From bcf480b4ddfdb82f810ce537a96909ec797c1f5f Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Fri, 7 Mar 2008 14:30:17 +0000
Subject: [PATCH] add in analysis row for each similarity qualifier added
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@7208 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
uk/ac/sanger/artemis/chado/ArtemisUtils.java | 1 +
uk/ac/sanger/artemis/chado/GmodDAO.java | 10 ++++++++++
uk/ac/sanger/artemis/chado/IBatisDAO.java | 5 +++++
uk/ac/sanger/artemis/util/DatabaseDocument.java | 10 ++++++++--
4 files changed, 24 insertions(+), 2 deletions(-)
diff --git a/uk/ac/sanger/artemis/chado/ArtemisUtils.java b/uk/ac/sanger/artemis/chado/ArtemisUtils.java
index b40c6b273..2c357a12a 100644
--- a/uk/ac/sanger/artemis/chado/ArtemisUtils.java
+++ b/uk/ac/sanger/artemis/chado/ArtemisUtils.java
@@ -323,6 +323,7 @@ public class ArtemisUtils
";");
analysis.setProgram((String) qualifier_strings.get(0));
+ analysis.setProgramVersion("1.0");
// primary dbxref
DbXRef dbXRef_1 = new DbXRef();
diff --git a/uk/ac/sanger/artemis/chado/GmodDAO.java b/uk/ac/sanger/artemis/chado/GmodDAO.java
index bf7ad170a..a9e41d916 100644
--- a/uk/ac/sanger/artemis/chado/GmodDAO.java
+++ b/uk/ac/sanger/artemis/chado/GmodDAO.java
@@ -150,6 +150,16 @@ public abstract class GmodDAO
}
+ public List getFeaturesByOrganism(Organism organism)
+ {
+ return null;
+ }
+
+ public List getFeaturesByUniqueNames(List name)
+ {
+ return null;
+ }
+
//////
////// SchemaDaoI
//////
diff --git a/uk/ac/sanger/artemis/chado/IBatisDAO.java b/uk/ac/sanger/artemis/chado/IBatisDAO.java
index a177ab2d0..76612f15e 100644
--- a/uk/ac/sanger/artemis/chado/IBatisDAO.java
+++ b/uk/ac/sanger/artemis/chado/IBatisDAO.java
@@ -943,6 +943,11 @@ public class IBatisDAO extends GmodDAO
subjectLoc.setFeatureByFeatureId(matchFeature);
sqlMap.insert("insertFeatureLoc", subjectLoc);
+
+ // insert analysis
+ Integer analysisId = (Integer) sqlMap.insert("insertAnalysis", analysisFeature.getAnalysis());
+ analysisFeature.getAnalysis().setAnalysisId(analysisId.intValue());
+
// insert analysis feature
matchFeature.setFeatureId(matchFeatureId);
analysisFeature.setFeature(matchFeature);
diff --git a/uk/ac/sanger/artemis/util/DatabaseDocument.java b/uk/ac/sanger/artemis/util/DatabaseDocument.java
index 4913545b3..4de4caecf 100644
--- a/uk/ac/sanger/artemis/util/DatabaseDocument.java
+++ b/uk/ac/sanger/artemis/util/DatabaseDocument.java
@@ -2240,9 +2240,9 @@ public class DatabaseDocument extends Document
schema_list = dao.getOrganisms();
- Organism org = new Organism();
+ /*Organism org = new Organism();
org.setCommonName("web");
- schema_list.add(org);
+ schema_list.add(org);*/
final List pg_schemas = dao.getSchema();
@@ -2271,6 +2271,12 @@ public class DatabaseDocument extends Document
final Organism organism = (Organism)it.next();
String orgName = organism.getCommonName();
+ if(orgName == null || orgName.equals(""))
+ {
+ orgName = organism.getGenus() + "." + organism.getSpecies();
+ organism.setCommonName(orgName);
+ }
+
// search to see if this is in its own schema
Iterator schemasIt = pg_schemas.iterator();
while(schemasIt.hasNext())
--
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