ibatis config

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@3802 ee4ac58c-ac51-4696-9907-e4b3aa274f04

artemis_sqlmap/Cvterm.xml

+<?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="Cvterm"> 
+ 
+    <resultMap id="select-cvterm-names-result" class="uk.ac.sanger.ibatis.Cvterm">
+   	<result property="id" column="cvterm_id"/>
+  	<result property="name" column="name"/>
+     </resultMap>
+
+    <!-- look up cvterms names and id -->
+     <select id="getCvterm" resultMap="select-cvterm-names-result"> 
+   	SELECT  
+	  cvterm.CVTERM_ID, cvterm.NAME
+        FROM cvterm, cv WHERE cv.cv_id = cvterm.cv_id
+     </select> 
+ 
+</sqlMap> 

artemis_sqlmap/Feature.xml

+<?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="Feature"> 
+ 
+    <resultMap id="select-feature-properties-result" class="uk.ac.sanger.ibatis.Feature">
+        <result property="timelastmodified" column="timelastmodified"/>
+   	<result property="id" column="id"/>
+  	<result property="object_id" column="object_id"/>
+        <result property="strand" column="strand"/>
+        <result property="fmin" column="fmin"/>
+        <result property="fmax" column="fmax"/>
+        <result property="uniquename" column="uniquename"/>
+        <result property="type_id" column="type_id"/>
+        <result property="prop_type_id" column="prop_type_id"/>
+        <result property="value" column="value"/>
+     </resultMap>
+
+     <resultMap id="select-feature-sequence-result" class="uk.ac.sanger.ibatis.Feature">
+        <result property="name" column="name"/>
+        <result property="residues" column="residues"/>
+     </resultMap>
+    
+     <resultMap id="select-feature-with-residues-result" class="uk.ac.sanger.ibatis.Feature">
+        <result property="abbreviation" column="abbreviation"/>
+        <result property="name" column="name"/>
+        <result property="id" column="feature_id"/>
+        <result property="type_id" column="type_id"/>
+     </resultMap>
+
+     <!-- get feature name -->
+     <select id="getFeatureName" parameterClass="java.lang.String" resultClass="java.lang.String"> 
+   	SELECT  
+	  name
+        FROM feature WHERE feature_id=#value#
+     </select> 
+
+     <select id="getGffLine" parameterClass="int" resultMap="select-feature-properties-result">
+        SELECT
+          timelastmodified, 
+          feature.feature_id AS id, 
+          object_id, 
+          strand, 
+          fmin, 
+          fmax, 
+          uniquename,
+          feature.type_id AS type_id,  
+          featureprop.type_id AS prop_type_id, 
+          featureprop.value AS value
+        FROM  featureloc, feature
+        LEFT JOIN feature_relationship ON feature_relationship.subject_id=feature.feature_id
+        LEFT JOIN featureprop ON featureprop.feature_id=feature.feature_id
+        WHERE srcfeature_id=#value# and  featureloc.feature_id=feature.feature_id
+        and (featureloc.rank=feature_relationship.rank OR feature_relationship.rank IS NULL)
+        ORDER BY feature.type_id,  uniquename
+     </select>
+ 
+    <select id="getSequence" parameterClass="int" resultMap="select-feature-sequence-result">
+       SELECT
+         name, 
+         residues 
+       FROM feature 
+       WHERE feature_id=#value#
+    </select>
+
+    <select id="getResidueType" resultClass="java.lang.String">
+       SELECT DISTINCT type_id FROM feature WHERE residues notnull
+    </select>
+
+    <select id="getResidueFeatures" parameterClass="java.util.List" resultMap="select-feature-with-residues-result">
+       SELECT 
+         abbreviation, 
+         name, 
+         feature_id, 
+         type_id 
+       FROM organism, feature WHERE
+         organism.organism_id=feature.organism_id AND
+         residues notnull
+         <iterate prepend="AND" conjunction="OR" open="(" close=")">
+           type_id=#[]#
+         </iterate>
+       ORDER BY abbreviation
+    </select>
+</sqlMap> 

artemis_sqlmap/Organism.xml

+<?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="Organism"> 
+ 
+      <!-- Use primitive wrapper type (e.g. Integer) as parameter and allow results to 
+            be auto-mapped results to Organism object (JavaBean) properties --> 
+      <select id="getOrganism" parameterClass="java.lang.String" resultClass="uk.ac.sanger.ibatis.Organism"> 
+   	SELECT  
+	  ORGANISM_ID as id,
+	  ABBREVIATION, 
+	  GENUS,
+	  SPECIES,
+	  COMMON_NAME,
+	  COMMENT
+ 	FROM Organism WHERE COMMON_NAME = #value# 
+      </select> 
+ 
+</sqlMap> 

artemis_sqlmap/chado_iBatis_config.properties

+# This is just a simple properties file that simplifies automated configuration 
+# of the SQL Maps configuration file (e.g. by Ant builds or continuous  
+# integration tools for different environments... etc.) 
+# These values can be used in any property value in the file above (e.g. ${driver}) 
+# Using a properties file such as this is completely optional.   
+ 
+driver=org.postgresql.Driver
+url=jdbc:postgresql://localhost:2999/test
+username=tjc

artemis_sqlmap/chado_iBatis_config.xml

+<?xml version="1.0" encoding="UTF-8" ?> 
+ 
+<!DOCTYPE sqlMapConfig 
+    PUBLIC "-//iBATIS.com//DTD SQL Map Config 2.0//EN" 
+    "http://www.ibatis.com/dtd/sql-map-config-2.dtd"> 
+ 
+<!-- Always ensure to use the correct XML header as above! --> 
+ 
+<sqlMapConfig> 
+ 
+  <!-- The properties (name=value) in the file specified here can be used placeholders in this config  
+         file (e.g. ${driver}.  The file is usually relative to the classpath and is optional.  --> 
+ 
+  <!--
+  <properties resource="artemis_sqlmap/chado_iBatis_config.properties" /> 
+  -->
+
+  <!-- These settings control SqlMap configuration details, primarily to do with transaction  
+         management.  They are all optional (see the Developer Guide for more).  --> 
+ 
+  <settings 
+    cacheModelsEnabled="true" 
+    enhancementEnabled="true" 
+    lazyLoadingEnabled="true" 
+    maxRequests="32" 
+    maxSessions="10" 
+    maxTransactions="5" 
+    useStatementNamespaces="false" 
+  /> 
+ 
+  <!-- Type aliases allow you to use a shorter name for long fully qualified class names. --> 
+ 
+  <typeAlias alias="order" type="testdomain.Order"/> 
+ 
+  <!-- Configure a datasource to use with this SQL Map using SimpleDataSource. 
+         Notice the use of the properties from the above resource --> 
+ 
+  <transactionManager type="JDBC" > 
+    <dataSource type="SIMPLE"> 
+      <property name="JDBC.Driver" value="org.postgresql.Driver"/> 
+      <property name="JDBC.ConnectionURL" value="jdbc:postgresql://${chado}"/> 
+      <property name="JDBC.Username" value="${username}"/> 
+      <property name="JDBC.Password" value="${password}"/> 
+    </dataSource> 
+  </transactionManager> 
+ 
+  <!-- Identify all SQL Map XML files to be loaded by this SQL map.  Notice the paths  
+         are relative to the classpath.  For now, we only have one... --> 
+ 
+  <sqlMap resource="artemis_sqlmap/Organism.xml" /> 
+  <sqlMap resource="artemis_sqlmap/Cvterm.xml" />
+  <sqlMap resource="artemis_sqlmap/Feature.xml" />
+
+</sqlMapConfig> 
+