From 3a661bc27b89dddcb402ebccdc39f67a2c62d6e3 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Fri, 8 May 2009 12:53:49 +0000
Subject: [PATCH] load a pub_dbxref when a pub is created
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10763 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
uk/ac/sanger/artemis/chado/GmodDAO.java | 39 ++++++++++++++++++++++-
uk/ac/sanger/artemis/chado/IBatisDAO.java | 6 ++++
uk/ac/sanger/artemis/chado/JdbcDAO.java | 9 +++---
3 files changed, 49 insertions(+), 5 deletions(-)
diff --git a/uk/ac/sanger/artemis/chado/GmodDAO.java b/uk/ac/sanger/artemis/chado/GmodDAO.java
index 69e733f19..ba10e0aaa 100644
--- a/uk/ac/sanger/artemis/chado/GmodDAO.java
+++ b/uk/ac/sanger/artemis/chado/GmodDAO.java
@@ -36,6 +36,7 @@ import org.gmod.schema.general.Db;
import org.gmod.schema.general.DbXRef;
import org.gmod.schema.organism.Organism;
import org.gmod.schema.pub.Pub;
+import org.gmod.schema.pub.PubDbXRef;
import org.gmod.schema.sequence.Feature;
import org.gmod.schema.sequence.FeatureCvTerm;
import org.gmod.schema.sequence.FeatureCvTermDbXRef;
@@ -48,7 +49,8 @@ import uk.ac.sanger.artemis.util.DatabaseDocument;
public abstract class GmodDAO
implements SequenceDaoI, SchemaDaoI, OrganismDaoI, CvDaoI, PubDaoI, GeneralDaoI
{
-
+ private static org.apache.log4j.Logger logger4j =
+ org.apache.log4j.Logger.getLogger(GmodDAO.class);
public abstract List getOrganismsContainingSrcFeatures();
public abstract List getSimilarityMatchesByFeatureIds(final List featureIds);
public abstract List getSimilarityMatches(final Integer srcFeatureId);
@@ -472,11 +474,45 @@ public abstract class GmodDAO
insertPub(pub);
pubResult = getPubByUniqueName(pub);
+
+ // add PubDbXRef
+ loadPubDbXRef(pubResult);
}
return pubResult;
}
+ /**
+ * Create PubDbXRef for new Pub's and to handle links to
+ * links to eg, pubmed.
+ * @param pub
+ */
+ private void loadPubDbXRef(final Pub pub)
+ {
+ try
+ {
+ int index = pub.getUniqueName().indexOf(':');
+ if (index > -1)
+ {
+ DbXRef dbXRef = new DbXRef();
+ dbXRef.setAccession(pub.getUniqueName().substring(index + 1));
+ Db db = new Db();
+ db.setName(pub.getUniqueName().substring(0, index));
+ dbXRef.setDb(db);
+ dbXRef = loadDbXRef(dbXRef);
+
+ PubDbXRef pubDbXRef = new PubDbXRef();
+ pubDbXRef.setDbXRef(dbXRef);
+ pubDbXRef.setPub(pub);
+ insertPubDbXRef(pubDbXRef);
+ }
+ }
+ catch (Exception e)
+ {
+ logger4j.warn("GmodDAO.loadPubDbXRef() :: "+e.getMessage());
+ }
+ }
+
/**
* Insert a feature_cvterm and associated feature_cvtermprop's,
* feature_cvterm_dbxref's and feature_cvterm_pub.
@@ -547,6 +583,7 @@ public abstract class GmodDAO
protected abstract void insertDbXRef(DbXRef dbXRef);
protected abstract Pub getPubByUniqueName(Pub pub);
protected abstract void insertPub(Pub pub);
+ protected abstract void insertPubDbXRef(PubDbXRef pubDbXRef);
protected abstract void insertFeatureCvTerm(final FeatureCvTerm feature_cvterm);
protected abstract int getCurrval(String seq_id);
protected abstract void insertFeatureCvTermProp(FeatureCvTermProp featureCvTermProp);
diff --git a/uk/ac/sanger/artemis/chado/IBatisDAO.java b/uk/ac/sanger/artemis/chado/IBatisDAO.java
index 47ac96692..e1f66ade5 100644
--- a/uk/ac/sanger/artemis/chado/IBatisDAO.java
+++ b/uk/ac/sanger/artemis/chado/IBatisDAO.java
@@ -47,6 +47,7 @@ import org.gmod.schema.general.Db;
import org.gmod.schema.general.DbXRef;
import org.gmod.schema.organism.Organism;
import org.gmod.schema.pub.Pub;
+import org.gmod.schema.pub.PubDbXRef;
import org.gmod.schema.analysis.AnalysisFeature;
import org.gmod.schema.cv.Cv;
import org.gmod.schema.cv.CvTerm;
@@ -1236,6 +1237,11 @@ public class IBatisDAO extends GmodDAO
sqlMap.insert("insertPub", pub);
}
+ protected void insertPubDbXRef(PubDbXRef pubDbXRef)
+ {
+ sqlMap.insert("insertPubDbXRef", pubDbXRef);
+ }
+
public void startTransaction() throws SQLException
{
diff --git a/uk/ac/sanger/artemis/chado/JdbcDAO.java b/uk/ac/sanger/artemis/chado/JdbcDAO.java
index 2d7c4d05e..a4b0b7975 100644
--- a/uk/ac/sanger/artemis/chado/JdbcDAO.java
+++ b/uk/ac/sanger/artemis/chado/JdbcDAO.java
@@ -2285,8 +2285,9 @@ public class JdbcDAO extends GmodDAO
throw new RuntimeException(sqle);
}
}
-
-
-
-
+
+ protected void insertPubDbXRef(PubDbXRef pubDbXRef)
+ {
+
+ }
}
--
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