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Fetches and Translates rdf data from RDB using D2RMap.

Example

java org.vivoweb.harvester.fetch.D2RMapFetch -o config/recordHandlers/JDBCXMLRecordHandler.xml -u config/tasks/D2RMapFetchTask.d2r.xml -s person.rdf

Parameters

-u [d2r file] - D2RMap Configuration File Path (Required)

Example configuration files using MySQL and Oracle

See the D2R spec for details of d2r elements.

Example 1:

<?xml version="1.0"?>
<d2r:Map xmlns:d2r="http://www.wiwiss.fu-berlin.de/suhl/bizer/D2RMap/0.1#" d2r:versionInfo="$Id: iswcMap.d2r,xml, v 0.1 2003/01/15 19:44:09 Chris Exp $">
        <d2r:Prepend><![CDATA[<?xml version="1.0" encoding="UTF-8" ?>]]></d2r:Prepend>
        <d2r:ProcessorMessage d2r:outputFormat="RDF/XML"/>
        <d2r:DBConnection d2r:jdbcDriver="com.mysql.jdbc.Driver" d2r:jdbcDSN="jdbc:mysql://localhost:3306/injest_test" d2r:username="user" d2r:password="pw"/>
        <d2r:Namespace d2r:prefix="owl" d2r:namespace="http://www.w3.org/2002/07/owl#"/>
        <d2r:Namespace d2r:prefix="rdf" d2r:namespace="http://www.w3.org/1999/02/22-rdf-syntax-ns#"/>
        <d2r:Namespace d2r:prefix="xsd" d2r:namespace="http://www.w3.org/2001/XMLSchema#"/>
        <d2r:Namespace d2r:prefix="rdfs" d2r:namespace="http://www.w3.org/2000/01/rdf-schema#"/>
        <d2r:Namespace d2r:prefix="core" d2r:namespace="http://vivoweb.org/ontology/core#"/>
        <d2r:Namespace d2r:prefix="foaf" d2r:namespace="http://xmlns.com/foaf/0.1/"/>
        <d2r:Namespace d2r:prefix="vivo" d2r:namespace="http://vivoweb.org/ontology/core#"/>

        <!-- Person -->
        <!-- Note: d2r:groupBy and d2r:column Strings needs to be ALL CAPITALS unless running a case sensitive RDBMS like MySQL on Linux/Unix -->
        <d2r:ClassMap d2r:type="foaf:Person" 
                 d2r:sql="select personID as PERSONID, firstName as FIRSTNAME, 
                                middleName as MIDDLENAME, lastName as LASTNAME, title as TITLE 
                                from injest_test.people" 
                 d2r:groupBy="PERSONID"  
                 d2r:uriPattern="http://example.org/vivo/individual/@<at:var at:name="PERSONID" />@">
                <d2r:DatatypePropertyBridge d2r:property="rdfs:label" d2r:column="PERSONID"/>
                <d2r:DatatypePropertyBridge d2r:property="foaf:firstName" d2r:column="FIRSTNAME"/>
                <d2r:DatatypePropertyBridge d2r:property="core:middleName" d2r:column="MIDDLENAME"/>
                <d2r:DatatypePropertyBridge d2r:property="foaf:lastName" d2r:column="LASTNAME"/>
                <d2r:DatatypePropertyBridge d2r:property="vivo:preferredTitle" d2r:column="TITLE"/>
        </d2r:ClassMap>

</d2r:Map>   

Example 2:

<?xml version="1.0" encoding="UTF-8"?>
<d2r:Map xmlns:d2r="http://www.wiwiss.fu-berlin.de/suhl/bizer/D2RMap/0.1#" d2r:versionInfo="$Id: iswcMap.d2r,xml, v 0.1 2003/01/15 19:44:09 Chris Exp $">
	<d2r:ProcessorMessage d2r:outputFormat="RDF/XML"/>
	<d2r:DBConnection d2r:jdbcDriver="oracle.jdbc.driver.OracleDriver" 
		d2r:jdbcDSN="jdbc:oracle:thin:@ldap://***/***,cn=OracleContext,ou=services,o=***" 
		d2r:username="***" d2r:password="***"/>
	<d2r:Namespace d2r:prefix="owl" d2r:namespace="http://www.w3.org/2002/07/owl#"/>
	<d2r:Namespace d2r:prefix="rdf" d2r:namespace="http://www.w3.org/1999/02/22-rdf-syntax-ns#"/>
	<d2r:Namespace d2r:prefix="xsd" d2r:namespace="http://www.w3.org/2001/XMLSchema#"/>
	<d2r:Namespace d2r:prefix="rdfs" d2r:namespace="http://www.w3.org/2000/01/rdf-schema#"/>
	<d2r:Namespace d2r:prefix="core" d2r:namespace="http://vivoweb.org/ontology/core#"/>
	<d2r:Namespace d2r:prefix="foaf" d2r:namespace="http://xmlns.com/foaf/0.1/"/>
	<d2r:Namespace d2r:prefix="wcmc" d2r:namespace="http://weill.cornell.edu/vivo/ontology/wcmc#"/>
	<d2r:Namespace d2r:prefix="j.0" d2r:namespace="http://vitro.mannlib.cornell.edu/ns/wcmc/people/"/>
	<d2r:Namespace d2r:prefix="j.6" d2r:namespace="http://vitro.mannlib.cornell.edu/ns/vitro/0.7#"/>

