Revision 36526
Added by Michele Artini over 9 years ago
| modules/dnet-node-services/trunk/src/main/java/eu/dnetlib/msro/worker/nodes/transform/GroovyUnaryFunction.java | ||
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package eu.dnetlib.msro.worker.nodes.transform; |
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import java.util.Map; |
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import com.google.common.base.Function; |
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public abstract class GroovyUnaryFunction implements Function<String, String> {
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private Map<String, String> params; |
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@Override |
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abstract public String apply(String input); |
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public Map<String, String> getParams() {
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return params; |
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} |
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public void setParams(final Map<String, String> params) {
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this.params = params; |
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} |
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} |
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| modules/dnet-node-services/trunk/src/main/java/eu/dnetlib/msro/worker/nodes/transform/ApplyXsltJobNode.java | ||
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| 29 | 29 |
protected String execute(final NodeToken token) throws Exception {
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@SuppressWarnings("unchecked")
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final ResultSet<String> inputRs = (ResultSet<String>) token.getEnv().getTransientAttribute(inputResultSetParam); |
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if (inputRs == null) { throw new ManagerServiceException("InputEprParam (" + inputResultSetParam + ") not found in ENV"); }
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if (inputRs == null) { throw new ManagerServiceException("InputResultSetParam (" + inputResultSetParam + ") not found in ENV"); }
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final Map<String, String> xsltParams = new HashMap<String, String>(); |
| 35 | 35 |
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| modules/dnet-node-services/trunk/src/main/java/eu/dnetlib/msro/worker/nodes/transform/CleanJobNode.java | ||
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| 32 | 32 |
protected String execute(final NodeToken token) throws Exception {
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@SuppressWarnings("unchecked")
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final ResultSet<String> inputRs = (ResultSet<String>) token.getEnv().getTransientAttribute(inputResultSetParam); |
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if (inputRs == null) { throw new ManagerServiceException("InputEprParam (" + inputResultSetParam + ") not found in ENV"); }
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if (inputRs == null) { throw new ManagerServiceException("InputResultSetParam (" + inputResultSetParam + ") not found in ENV"); }
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final CleaningRule rule = isClient.getResourceByCode(ruleId, CleaningRule.class); |
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| modules/dnet-node-services/trunk/src/main/java/eu/dnetlib/msro/worker/nodes/transform/GroovyJobNode.java | ||
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| 1 | 1 |
package eu.dnetlib.msro.worker.nodes.transform; |
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import java.io.IOException; |
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import java.util.Map; |
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import javax.annotation.Resource; |
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import javax.xml.ws.wsaddressing.W3CEndpointReference; |
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| 8 | 4 |
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import org.apache.commons.logging.Log; |
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import org.apache.commons.logging.LogFactory; |
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import org.springframework.beans.factory.annotation.Autowired; |
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import org.springframework.beans.factory.annotation.Required; |
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import com.google.common.collect.Maps; |
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import com.googlecode.sarasvati.Arc; |
| 15 | 9 |
import com.googlecode.sarasvati.NodeToken; |
| 16 | 10 |
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
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import eu.dnetlib.enabling.resultset.MappedResultSetFactory;
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import eu.dnetlib.enabling.resultset.client.utils.EPRUtils;
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import eu.dnetlib.msro.rmi.ManagerServiceException;
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import eu.dnetlib.common.services.locators.DnetServiceLocator;
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import eu.dnetlib.data.resultSet.ResultSetFactory; |
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import eu.dnetlib.data.resultSet.groovy.GroovyFactory;
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import eu.dnetlib.enabling.datastructures.GroovyRule;
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import eu.dnetlib.enabling.is.client.InformationServiceClient;
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| 22 | 16 |
import eu.dnetlib.msro.worker.nodes.SimpleJobNode; |
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import groovy.lang.GroovyShell;
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import groovy.util.GroovyScriptEngine;
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import eu.dnetlib.rmi.objects.resultSet.ResultSet;
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import eu.dnetlib.rmi.soap.exceptions.ManagerServiceException;
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| 26 | 20 |
public class GroovyJobNode extends SimpleJobNode {
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private static final Log log = LogFactory.getLog(GroovyJobNode.class); |
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private String inputResultSetParam; |
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private String outputResultSetParam; |
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private String ruleId; |
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/** |
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* used to transform the records using Groovy. |
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*/ |
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@Autowired |
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private InformationServiceClient isClient; |
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private MappedResultSetFactory mappedResultSetFactory; |
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@Autowired |
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private ResultSetFactory resultSetFactory; |
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private String inputEprParam; |
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private String outputEprParam; |
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private String transformationRuleId; |
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// private String groovyParams; |
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private GroovyFactory groovyFactory; |
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@Resource |
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private DnetServiceLocator serviceLocator; |
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private Map<String, String> retrieveGroovyParameter() {
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Map<String, String> out = Maps.newHashMap(); |
