;
- }
- pstmt.setString(param, uniquename);
-
- int rowCount = pstmt.executeUpdate();
- return rowCount;
- }
-
- /**
- * Write the time a feature was last accessed
- * @param uniquename the unique name of the feature
- * @param timestamp the time stamp to use,
- * if NULL use CURRENT_TIMESTAMP
- * @throws SQLException
- */
- public int writeTimeAccessioned
- (final String uniquename,
- final Timestamp timestamp)
- throws SQLException
- {
- String sql = "UPDATE "+
- "feature SET timeaccessioned=";
-
- if(timestamp == null)
- sql = sql +"CURRENT_TIMESTAMP";
- else
- sql = sql +"?";
-
- sql = sql + " WHERE uniquename= ?";
-
- PreparedStatement pstmt = conn.prepareStatement(sql);
-
- int param = 1;
- if(timestamp != null)
- {
- pstmt.setTimestamp(param, timestamp);
- param++;
- }
- pstmt.setString(param, uniquename);
-
- int rowCount = pstmt.executeUpdate();
- return rowCount;
- }
-
+
/**
* Appends a log entry to the log file
* @param logEntry entry to add to log file
@@ -1065,9 +1067,7 @@ public class JdbcDAO
{
bw.close();
}
- catch(IOException ioe2)
- {
- }
+ catch(IOException ioe2){}
}
}
diff --git a/uk/ac/sanger/artemis/util/DatabaseDocument.java b/uk/ac/sanger/artemis/util/DatabaseDocument.java
index a538fbd70f4dab1f6090e9dfdbbf024f97a5c9cb..1f21e457dfabbb3c26422fea6b4e830e394fdbb9 100644
--- a/uk/ac/sanger/artemis/util/DatabaseDocument.java
+++ b/uk/ac/sanger/artemis/util/DatabaseDocument.java
@@ -26,7 +26,6 @@ package uk.ac.sanger.artemis.util;
import uk.ac.sanger.artemis.io.ChadoCanonicalGene;
import uk.ac.sanger.artemis.io.GFFStreamFeature;
-import uk.ac.sanger.artemis.io.InvalidRelationException;
import uk.ac.sanger.artemis.io.ReadFormatException;
import uk.ac.sanger.artemis.chado.*;
import uk.ac.sanger.artemis.components.DatabaseEntrySource;
@@ -474,11 +473,12 @@ public class DatabaseDocument extends Document
this_buff = buffers[j];
}
+
chadoToGFF(feat, parentFeature.getUniquename(),
dbxrefs, synonym,
id_store, dao,
feat.getFeatureloc(), this_buff);
-
+
if( i%10 == 0 || i == feature_size-1)
progress_listener.progressMade("Read from database: " +
feat.getUniquename());
@@ -505,7 +505,7 @@ public class DatabaseDocument extends Document
for(int i=0; i<list.size(); i++)
{
alias = (FeatureSynonym)list.get(i);
- feature_id = alias.getFeature_id();
+ feature_id = new Integer(alias.getFeature().getId());
if(synonym.containsKey(feature_id))
value = (Vector)synonym.get(feature_id);
else
@@ -571,7 +571,7 @@ public class DatabaseDocument extends Document
{
//Feature transcript = new Feature();
- int id = ((FeatureRelationship) relations.get(i)).getSubject_id();
+ int id = ((FeatureRelationship) relations.get(i)).getSubject().getId();
//transcript.setId(id);
Feature transcript = dao.getFeatureById(id); //.getLazyFeature(transcript);
@@ -588,7 +588,7 @@ public class DatabaseDocument extends Document
for(int j = 0; j < transcipt_relations.size(); j++)
{
- id = ((FeatureRelationship) transcipt_relations.get(j)).getSubject_id();
+ id = ((FeatureRelationship) transcipt_relations.get(j)).getSubject().getId();
//Feature child = new Feature();
