From a14d27d941924ac7156f805bd5dd1af2592d619d Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Wed, 10 Dec 2008 15:43:02 +0000
Subject: [PATCH] add OrganismProp
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@9582 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
artemis_sqlmap/Organism.xml | 16 +++++++++++++---
artemis_sqlmap/OrganismProp.xml | 20 ++++++++++++++++++++
artemis_sqlmap/chado_iBatis_config.xml | 1 +
3 files changed, 34 insertions(+), 3 deletions(-)
create mode 100644 artemis_sqlmap/OrganismProp.xml
diff --git a/artemis_sqlmap/Organism.xml b/artemis_sqlmap/Organism.xml
index 15bb06d12..8b03b450a 100644
--- a/artemis_sqlmap/Organism.xml
+++ b/artemis_sqlmap/Organism.xml
@@ -10,7 +10,17 @@
<flushInterval hours="24"/>
<property name="cache-size" value="100" />
</cacheModel>
-
+
+ <resultMap id="map-organism" class="org.gmod.schema.organism.Organism">
+ <result property="organismId" column="organismId"/>
+ <result property="abbreviation" column="abbreviation"/>
+ <result property="commonName" column="commonName"/>
+ <result property="genus" column="genus"/>
+ <result property="species" column="species"/>
+ <result property="comment" column="comment"/>
+ <result property="organismProps" column="organismId" select="getOrganismPropByOrganismIdLazy"/>
+ </resultMap>
+
<select id="getOrganism"
resultClass="org.gmod.schema.organism.Organism">
SELECT organism_id AS organismId, abbreviation, genus, species, common_name AS commonName, comment
@@ -60,7 +70,7 @@
</isNull>
</select>
- <select id="getOrganismsContainingSrcFeatures" resultClass="org.gmod.schema.organism.Organism">
+ <select id="getOrganismsContainingSrcFeatures" resultMap="map-organism">
SELECT DISTINCT ON( feature.organism_id )
organism.organism_id AS organismId, abbreviation, genus, species, common_name AS commonName, comment
FROM feature
@@ -70,7 +80,7 @@
AND ( <include refid="source_feature_cvterm_names"/> )
</select>
- <select id="getTopLevelOrganisms" resultClass="org.gmod.schema.organism.Organism">
+ <select id="getTopLevelOrganisms" resultMap="map-organism">
SELECT DISTINCT ON( feature.organism_id )
organism.organism_id AS organismId, abbreviation, genus, species, common_name AS commonName, comment
FROM feature
diff --git a/artemis_sqlmap/OrganismProp.xml b/artemis_sqlmap/OrganismProp.xml
new file mode 100644
index 000000000..66394bb3c
--- /dev/null
+++ b/artemis_sqlmap/OrganismProp.xml
@@ -0,0 +1,20 @@
+<?xml version="1.0" encoding="UTF-8" ?>
+
+<!DOCTYPE sqlMap
+ PUBLIC "-//ibatis.apache.org//DTD SQL Map 2.0//EN"
+ "http://ibatis.apache.org/dtd/sql-map-2.dtd">
+
+<sqlMap namespace="OrganismProp">
+ <resultMap id="map-organismprop-with-cvterm-lazy"
+ class="org.gmod.schema.organism.OrganismProp">
+ <result property="value" column="value" />
+ <result property="rank" column="rank" />
+ <result property="cvTerm" column="type_id" select="getCvtermByCvTermId" />
+ </resultMap>
+
+ <select id="getOrganismPropByOrganismIdLazy" resultMap="map-organismprop-with-cvterm-lazy">
+ SELECT type_id, value, rank
+ FROM organismprop
+ WHERE organism_id=#organism_id#
+ </select>
+</sqlMap>
diff --git a/artemis_sqlmap/chado_iBatis_config.xml b/artemis_sqlmap/chado_iBatis_config.xml
index b8d1d1ef3..7f3e3b128 100644
--- a/artemis_sqlmap/chado_iBatis_config.xml
+++ b/artemis_sqlmap/chado_iBatis_config.xml
@@ -82,6 +82,7 @@
<sqlMap resource="artemis_sqlmap/Pub.xml" />
<sqlMap resource="artemis_sqlmap/Feature.xml" />
<sqlMap resource="artemis_sqlmap/Organism.xml" />
+ <sqlMap resource="artemis_sqlmap/OrganismProp.xml" />
<sqlMap resource="artemis_sqlmap/FeatureCvTerm.xml" />
<sqlMap resource="artemis_sqlmap/FeatureCvTermDbXRef.xml" />
<sqlMap resource="artemis_sqlmap/FeatureCvTermProp.xml" />
--
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