-
tjc authored
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13746 ee4ac58c-ac51-4696-9907-e4b3aa274f04
tjc authoredgit-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13746 ee4ac58c-ac51-4696-9907-e4b3aa274f04
Feature.xml 22.65 KiB
<?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">
<typeAlias alias="Feature"
type="org.gmod.schema.sequence.Feature"/>
<cacheModel id="feature-cache" type ="LRU" readOnly="true">
<flushInterval hours="24"/>
<flushOnExecute statement="insertFeature"/>
<flushOnExecute statement="updateFeature"/>
<flushOnExecute statement="deleteFeature"/>
<flushOnExecute statement="deleteFeatureById"/>
<property name="cache-size" value="10" />
</cacheModel>
<parameterMap id="schema-cvlist"
class="Feature">
<parameter property="schema" javaType="java.lang.String"/>
<parameter property="featureCvTerms" javaType="java.util.List"/>
</parameterMap>
<!-- resultMap templates below -->
<resultMap id="template-basicfeature" class="Feature">
<result property="timeLastModified" column="timelastmodified"/>
<result property="featureId" column="id"/>
<result property="uniqueName" column="uniquename"/>
<result property="name" column="feature_name"/>
<result property="seqLen" column="seqlen" nullValue="-1" />
<result property="obsolete" column="obsolete" />
</resultMap>
<resultMap id="template-basicfeature-all-lazy" class="Feature"
extends="template-basicfeature">
<result property="cvTerm" column="type_id" select="getCvtermByCvTermId" />
<result property="dbXRef" column="dbXRefId"
select="getDbXRefByDbXRefId" />
<result property="featureLocsForFeatureId" column="{id=id}"
select="getFeatureLoc" />
<result property="featureProps" column="{feature_id=id}"
select="getFeaturePropByFeatureId" />
<result property="featureDbXRefs" column="{featureId=id}"
select="getFeatureDbXRef" />
<result property="featureRelationshipsForObjectId" column="{object_id=id}"
select="getFeatureRelationship" />
<result property="featureRelationshipsForSubjectId" column="{subject_id=id}"
select="getFeatureRelationship" />
<result property="featureSynonyms" column="{feature.uniqueName=uniqueName}"
select="getLazyFeatureSynonymsByUniquename" />
<result property="organism" column="{organismId=organismId}"
select="getOrganism" />
</resultMap>
<resultMap id="template-feature" class="Feature"
extends="template-basicfeature">
<result property="organism.organismId" column="organism_id"/>
<result property="dbXRef" resultMap="DbXRef.select-dbxref" />
<result property="featureProps" resultMap="FeatureProp.map-featureprop" />
<result property="featureRelationshipsForSubjectId"
resultMap="FeatureRelationship.map-feature-relationship-for-objectId" />
<result property="featureLoc.strand" column="strand" nullValue="0"/>
<result property="featureLoc.fmin" column="fmin" nullValue="-1"/>
<result property="featureLoc.fmax" column="fmax" nullValue="0"/>
<result property="featureLoc.phase" column="phase"/> <result property="featureLoc.fminPartial" column="is_fmin_partial"/>
<result property="featureLoc.fmaxPartial" column="is_fmax_partial"/>
<result property="cvTerm.cvTermId" column="type_id"/>
<result property="featureSynonyms" column="{feature.uniqueName=uniqueName}"
select="getLazyFeatureSynonymsByUniquename" />
