diff --git a/artemis_sqlmap/Feature.xml b/artemis_sqlmap/Feature.xml
index e1ab4fe138acb9061b04a22f48bbabcd4206a455..e646d050b46a19e02e37d4b571e7a3c7dc89962d 100644
--- a/artemis_sqlmap/Feature.xml
+++ b/artemis_sqlmap/Feature.xml
@@ -7,6 +7,12 @@
<sqlMap namespace="Feature">
+ <typeAlias alias="ChadoFeature"
+ type="uk.ac.sanger.artemis.chado.ChadoFeature"/>
+
+ <typeAlias alias="ChadoTransaction"
+ type="uk.ac.sanger.artemis.chado.ChadoTransaction"/>
+
<resultMap id="select-cvterm-names-result" class="uk.ac.sanger.artemis.chado.Cvterm">
<result property="id" column="cvterm_id"/>
<result property="name" column="name"/>
@@ -19,7 +25,7 @@
</parameterMap>
<resultMap id="select-feature-properties-result"
- class="uk.ac.sanger.artemis.chado.ChadoFeature">
+ class="ChadoFeature">
<result property="timelastmodified" column="timelastmodified"/>
<result property="id" column="id"/>
<result property="feature_relationship.object_id" column="object_id"/>
@@ -34,7 +40,7 @@
</resultMap>
<resultMap id="select-feature-result"
- class="uk.ac.sanger.artemis.chado.ChadoFeature">
+ class="ChadoFeature">
<result property="timelastmodified" column="timelastmodified"/>
<result property="id" column="id"/>
<result property="uniquename" column="uniquename"/>
@@ -48,23 +54,24 @@
<result property="featureprop.cvterm" column="prop_type_id" select="selectCvterm" />
<result property="featureprop.value" column="value" />
<result property="featureprop.rank" column="rank" />
+ <result property="organism" column="organism_id" select="selectOrganism" />
</resultMap>
<resultMap id="select-feature-sequence-result"
- class="uk.ac.sanger.artemis.chado.ChadoFeature">
+ class="ChadoFeature">
<result property="name" column="name"/>
<result property="residues" column="residues"/>
</resultMap>
<resultMap id="select-feature-with-residues-result"
- class="uk.ac.sanger.artemis.chado.ChadoFeature">
+ class="ChadoFeature">
<result property="organism.abbreviation" column="abbreviation"/>
<result property="name" column="name"/>
<result property="id" column="feature_id"/>
<result property="cvterm.id" column="type_id"/>
</resultMap>
-
+
<!-- look up cvterms names and id -->
<select id="selectCvterm" resultMap="select-cvterm-names-result">
SELECT cvterm_id, name
@@ -72,15 +79,22 @@
WHERE cvterm_id=#value#
</select>
+ <select id="selectOrganism" resultClass="uk.ac.sanger.artemis.chado.ChadoOrganism">
+ SELECT organism_id AS id, abbreviation, genus, species, common_name, comment
+ FROM organism
+ WHERE organism_id=#value#
+ </select>
+
+
<!-- get feature name -->
- <select id="getFeatureName" parameterClass="uk.ac.sanger.artemis.chado.ChadoFeature"
+ <select id="getFeatureName" parameterClass="ChadoFeature"
resultClass="java.lang.String">
SELECT name
FROM $schema$.feature WHERE feature_id=$id$
</select>
<!-- get feature id -->
- <select id="getFeatureID" parameterClass="uk.ac.sanger.artemis.chado.ChadoTransaction"
+ <select id="getFeatureID" parameterClass="ChadoTransaction"
resultClass="java.lang.Integer">
SELECT feature_id FROM $schema$.feature WHERE
<iterate property="uniquename" conjunction="OR">
@@ -88,7 +102,7 @@
</iterate>
</select>
- <select id="getGffLine" parameterClass="uk.ac.sanger.artemis.chado.ChadoFeature"
+ <select id="getGffLine" parameterClass="ChadoFeature"
resultMap="select-feature-properties-result">
SELECT
timelastmodified,
@@ -119,7 +133,7 @@
ORDER BY f.type_id, uniquename
</select>
- <select id="getSequence" parameterClass="uk.ac.sanger.artemis.chado.ChadoFeature"
+ <select id="getSequence" parameterClass="ChadoFeature"
resultMap="select-feature-sequence-result">