	<!-- WCMC Consortium -->
	<d2r:ClassMap d2r:id="ConsortiumParent" d2r:type="core:University" 
		d2r:sql="select DB.ORG.ofa_institute_fk as OFA_INSTITUTE_FK, 
DB.ORG.vivo_organization_name as ORGANIZATION_NAME, 
DB.VIVO_ORGUNIT_PREFIX.vivo_orgunit_prefix_name as PREFIX_NAME, 
DB.VIVO_UNIT.vivo_unit_pk as UNIT_PK 
from DB.ORG 
inner join DB.VIVO_ORGUNIT_PREFIX on DB.ORG.vivo_orgunit_prefix_fk=DB.VIVO_ORGUNIT_PREFIX.vivo_orgunit_prefix_pk 
inner join DB.VIVO_UNIT on DB.VIVO_UNIT.vivo_organization_fk=DB.ORG.vivo_organization_pk 
where DB.ORG.vivo_organization_pk=90041" 
		d2r:groupBy="OFA_INSTITUTE_FK"  d2r:uriPattern="http://vivo.med.cornell.edu/individual/org-@<at:var at:name="OFA_INSTITUTE_FK" />@">
		<d2r:DatatypePropertyBridge d2r:property="rdfs:label" d2r:column="ORGANIZATION_NAME"/>
		<d2r:ObjectPropertyBridge d2r:property="core:hasSubOrganization" d2r:referredClass="ConsortiumChild" d2r:referredGroupBy="UNIT_PK"/>
	</d2r:ClassMap>
	
	<d2r:ClassMap d2r:id="ConsortiumChild" d2r:type="core:Consortium" 
		d2r:sql="select DB.VIVO_UNIT.vivo_unit_pk as UNIT_PK, 
DB.ORG.ofa_institute_fk as OFA_INSTITUTE_FK, 
DB.VIVO_UNIT.vivo_unit_name as UNIT_NAME, 
DB.VIVO_UNIT.description as OVERVIEW,
DB.VIVO_ORGUNIT_PREFIX.vivo_orgunit_prefix_name as PREFIX_NAME
from DB.VIVO_UNIT 
inner join DB.VIVO_ORGUNIT_PREFIX on DB.VIVO_UNIT.vivo_orgunit_prefix_fk=DB.VIVO_ORGUNIT_PREFIX.vivo_orgunit_prefix_pk 
inner join DB.ORG on DB.VIVO_UNIT.vivo_organization_fk=DB.ORG.vivo_organization_pk 
where DB.VIVO_ORGUNIT_PREFIX.vivo_orgunit_prefix_pk=13 and DB.ORG.vivo_organization_pk=90041" 
		d2r:groupBy="UNIT_PK"  d2r:uriPattern="http://vivo.med.cornell.edu/individual/org-u@<at:var at:name="UNIT_PK" />@">
		<d2r:DatatypePropertyBridge d2r:property="rdfs:label" d2r:column="UNIT_NAME"/>
		<d2r:DatatypePropertyBridge d2r:property="core:overview" d2r:column="OVERVIEW"/>
		<d2r:ObjectPropertyBridge d2r:property="core:subOrganizationWithin" d2r:referredClass="ConsortiumParent" d2r:referredGroupBy="OFA_INSTITUTE_FK"/>
	</d2r:ClassMap>

</d2r:Map>

-o [config file] - Record Handler configuration file path (Required)

Example Record Handler configuration file

This config file redirects any .rdf output to the directory XMLVault/JDBCRDF.

<?xml version="1.0" encoding="UTF-8"?>
<RecordHandler type="org.vivoweb.harvester.util.repo.TextFileRecordHandler">
        <Param name="fileDir">XMLVault/JDBCRDF</Param>
</RecordHandler>

-s [output file] - D2RMap output file name

The file name to use for any rdf output.

The directory for this file should be specified with the Record Handler config file's "fileDir" parameter, which is passed via the -o argument. In this above example, this is set to XMLVault/JDBCRDF.


-O [output override] - Output Override (Optional)

Override the RH_PARAM of output recordhandler.