<result property="featureDbXRefs" column="{featureId=id}"
select="getFeatureDbXRef" />
<result property="featurePubs" column="{featureId=id}" select="getFeaturePubsByFeature"/>
</resultMap>
<!-- resultMap proper below -->
<resultMap id="map-feature" class="Feature"
groupBy="featureId" extends="template-feature">
<result property="featureCvTerms" column="{{uniqueName=uniquename}}"
select="getFeatureCvTermsByFeature"/>
</resultMap>
<resultMap id="map-feature-no-rank" class="Feature"
groupBy="featureId" extends="template-feature">
<result property="featureCvTerms" column="{{uniqueName=uniquename}}"
select="getFeatureCvTermsNoRankByFeature"/>
</resultMap>
<!-- mapping for feature table and lazy loading -->
<resultMap id="map-feature-lazy-no-residues" class="Feature"
extends="template-basicfeature-all-lazy">
<result property="featureCvTerms" column="{{uniqueName=uniquename}}"
select="getFeatureCvTermsByFeature"/>
</resultMap>
<resultMap id="map-feature-lazy" class="Feature"
extends="template-basicfeature-all-lazy">
<result property="featureCvTerms" column="{{uniqueName=uniquename}}"
select="getFeatureCvTermsByFeature"/>
<result property="residues" column="residues" />
</resultMap>
<resultMap id="map-feature-lazy-no-rank" class="Feature"
extends="template-basicfeature-all-lazy">
<result property="featureCvTerms" column="{{uniqueName=uniquename}}"
select="getFeatureCvTermsNoRankByFeature"/>
<result property="residues" column="residues" />
</resultMap>
<resultMap id="map-feature-name-lazy" class="Feature">
<result property="featureId" column="id"/>
<result property="uniqueName" column="uniquename"/>
<result property="cvTerm.name" column="name" />
<result property="featureRelationshipsForSubjectId" column="{subject_id=id}"
select="getParentFeatureRelationship" />
</resultMap>
<resultMap id="map-feature-withprop" class="Feature"
groupBy="featureId" extends="template-basicfeature">
<result property="cvTerm" column="type_id" select="getCvtermByCvTermId" />
<result property="featureProps" resultMap="FeatureProp.map-featureprop" />
<result property="featureDbXRefs" column="{featureId=id}"
select="getFeatureDbXRef" />
<result property="dbXRef" resultMap="DbXRef.select-dbxref" />
</resultMap>
<resultMap id="map-feature-residues" class="Feature">
<result property="residues" column="residues"/>
<result property="seqLen" column="seqLen"/>
<result property="featureLoc.fmin" column="fmin" nullValue="-1"/>
<result property="featureLoc.fmax" column="fmax" nullValue="0"/>
<result property="featureLoc.strand" column="strand" nullValue="0" /> <result property="featureLoc.phase" column="phase" nullValue="0" />
</resultMap>
<resultMap id="map-similaritymatch-lazy" class="Feature"
groupBy="featureId" extends="template-basicfeature">
<result property="cvTerm.cvTermId" column="type_id" />
<result property="featureLocsForFeatureId" column="{id=id}"
select="getFeatureLoc" />
<result property="featureProps" column="{feature_id=id}"
select="getFeaturePropByFeatureId" />
<result property="featureDbXRefs" column="{featureId=id}"
select="getFeatureDbXRef" />
<result property="dbXRef" column="dbXRefId"
select="getDbXRefByDbXRefId" />
<result property="analysisFeatures" column="{feature_id=id}"
select="getAnalysisFeaturesByFeatureId" />