//child.setId(((FeatureRelationship) transcipt_relations.get(j))
// .getSubject_id());
@@ -644,7 +644,7 @@ public class DatabaseDocument extends Document
if(feat.getFeature_relationship() != null)
{
FeatureRelationship feat_relationship = feat.getFeature_relationship();
- parent_id = Integer.toString(feat_relationship.getObject_id());
+ parent_id = Integer.toString(feat_relationship.getObject().getId());
long parent_type_id = feat_relationship.getCvterm().getCvtermId();
parent_relationship = feat_relationship.getCvterm().getName();
@@ -660,9 +660,9 @@ public class DatabaseDocument extends Document
{
FeatureRelationship feat_relationship =
(FeatureRelationship)relations.get(i);
- parent_id = Integer.toString(feat_relationship.getObject_id());
+ parent_id = Integer.toString(feat_relationship.getObject().getId());
System.out.println("HERE "+i+" "+feat_relationship.getCvterm().getName()+ " "+
- feat_relationship.getObject_id()+" "+feat_relationship.getSubject_id()+ " parent_id="+ parent_id);
+ feat_relationship.getObject().getId()+" "+feat_relationship.getSubject().getId()+ " parent_id="+ parent_id);
parent_relationship = feat_relationship.getCvterm().getName();
}
}
@@ -1033,26 +1033,26 @@ public class DatabaseDocument extends Document
Vector names_checked = new Vector();
for(i = 0; i < sql.size(); i++)
{
- ChadoTransaction tsn = (ChadoTransaction) sql.get(i);
-
- if(tsn.getType() != ChadoTransaction.INSERT_FEATURE ||
- tsn.getType() != ChadoTransaction.DELETE_FEATURE)
- {
- final List uniquename = tsn.getUniquename();
-
- for(int j=0; j<uniquename.size(); j++)
- {
- if(names_checked.contains((String)uniquename.get(j)))
- continue;
+ ChadoTransaction tsn = (ChadoTransaction)sql.get(i);
+ if( (tsn.getType() == ChadoTransaction.INSERT ||
+ tsn.getType() == ChadoTransaction.DELETE) &&
+ tsn.getFeatureObject() instanceof Feature )
+ continue;
- names_checked.add((String)uniquename.get(j));
- unchanged = checkFeatureTimestamp(schema,
- (String)uniquename.get(j),
+ final String uniquename = tsn.getUniquename();
+
+ if(uniquename == null)
+ continue;
+ if(names_checked.contains(uniquename))
+ continue;
+
+ names_checked.add(uniquename);
+
+ unchanged = checkFeatureTimestamp(schema,
+ uniquename,
tsn.getLastModified(), dao);
- if(!unchanged)
- return 0;
- }
- }
+ if(!unchanged)
+ return 0;
}
try
@@ -1067,65 +1067,76 @@ public class DatabaseDocument extends Document
ChadoTransaction tsn = (ChadoTransaction) sql.get(i);
if(tsn.getType() == ChadoTransaction.UPDATE)
- dao.updateAttributes(tsn);
+ {
+ if(tsn.getFeatureObject() instanceof Feature)
+ {
+ Feature feature = (Feature)tsn.getFeatureObject();
+
+ if(feature.getUniquename() != null)
+ {
+ final String uniquename;
+ if(tsn.getOldUniquename() != null)
+ uniquename = (String)tsn.getOldUniquename();
+ else
+ uniquename = feature.getUniquename();
+
+ Feature old_feature
+ = dao.getFeatureByUniqueName(uniquename);
+ feature.setId( old_feature.getId() );
+
+ tsn.setOldUniquename(feature.getUniquename());
+ }
+ }
+ dao.merge(tsn.getFeatureObject());
+ //dao.updateAttributes(tsn);
+ }