SELECT
name,
@@ -158,12 +172,13 @@
</select>
<select id="getFeature" resultMap ="select-feature-result"
- parameterClass="uk.ac.sanger.artemis.chado.ChadoFeature">
+ parameterClass="ChadoFeature">
SELECT
#schema# AS schema,
timelastmodified,
f.feature_id AS id,
uniquename,
+ organism_id,
name,
f.type_id,
seqlen AS length,
@@ -193,13 +208,13 @@
</select>
<select id="getOrganismID" resultClass="java.lang.Integer"
- parameterClass="uk.ac.sanger.artemis.chado.ChadoFeature">
+ parameterClass="ChadoFeature">
SELECT organism_id FROM $schema$.feature f WHERE
f.feature_id=$featureloc.srcfeature_id$
</select>
<select id="getTimeLastModified" resultClass="java.sql.Timestamp"
- parameterClass="uk.ac.sanger.artemis.chado.ChadoFeature">
+ parameterClass="ChadoFeature">
SELECT timelastmodified FROM $schema$.feature f WHERE
f.uniquename=#uniquename#
</select>
@@ -213,7 +228,7 @@
<!-- WRITE BACK METHODS -->
<update id="updateAttributes"
- parameterClass="uk.ac.sanger.artemis.chado.ChadoTransaction">
+ parameterClass="ChadoTransaction">
UPDATE $schema$.$chadoTable$
SET
<iterate property="properties" conjunction=",">
@@ -240,7 +255,7 @@
</update>
<insert id="insertAttributes"
- parameterClass="uk.ac.sanger.artemis.chado.ChadoTransaction">
+ parameterClass="ChadoTransaction">
INSERT INTO $schema$.$chadoTable$
(
feature_id
@@ -257,7 +272,7 @@
</insert>
<delete id="deleteAttributes"
- parameterClass="uk.ac.sanger.artemis.chado.ChadoTransaction">
+ parameterClass="ChadoTransaction">
DELETE FROM $schema$.$chadoTable$
WHERE
<iterate property="constraint" conjunction="AND">
@@ -268,7 +283,7 @@
</delete>
<insert id="insertFeature"
- parameterClass="uk.ac.sanger.artemis.chado.ChadoFeature">
+ parameterClass="ChadoFeature">
INSERT INTO $schema$.feature
( feature_id, organism_id, name, uniquename, type_id )
VALUES
@@ -280,7 +295,7 @@
</insert>
<insert id="insertFeatureLoc"
- parameterClass="uk.ac.sanger.artemis.chado.ChadoFeature">
+ parameterClass="ChadoFeature">
INSERT INTO $schema$.featureloc
( featureloc_id, feature_id, srcfeature_id, fmin, fmax, strand, phase )
VALUES
@@ -294,7 +309,7 @@
</insert>
<delete id="deleteFeature"
- parameterClass="uk.ac.sanger.artemis.chado.ChadoFeature">
+ parameterClass="ChadoFeature">
DELETE FROM $schema$.feature
WHERE uniquename=#uniquename#
</delete>
diff --git a/artemis_sqlmap/chado_iBatis_config.properties b/artemis_sqlmap/chado_iBatis_config.properties
index f1f289fc28fa76bd3727a78b33a6270790ef4906..60d72ac34cc2e830d617b70c1d80ee8e1d867d06 100644
--- a/artemis_sqlmap/chado_iBatis_config.properties
+++ b/artemis_sqlmap/chado_iBatis_config.properties
@@ -4,6 +4,6 @@
# 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
+jdbc.drivers=org.postgresql.Driver
+chado=localhost:2996/chado
+username=lbraziliensis
diff --git a/artemis_sqlmap/chado_iBatis_config.xml b/artemis_sqlmap/chado_iBatis_config.xml
index daad978d8755c1872ce332f48ce2c86a066d05db..5bcf8906074398507de4cbc9e6639531c62b812d 100644
--- a/artemis_sqlmap/chado_iBatis_config.xml
+++ b/artemis_sqlmap/chado_iBatis_config.xml
@@ -1,32 +1,31 @@
<?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">
-
+ <!DOCTYPE sqlMapConfig
+ PUBLIC "-//ibatis.apache.org//DTD SQL Map Config 2.0//EN"
+ "http://ibatis.apache.org/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"
+ <settings
+ cacheModelsEnabled="true"
+ enhancementEnabled="true"
+ lazyLoadingEnabled="true"
+ maxRequests="128"
+ maxSessions="10"
+ maxTransactions="5"
+ useStatementNamespaces="false"
/>
+
<!-- Type aliases allow you to use a shorter name for long fully qualified class names. -->