</resultMap>
<resultMap id="map-clusterfeature" class="Feature"
groupBy="featureId">
<result property="featureId" column="id"/>
<result property="uniqueName" column="cluster_name"/>
<result property="cvTerm.name" column="cluster_cvterm"/>
<result property="featureProps" column="{feature_id=id}"
select="getFeaturePropByFeatureId" />
<result property="featureRelationshipsForSubjectId"
resultMap="FeatureRelationship.map-feature-relationship-for-subjectId" />
<result property="analysisFeatures" resultMap="AnalysisFeature.map-analysisfeature" />
</resultMap>
<resultMap id="map-feature-with-residues-result" class="Feature">
<result property="uniqueName" column="uniquename"/>
<result property="featureId" column="feature_id"/>
<result property="cvTerm.cvTermId" column="type_id"/>
<result property="cvTerm.name" column="cvterm_name"/>
<!--<result property="cvTerm" column="type_id" select="getCvtermByCvTermId" />-->
<result property="organism" column="{organismId=organism_id}"
select="getOrganism" />
</resultMap>
<!-- SQL -->
<!-- get feature -->
<sql id="sql-feature">
SELECT
timelastmodified,
f.feature_id AS id,
f.organism_id,
f.is_obsolete AS obsolete,
dbx.*,
db.*,
fr.feature_relationship_id,
fr.object_id,
fr.type_id AS relation_type_id,
fr.rank,
fr.value AS relation_value,
fl.strand,
fmin,
fmax,
f.name AS feature_name,
uniquename,
f.type_id,
f.seqlen,
fp.featureprop_id,
fp.type_id AS prop_type_id,
fp.rank AS prop_rank,
fp.value,
fl.phase, fl.is_fmin_partial,
fl.is_fmax_partial
FROM feature f
LEFT JOIN featureloc fl ON ( f.feature_id = fl.feature_id )
LEFT JOIN feature_relationship fr ON fr.subject_id = f.feature_id
LEFT JOIN featureprop fp ON fp.feature_id = f.feature_id
LEFT JOIN dbxref dbx ON f.dbxref_id = dbx.dbxref_id
LEFT JOIN db ON dbx.db_id = db.db_id
WHERE
<dynamic>
<isGreaterThan property="featureLoc.featureBySrcFeatureId.featureId" compareValue="0">
srcfeature_id=$featureLoc.featureBySrcFeatureId.featureId$
<isGreaterThan property="cvTerm.cvTermId" compareValue="0" prepend="AND">
( is_analysis=#analysis# OR f.type_id!=$cvTerm.cvTermId$ )
</isGreaterThan>
</isGreaterThan>
<isGreaterEqual property="featureLoc.fmin" compareValue="0" prepend="AND">
<![CDATA[ fl.fmin >= $featureLoc.fmin$ AND fl.fmax < $featureLoc.fmax$ ]]>
</isGreaterEqual>
<isNotNull property="uniqueName">
uniquename LIKE #uniqueName#
</isNotNull>
</dynamic>
</sql>
<select id="getFeature" parameterClass="Feature"
resultMap="map-feature">
<include refid="sql-feature"/>
</select>
<select id="getFeatureNoFeatureCvTermRank" parameterClass="Feature"
resultMap="map-feature-no-rank">
<include refid="sql-feature"/>
</select>
<sql id="sql-lazy-feature">
SELECT
timelastmodified,
f.feature_id AS id,
uniquename,
organism_id AS organismId,
f.is_obsolete AS obsolete,
f.name AS feature_name,
f.type_id,
f.dbxref_id AS dbXRefId,
f.seqlen,
residues
FROM feature f
<dynamic>
<isNotNull property="cvTerm.name">
LEFT JOIN cvterm ON f.type_id=cvterm.cvterm_id
</isNotNull>
</dynamic>
<dynamic prepend="WHERE">
<isGreaterThan property="featureId" compareValue="0">
f.feature_id=$featureId$
</isGreaterThan>
<isNotNull property="uniqueName" prepend="AND">
<isNotNull property="featureSynonyms">
<iterate property="featureSynonyms" conjunction="OR" open="(" close=") OR">