else if(tsn.getType() == ChadoTransaction.INSERT)
- dao.insertAttributes(tsn);
+ {
+ // set srcfeature_id
+ if(tsn.getFeatureObject() instanceof Feature)
+ {
+ FeatureLoc featureloc = ((Feature)tsn.getFeatureObject()).getFeatureloc();
+ featureloc.setSrcfeature_id(Integer.parseInt(feature_id));
+ }
+ dao.persist(tsn.getFeatureObject());
+ //dao.insertAttributes(tsn);
+ }
else if(tsn.getType() == ChadoTransaction.DELETE)
- dao.deleteAttributes(tsn);
- else if(tsn.getType() == ChadoTransaction.INSERT_FEATURE)
- dao.insertFeature(tsn, feature_id);
- else if(tsn.getType() == ChadoTransaction.DELETE_FEATURE)
- dao.deleteFeature(tsn);
- else if(tsn.getType() == ChadoTransaction.DELETE_DBXREF)
- dao.deleteFeatureDbxref(tsn);
- else if(tsn.getType() == ChadoTransaction.INSERT_DBXREF)
- dao.insertFeatureDbxref(tsn);
- else if(tsn.getType() == ChadoTransaction.DELETE_ALIAS)
- dao.deleteFeatureAlias(tsn);
- else if(tsn.getType() == ChadoTransaction.INSERT_ALIAS)
- dao.insertFeatureAlias(tsn);
- else if(tsn.getType() == ChadoTransaction.UPDATE_FEATURE_RELATIONSHIP)
- dao.updateFeatureRelationshipsForSubjectId(tsn);
+ dao.delete(tsn.getFeatureObject());
}
//
// update timelastmodified timestamp
- Timestamp ts = null;
- Timestamp ts2;
+ Timestamp ts = new Timestamp(new java.util.Date().getTime());
names_checked = new Vector();
for(int j = 0; j < sql.size(); j++)
{
- ChadoTransaction tsn = (ChadoTransaction) sql.get(j);
-
- if(tsn.getType() != ChadoTransaction.INSERT_FEATURE &&
- tsn.getType() != ChadoTransaction.DELETE_FEATURE)
- {
- final List uniquename = tsn.getUniquename();
-
- // update timelastmodified timestamp
- for(int k = 0; k < uniquename.size(); k++)
- {
- if(names_checked.contains((String) uniquename.get(k)))
- continue;
-
- names_checked.add((String) uniquename.get(k));
-
- dao.writeTimeLastModified((String) uniquename.get(k), ts);
-
- Feature feature = dao.getFeatureByUniqueName((String) uniquename.get(k));
- ts2 = feature.getTimelastmodified();
- if(ts2 == null)
- continue;
+ ChadoTransaction tsn = (ChadoTransaction)sql.get(j);
+
+ if( (tsn.getType() == ChadoTransaction.INSERT ||
+ tsn.getType() == ChadoTransaction.DELETE) &&
+ tsn.getFeatureObject() instanceof Feature )
+ continue;
+
+ final String uniquename = tsn.getUniquename();
+ if(uniquename == null)
+ continue;
+
+ if(names_checked.contains(uniquename))
+ continue;
- if(ts == null)
- ts = ts2;
+ names_checked.add(uniquename);
- GFFStreamFeature gff_feature = (GFFStreamFeature) tsn
- .getFeatureObject();
-
- gff_feature.setLastModified(ts);
- }
+ Feature feature = dao.getFeatureByUniqueName(uniquename);
+ if(feature != null)
+ {
+ feature.setTimelastmodified(ts);
+ dao.merge(feature);
}
+
+ GFFStreamFeature gff_feature = (GFFStreamFeature) tsn
+ .getGff_feature();
+ gff_feature.setLastModified(ts);
}
if(dao instanceof IBatisDAO &&
@@ -1173,6 +1184,8 @@ public class DatabaseDocument extends Document
throws SQLException
{
Feature feature = dao.getFeatureByUniqueName(uniquename);
+ if(feature == null)
+ return true;
Timestamp now = feature.getTimelastmodified();
if(now != null && timestamp != null)