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From: <yo...@us...> - 2010-03-01 15:49:14
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Revision: 521
http://treebase.svn.sourceforge.net/treebase/?rev=521&view=rev
Author: youjun
Date: 2010-03-01 15:49:04 +0000 (Mon, 01 Mar 2010)
Log Message:
-----------
optimize taxonlabeldao queries
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/taxon/TaxonLabelDAO.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/dao/taxon/TaxonLabelDAO.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/dao/taxon/TaxonLabelDAO.java 2010-02-26 16:02:32 UTC (rev 520)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/dao/taxon/TaxonLabelDAO.java 2010-03-01 15:49:04 UTC (rev 521)
@@ -409,12 +409,13 @@
return result;
}
-
+ // need refactoring later
+ //all the sql statement should go to same file or class
public Collection<Matrix> findMatrices(Taxon t) {
Query q = getSession()
- .createQuery("select distinct m from Matrix m, TaxonLabel tl where " +
- "tl member of m.taxa.taxonLabelList and tl.taxonVariant.taxon = :t");
- q.setParameter("t", t);
+ .createSQLQuery("select distinct m.* from matrix m join matrixrow using(matrix_id) join taxonlabel " +
+ "using (taxonlabel_id) join taxonvariant using (taxonvariant_id) where taxon_id = :id").addEntity(Matrix.class);
+ q.setParameter("id", t.getId());
Collection<Matrix> result = q.list();
return result;
}
@@ -436,8 +437,11 @@
*/
public Collection<PhyloTree> findTrees(Taxon t) {
Query q = getSession()
- .createQuery("select pt from PhyloTree pt, TaxonLabel tl where " +
- "tl member of pt.treeBlock.taxonLabelSet.taxonLabelList and tl.taxonVariant.taxon = :t");
+ .createQuery("select distinct pt from PhyloTree pt inner join fetch pt.treeNodes tn where " +
+ "tn.taxonLabel.taxonVariant.taxon = :t");
+
+ //("select pt from PhyloTree pt, TaxonLabel tl where " +
+ // "tl member of pt.treeBlock.taxonLabelSet.taxonLabelList and tl.taxonVariant.taxon = :t");
q.setParameter("t", t);
Collection<PhyloTree> result = new HashSet<PhyloTree>();
for (Object o: q.list()) { // Can't select distinct over phylotrees today 20081204 mjd
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From: <yo...@us...> - 2010-03-23 14:51:01
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Revision: 650
http://treebase.svn.sourceforge.net/treebase/?rev=650&view=rev
Author: youjun
Date: 2010-03-23 14:50:54 +0000 (Tue, 23 Mar 2010)
Log Message:
-----------
eliminate repeat results return by findByStudy
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/taxon/TaxonLabelDAO.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/dao/taxon/TaxonLabelDAO.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/dao/taxon/TaxonLabelDAO.java 2010-03-23 13:45:53 UTC (rev 649)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/dao/taxon/TaxonLabelDAO.java 2010-03-23 14:50:54 UTC (rev 650)
@@ -81,7 +81,7 @@
// ALERT: the result might not be unique since mesquite allows duplicated taxonlabels
// in the same tree.
// returnVal = (TaxonLabel) c.uniqueResult();
-
+ c.setResultTransformer(Criteria.DISTINCT_ROOT_ENTITY);
returnVal = c.list();
}
return returnVal;
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From: <yo...@us...> - 2010-03-26 20:45:02
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Revision: 657
http://treebase.svn.sourceforge.net/treebase/?rev=657&view=rev
Author: youjun
Date: 2010-03-26 20:44:55 +0000 (Fri, 26 Mar 2010)
Log Message:
-----------
add method to clen orphan value in taxonlabel and taxonlabelset
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/taxon/TaxonLabelDAO.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/dao/taxon/TaxonLabelDAO.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/dao/taxon/TaxonLabelDAO.java 2010-03-24 12:59:35 UTC (rev 656)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/dao/taxon/TaxonLabelDAO.java 2010-03-26 20:44:55 UTC (rev 657)
@@ -460,4 +460,24 @@
}
return result;
}
+
+ public void clean(TaxonLabelSet tSet) {
+ // TODO Auto-generated method stub
+ Query q = getSession()
+ .createQuery("select count(*) from TreeBlock tb where tb.taxonLabelSet = :ts");
+ q.setParameter("ts", tSet);
+ int count=((Integer)q.iterate().next()).intValue();
+
+ q = getSession()
+ .createQuery("select count(*) from Matrix m where m.taxa = :ts");
+ q.setParameter("ts", tSet);
+ count += ((Integer)q.iterate().next()).intValue();
+
+ if(count==0)deletePersist(tSet);
+ }
+
+ public void clean(List<TaxonLabel> tList) {
+ // TODO Auto-generated method stub
+
+ }
}
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From: <yo...@us...> - 2010-03-27 01:02:57
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Revision: 658
http://treebase.svn.sourceforge.net/treebase/?rev=658&view=rev
Author: youjun
Date: 2010-03-27 01:02:51 +0000 (Sat, 27 Mar 2010)
Log Message:
-----------
finish modification
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/taxon/TaxonLabelDAO.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/dao/taxon/TaxonLabelDAO.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/dao/taxon/TaxonLabelDAO.java 2010-03-26 20:44:55 UTC (rev 657)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/dao/taxon/TaxonLabelDAO.java 2010-03-27 01:02:51 UTC (rev 658)
@@ -478,6 +478,18 @@
public void clean(List<TaxonLabel> tList) {
// TODO Auto-generated method stub
-
+ for(TaxonLabel tl : tList){
+ Query q = getSession()
+ .createQuery("select count(*) from PhyloTreeNode pn where pn.taxonLabel = :tl");
+ q.setParameter("tl", tl);
+ int count=((Integer)q.iterate().next()).intValue();
+
+ q = getSession()
+ .createQuery("select count(*) from MatrixRow mr where mr.taxonLabel = :tl");
+ q.setParameter("tl", tl);
+ count += ((Integer)q.iterate().next()).intValue();
+
+ if(count==0)deletePersist(tl);
+ }
}
}
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From: <yo...@us...> - 2010-04-11 14:40:26
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Revision: 682
http://treebase.svn.sourceforge.net/treebase/?rev=682&view=rev
Author: youjun
Date: 2010-04-11 14:40:20 +0000 (Sun, 11 Apr 2010)
Log Message:
-----------
clean sub_taxonlabel table before delete a taxonlabel
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/taxon/TaxonLabelDAO.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/dao/taxon/TaxonLabelDAO.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/dao/taxon/TaxonLabelDAO.java 2010-04-09 03:30:14 UTC (rev 681)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/dao/taxon/TaxonLabelDAO.java 2010-04-11 14:40:20 UTC (rev 682)
@@ -489,7 +489,11 @@
q.setParameter("tl", tl);
count += ((Long)q.iterate().next()).intValue();
- if(count==0)deletePersist(tl);
+ if(count==0){
+ Submission sub=tl.getSubmission();
+ if(sub!=null)sub.removeTaxonLabel(tl);
+ deletePersist(tl);
+ }
}
}
}
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