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String query = "for $x in collection('/db/DRIVER/GroovyProcessingDSResource/GroovyProcessingDSResourceType')"
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+ "where $x[.//RESOURCE_IDENTIFIER/@value='" + transformationRuleId + "']" |
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+ "return concat($x//GROOVY_CLASSPATH/text(),':::',$x//GROOVY_DNETCLASS/text())"; |
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try {
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String result = serviceLocator.getService(ISLookUpService.class).quickSearchProfile(query).get(0); |
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if (result == null) { return null; }
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String[] data = result.trim().split(":::");
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if (data.length == 2) {
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out.put("classpath", data[0]);
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out.put("mainClass", data[1]);
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} |
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return out; |
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} catch (Exception e) {
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log.error(e); |
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return null; |
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} |
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} |
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@Override |
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protected String execute(final NodeToken token) throws Exception {
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final String inputEprString = token.getEnv().getAttribute(inputEprParam); |
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if (inputEprString == null || inputEprString.isEmpty()) { throw new ManagerServiceException("InputEprParam (" + inputEprParam + ") not found in ENV"); }
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final W3CEndpointReference inputEpr = new EPRUtils().getEpr(inputEprString); |
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String groovyClasspath, groovyDnetClass; |
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Map<String, String> prop = retrieveGroovyParameter(); |
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groovyClasspath = prop.get("classpath");
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groovyDnetClass = prop.get("mainClass");
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W3CEndpointReference epr = transformGroovy(inputEpr, groovyClasspath, groovyDnetClass, parseJsonParameters(token)); |
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token.getEnv().setAttribute(outputEprParam, epr.toString()); |
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return Arc.DEFAULT_ARC; |
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} |
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@SuppressWarnings("unchecked")
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final ResultSet<String> inputRs = (ResultSet<String>) token.getEnv().getTransientAttribute(inputResultSetParam); |
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if (inputRs == null) { throw new ManagerServiceException("InputResultSetParam (" + inputResultSetParam + ") not found in ENV"); }
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private W3CEndpointReference transformGroovy(final W3CEndpointReference source, |
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final String groovyClasspath, |
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final String groovyDnetClass, |
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final Map<String, String> params) throws ClassNotFoundException, IOException {
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final GroovyRule rule = isClient.getResourceByCode(ruleId, GroovyRule.class); |
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GroovyScriptEngine gse = new GroovyScriptEngine(groovyClasspath); |
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gse.getGroovyClassLoader().loadClass(groovyDnetClass); |
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log.info("***********************************************");
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log.info("Loaded Groovy classes:");
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for (Class<?> c : gse.getGroovyClassLoader().getLoadedClasses()) {
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log.info(c.getCanonicalName()); |
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} |
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log.info("***********************************************");
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GroovyShell groovyShell = new GroovyShell(gse.getGroovyClassLoader()); |
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final ResultSet<String> outputRs = resultSetFactory.transform(inputRs, groovyFactory.createGroovyFunction(rule, null)); |
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Object go = groovyShell.evaluate("new " + groovyDnetClass + "()");
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if (go instanceof GroovyUnaryFunction) {
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GroovyUnaryFunction groovyUnaryFunction = (GroovyUnaryFunction) go; |
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if (params != null) {
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groovyUnaryFunction.setParams(params); |
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} |
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return mappedResultSetFactory.createMappedResultSet(source, groovyUnaryFunction); |
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} else {
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throw new RuntimeException("Groovy object " + go + " is not supported");
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} |
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token.getEnv().setAttribute(outputResultSetParam, outputRs.toString()); |
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return Arc.DEFAULT_ARC; |
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} |
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public MappedResultSetFactory getMappedResultSetFactory() {
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return mappedResultSetFactory;
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public String getInputResultSetParam() {
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return inputResultSetParam;
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} |
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@Required |
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public void setMappedResultSetFactory(final MappedResultSetFactory mappedResultSetFactory) {
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this.mappedResultSetFactory = mappedResultSetFactory; |
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public void setInputResultSetParam(final String inputResultSetParam) {
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this.inputResultSetParam = inputResultSetParam; |
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} |
| 115 | 59 |
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public String getInputEprParam() {
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return inputEprParam;
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public String getOutputResultSetParam() {
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return outputResultSetParam;
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} |
| 119 | 63 |
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public void setInputEprParam(final String inputEprParam) {
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this.inputEprParam = inputEprParam;
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public void setOutputResultSetParam(final String outputResultSetParam) {
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this.outputResultSetParam = outputResultSetParam;
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} |
| 123 | 67 |
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public String getOutputEprParam() {