f.feature_id=#featureSynonyms[].feature.featureId#
</iterate>
</isNotNull>
( uniquename LIKE #uniqueName# )
</isNotNull>
<isGreaterThan property="cvTerm.cvTermId" compareValue="0" prepend="AND">
f.type_id=$cvTerm.cvTermId$ </isGreaterThan>
<isNotNull property="cvTerm.name" prepend="AND">
cvterm.name=#cvTerm.name#
</isNotNull>
</dynamic>
</sql>
<select id="getLazyFeature" resultMap ="map-feature-lazy"
parameterClass="Feature">
<include refid="sql-lazy-feature"/>
</select>
<select id="getLazyFeatureNoFeatureCvTermRank"
resultMap ="map-feature-lazy-no-rank"
parameterClass="Feature">
<include refid="sql-lazy-feature"/>
</select>
<sql id="sql-lazy-feature-exact-name">
SELECT
timelastmodified,
f.feature_id AS id,
uniquename,
organism_id AS organismId,
f.is_obsolete AS obsolete,
f.name AS feature_name,
f.type_id,
f.dbxref_id AS dbXRefId,
f.seqlen,
residues
FROM feature f
<dynamic>
<isNotNull property="cvTerm.name">
LEFT JOIN cvterm ON f.type_id=cvterm.cvterm_id
</isNotNull>
</dynamic>
WHERE ( uniquename = #uniqueName# )
<isGreaterThan property="cvTerm.cvTermId" compareValue="0" prepend="AND">
f.type_id=$cvTerm.cvTermId$
</isGreaterThan>
<isNotNull property="cvTerm.name" prepend="AND">
cvterm.name=#cvTerm.name#
</isNotNull>
</sql>
<select id="getLazyFeatureExact" resultMap ="map-feature-lazy"
parameterClass="Feature">
<include refid="sql-lazy-feature-exact-name"/>
</select>
<select id="getLazyFeatureExactNoFeatureCvTermRank"
resultMap ="map-feature-lazy-no-rank"
parameterClass="Feature">
<include refid="sql-lazy-feature-exact-name"/>
</select>
<select id="getLazyFeatureNoResiduesById" resultMap ="map-feature-lazy-no-residues"
cacheModel="feature-cache">
SELECT timelastmodified,
f.feature_id AS id,
uniquename,
organism_id AS organismId,
f.is_obsolete AS obsolete,
f.name AS feature_name,
f.type_id,
f.dbxref_id AS dbXRefId,
f.seqlen
FROM feature f
WHERE f.feature_id=$featureId$
</select>
<select id="getFeaturesByListOfIds" resultMap ="map-feature-withprop">
SELECT
timelastmodified,
f.feature_id AS id,
uniquename,
organism_id AS organismId,
f.is_obsolete AS obsolete,
f.name AS feature_name,
f.type_id,
f.dbxref_id AS dbXRefId,
f.seqlen,
fp.type_id AS prop_type_id, fp.rank AS prop_rank, fp.value, fp.featureprop_id,
dbxref.*, db.*
FROM feature f
LEFT JOIN featureprop fp ON fp.feature_id=f.feature_id
LEFT JOIN dbxref ON f.dbxref_id=dbxref.dbxref_id
LEFT JOIN db ON dbxref.db_id=db.db_id
WHERE f.feature_id IN <iterate open="(" close=")" conjunction=","> $[]$ </iterate>
</select>
<sql id="selectSimilarityMatch">
SELECT
timelastmodified,
f.feature_id AS id,
f.uniquename,
f.is_obsolete AS obsolete,
f.type_id,
f.dbxref_id AS dbXRefId,
f.name AS feature_name,
f.seqlen,
f.residues
FROM feature f
<!--LEFT JOIN featureloc fl ON f.feature_id=fl.feature_id
LEFT JOIN analysisfeature af ON f.feature_id=af.feature_id
LEFT JOIN analysis a ON af.analysis_id=a.analysis_id-->
WHERE f.feature_id IN
</sql>
<!-- Returns matches for all features on a given srcfeature -->
<select id="getLazySimilarityMatches" parameterClass="java.lang.Integer"
resultMap="map-similaritymatch-lazy">
<include refid="selectSimilarityMatch"/>
( SELECT feature_id FROM featureloc WHERE srcfeature_id IN
