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Overview

This class enables translation of XML into RDF using a XSL File. The main intent of this class is that the user will define the translation from the target data source's schema into XML/RDF that follows the VIVO ontology's schema. This means that without recompiling users can create Harvesting methods from various XML sources using different XSL files for each.

The author of the XSL file needs to have knowledge of the incoming data and the ontology of the vivo being harvested into. If there is an ontology specialist available they should investigate the post translated RDF/XML to be certain that the data is being placed in the proper format.

This class uses Saxon's implementation of an xsl translator as it translates between RecordHandlers.

Parameters

Short Option

Long Option

Parameter Value Map

Description

Required

i

input

CONFIG_FILE

config file for input record handler

true

I

inputOverride

RH_PARAM

override the RH_PARAM of input record handler using VALUE

false

o

output

CONFIG_FILE

config file for output record handler

true

O

outputOverride

RH_PARAM

override the RH_PARAM of output record handler using VALUE

false

x

xslFile

XSL_FILE

the stylesheet to use for translating records from input to output

true

f

force

 

force translation of all input records, even if previously processed

false

Variables

Name

Type

Visibility

Description

translationString

String

private

The translation xsl is the map that will reconstruct our input stream's document into the appropriate format

inStore

RecordHandler

protected

record handler for incoming records

outStore

RecordHandler

protected

record handler for storing records

Translation File

For each Translation File there will be a Detail Design of how the XSLT is designed to translate the original schema into the VIVO ontology's schema. The main change, aside from the VIVO ontology, is the format of XML/RDF. Each entity, including sub entities, is flattened. Links exist within each entity to the other entities its related to.

Flowchart

The XSLTranslator is an integral part of the standard JDBC fetch.

Tutorials on XSLT

Example XSLT Designs

Execution

Define Alias

XSLTranslator="java $OPTS Xms$MIN_MEM -Xmx$MAX_MEM -Dharvester-task=$HARVESTER_TASK -Dprocess-task=XSLTranslator -cp bin/harvester$VERSION.jar:bin/dependency/* org.vivoweb.harvester.translate.XSLTranslator"

Invocation

$XSLTranslator -i config/recordHandlers/PeopleSoft-Merge.xml -o config/recordHandlers/PeopleSoft-RDF.xml -x config/datamaps/PeopleSoftToVivo.xsl

Methods

setTranslation

Loads the file into memory as an attempt to speed up translations.

  1. create ByteArrayOutputStream
  2. copy the InputStream into ByteOutputStream
  3. create string from ByteOutputStream

execute

The execute method serves as a wrapper around the actual xml translation method.

  1. set translated and passed counters to zero
  2. loop through all the records in inStore
    1. create a ByteArrayOutputStream
    2. execute xmlTranslate with:
      1. a stream based off the loop's record
      2. a stream based off translationString
      3. the new ByteArrayOutputStream
    3. add translated record to outStore.

xmlTranslate

This Method uses the Javax xml transform factory to apply the xsl

  1. create javax.xml.transform.stream.StreamResult from the OutputStream
  2. create javax.xml.transform.Source from the InputStream
  3. create javax.xml.transform.Source from the translationStream (of type InputStream)
  4. use javax.xml.transform.TransformerFactory to apply the transform on the input to produce the output.