( SELECT feature_id FROM featureloc WHERE srcfeature_id=$value$) )
ORDER BY f.feature_id
</select>
<!-- Returns matches for a list of feature_id's -->
<select id="getLazySimilarityMatchesByFeatureIds" parameterClass="java.util.List"
resultMap="map-similaritymatch-lazy">
<include refid="selectSimilarityMatch"/>
( SELECT feature_id FROM featureloc WHERE srcfeature_id IN
<iterate open="(" close=")" conjunction=","> $[]$ </iterate>
)
ORDER BY f.feature_id
</select>
<!-- Returns cluster/ortholog/paralog for a list of feature_id's -->
<select id="getLazyClustersByFeatureIds" parameterClass="java.util.List"
resultMap="map-clusterfeature">
SELECT
f.feature_id AS id,
f.uniquename AS cluster_name,
cv_f.name AS cluster_cvterm,
f1.uniquename AS subject_name,
fr.subject_id,
cv_fr.name AS fr_name,
common_name AS subject_common_name,
cv_f1.name AS subject_cvterm,
rawscore, normscore, significance, identity, a.analysis_id,
a.name, description, program, programversion, algorithm, sourcename, sourceversion,sourceuri, timeexecuted
FROM feature f
LEFT JOIN feature_relationship fr ON f.feature_id=fr.object_id
LEFT JOIN analysisfeature af ON f.feature_id=af.feature_id
LEFT JOIN analysis a ON af.analysis_id=a.analysis_id
LEFT JOIN feature f1 ON f1.feature_id=subject_id
LEFT JOIN organism ON f1.organism_id=organism.organism_id
LEFT JOIN cvterm AS cv_f1 ON cv_f1.cvterm_id=f1.type_id
LEFT JOIN cvterm AS cv_fr ON cv_fr.cvterm_id=fr.type_id
LEFT JOIN cvterm AS cv_f ON cv_f.cvterm_id=f.type_id
WHERE f.feature_id IN <iterate open="(" close=")" conjunction=","> #[]# </iterate>
AND (cv_fr.name='orthologous_to' OR cv_fr.name='paralogous_to') <!-- cv_f.name LIKE '%match%' -->
</select>
<select id="getSchema" resultClass="java.lang.String">
SELECT schema_name FROM information_schema.schemata WHERE schema_name=schema_owner
ORDER BY schema_name
</select>
<select id="getResidueType" parameterClass="java.lang.String"
resultClass="java.lang.Long">
SELECT DISTINCT type_id FROM feature WHERE residues notnull
</select>
<sql id="source_feature_cvterm_names">
cvterm.name LIKE '%chromosome%' OR cvterm.name LIKE '%sequence%' OR
cvterm.name IN ('supercontig', 'ultra_scaffold', 'golden_path_region', 'contig', 'plasmid')
</sql>
<select id="getResidueFeatures" parameterClass="java.lang.Integer"
resultMap="map-feature-with-residues-result">
SELECT uniquename, feature_id, type_id, feature.organism_id,
cvterm.name AS cvterm_name
FROM cvterm
LEFT JOIN feature ON cvterm.cvterm_id=feature.type_id
WHERE <isNotNull> feature.organism_id=$value$ AND </isNotNull>
residues notnull AND residues != '' AND
( <include refid="source_feature_cvterm_names"/> )
ORDER BY uniquename
</select>
<select id="getTopLevelFeatures" parameterClass="java.lang.Integer"
resultMap="map-feature-with-residues-result">
SELECT feature.name, uniquename, feature_id, feature.type_id, feature.organism_id,
cvterm.name AS cvterm_name
FROM feature
JOIN cvterm on feature.type_id = cvterm.cvterm_id
JOIN featureprop using (feature_id)
WHERE <isNotNull> feature.organism_id=$value$ AND </isNotNull>
featureprop.type_id in (
SELECT cvterm_id FROM cvterm JOIN cv using (cv_id) WHERE cv.name = 'genedb_misc' AND cvterm.name = 'top_level_seq' )
ORDER BY uniquename
</select>
<select id="getResidueFeaturesByOrganismCommonName" parameterClass="java.lang.String"
resultMap="map-feature-with-residues-result">
SELECT uniquename, feature_id, type_id,
feature.organism_id
FROM cvterm
LEFT JOIN feature ON cvterm.cvterm_id=feature.type_id
WHERE <isNotNull> organism.common_name=#value# AND </isNotNull>
residues notnull AND residues != '' AND
( <include refid="source_feature_cvterm_names"/> )
ORDER BY uniquename
</select>
<select id="getResiduesByUniqueName" parameterClass="java.lang.String"
resultMap="map-feature-residues">
SELECT substr(residues, fl.fmin+1, fl.fmax-fl.fmin) AS residues,
length(residues) AS seqLen, fl.fmin, fl.fmax, fl.strand, fl.phase
FROM featureloc fl
LEFT JOIN feature f ON fl.srcfeature_id=f.feature_id
WHERE fl.feature_id=(SELECT feature_id FROM feature WHERE uniquename=#value#);
</select>
<select id="currval" resultClass="java.lang.Integer"
parameterClass="java.lang.String">
SELECT currval('$value$')
</select>
<!-- WRITE BACK METHODS -->
<!-- UPDATE -->
<update id="updateFeature"
parameterClass="Feature">
UPDATE feature
SET uniquename=#uniqueName#, is_obsolete=#obsolete#
<isNotEqual property="name" compareValue="0"> , name=#name# </isNotEqual>
<isNotNull property="cvTerm.cvTermId"> , type_id=$cvTerm.cvTermId$ </isNotNull>
<isNotNull property="timeLastModified"> , timelastmodified=#timeLastModified# </isNotNull>
WHERE feature_id=$featureId$
</update>
<update id="updateFeatureResidues"
parameterClass="uk.ac.sanger.artemis.chado.FeatureForUpdatingResidues">
UPDATE feature SET
residues=substring(residues from 1 for $startBase$) ||
<dynamic>
<isNotNull property="newSubSequence"> #newSubSequence# || </isNotNull>
</dynamic>
substring(residues from $endBase$ for $basesToEnd$),
seqlen=$seqLen$
WHERE
<isNotEqual property="featureId" compareValue="-1">feature_id=$featureId$</isNotEqual>
<isEqual property="featureId" compareValue="-1">
feature_id=(SELECT feature_id FROM feature WHERE uniquename=#uniqueName#)
</isEqual>
</update>
<!-- INSERT -->
<insert id="insertFeature"
parameterClass="Feature">
INSERT INTO feature
( feature_id, organism_id, name, uniquename, type_id
<isGreaterThan property="seqLen" compareValue="0"> , seqlen </isGreaterThan>
<isNotNull property="residues"> , residues </isNotNull>
<isNotNull property="dbXRef.dbXRefId"> , dbxref_id </isNotNull> )
VALUES
( nextval('feature_feature_id_seq'),
$organism.organismId$,
#name#, #uniqueName#,
$cvTerm.cvTermId$
<isGreaterThan property="seqLen" compareValue="0"> , $seqLen$ </isGreaterThan>
<isNotNull property="residues"> , #residues# </isNotNull>
<isNotNull property="dbXRef.dbXRefId"> , $dbXRef.dbXRefId$ </isNotNull> )
</insert>
<!--
<update id="updateRegionSequence"
parameterClass="Feature">
UPDATE feature SET
residues=substring(residues from 1 for $featureLoc.fmin$) ||
#residues,jdbcType=text# ||
substring(residues from $featureLoc.fmin$ for
(seqLen + $seqLen$)),
seqlen=(seqLen+$seqLen$)
WHERE feature_id=$featureLoc.featureBySrcFeatureId.featureId$
</update>
-->
<!-- DELETE -->
<delete id="deleteFeature"
parameterClass="Feature">
DELETE FROM feature
WHERE uniquename=#uniqueName# AND type_id=$cvTerm.cvTermId$
</delete>
<delete id="deleteFeatureById"
parameterClass="Feature">
DELETE FROM feature
WHERE feature_id=$featureId$
</delete>
</sqlMap>