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return outputEprParam;
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public String getRuleId() {
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return ruleId;
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} |
| 127 | 71 |
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public void setOutputEprParam(final String outputEprParam) {
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this.outputEprParam = outputEprParam;
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public void setRuleId(final String ruleId) {
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this.ruleId = ruleId;
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} |
| 131 | 75 |
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public String getTransformationRuleId() {
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return transformationRuleId;
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public GroovyFactory getGroovyFactory() {
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return groovyFactory;
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} |
| 135 | 79 |
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public void setTransformationRuleId(final String transformationRuleId) {
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this.transformationRuleId = transformationRuleId; |
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@Required |
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public void setGroovyFactory(final GroovyFactory groovyFactory) {
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this.groovyFactory = groovyFactory; |
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} |
| 139 | 84 |
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| 140 | 85 |
} |
| modules/dnet-node-services/trunk/src/main/java/eu/dnetlib/msro/worker/nodes/transform/MdBuilderJobNode.java | ||
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| 1 | 1 |
package eu.dnetlib.msro.worker.nodes.transform; |
| 2 | 2 |
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import java.io.IOException; |
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import java.net.URLEncoder; |
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import java.util.List; |
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import javax.xml.ws.wsaddressing.W3CEndpointReference; |
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import org.antlr.stringtemplate.StringTemplate; |
| 10 | 6 |
import org.apache.commons.io.IOUtils; |
| 11 | 7 |
import org.apache.commons.logging.Log; |
| 12 | 8 |
import org.apache.commons.logging.LogFactory; |
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import org.springframework.beans.factory.annotation.Autowired; |
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| 13 | 10 |
import org.springframework.beans.factory.annotation.Required; |
| 14 | 11 |
import org.springframework.core.io.Resource; |
| 15 | 12 |
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import com.googlecode.sarasvati.Arc; |
| 17 | 14 |
import com.googlecode.sarasvati.NodeToken; |
| 18 | 15 |
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; |
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; |
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import eu.dnetlib.enabling.resultset.XSLTMappedResultSetFactory; |
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import eu.dnetlib.enabling.resultset.client.utils.EPRUtils; |
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import eu.dnetlib.msro.rmi.ManagerServiceException; |
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import eu.dnetlib.common.services.locators.DnetServiceLocator; |
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import eu.dnetlib.data.resultSet.ResultSetFactory; |
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import eu.dnetlib.enabling.datastructures.Datasource; |
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import eu.dnetlib.miscutils.ApplyXslt; |
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import eu.dnetlib.msro.worker.nodes.SimpleJobNode; |
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import eu.dnetlib.rmi.objects.dsmanager.IfaceDesc; |
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import eu.dnetlib.rmi.objects.resultSet.ResultSet; |
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import eu.dnetlib.rmi.soap.DatasourceManagerService; |
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import eu.dnetlib.rmi.soap.exceptions.ManagerServiceException; |
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| 26 | 25 |
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| 27 | 26 |
public class MdBuilderJobNode extends SimpleJobNode {
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| 28 | 27 |
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| ... | ... | |
| 30 | 29 |
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| 31 | 30 |
private Resource mdBuilderTemplateXslt; |
| 32 | 31 |
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private String inputEprParam;
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private String outputEprParam;
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private String inputResultSetParam;
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private String outputResultSetParam;
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| 35 | 34 |
private String datasourceId; |
| 36 | 35 |
private String datasourceInterface; |
| 37 | 36 |
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private XSLTMappedResultSetFactory xsltMappedResultSetFactory; |
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@Autowired |
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private ResultSetFactory resultSetFactory; |
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| 39 | 39 |
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| 40 | 40 |
@javax.annotation.Resource |
| 41 | 41 |
private DnetServiceLocator serviceLocator; |
| 42 | 42 |
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| 43 | 43 |
@Override |
| 44 | 44 |
protected String execute(final NodeToken token) throws ManagerServiceException {
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final String inputEpr = token.getEnv().getAttribute(inputEprParam); |
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try {
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@SuppressWarnings("unchecked")
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final ResultSet<String> inputRs = (ResultSet<String>) token.getEnv().getTransientAttribute(inputResultSetParam); |
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| 46 | 48 |
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if ((inputEpr == null) || inputEpr.isEmpty()) throw new ManagerServiceException("InputEprParam (" + inputEprParam + ") not found in ENV");
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StringTemplate st = null; |
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try {
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final Datasource ds = serviceLocator.getService(DatasourceManagerService.class).getDatasource(datasourceId); |
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final IfaceDesc ifc = findIface(ds, datasourceInterface); |
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if (inputRs == null) { throw new ManagerServiceException("inputResultSetParam (" + inputResultSetParam + ") not found in ENV"); }
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StringTemplate st = null; |
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| 50 | 55 |
st = new StringTemplate(IOUtils.toString(getMdBuilderTemplateXslt().getInputStream())); |
| 51 | 56 |
st.setAttribute("datasourceId", datasourceId);
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st.setAttribute("xpath", getMetadataIdentifierPath());
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st.setAttribute("baseurl", URLEncoder.encode(getBaseUrl(), "UTF-8"));
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st.setAttribute("metadatanamespace", getMetadataNamespace());
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st.setAttribute("xpath", ifc.getExtraFields().get("metadata_identifier_path"));
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st.setAttribute("baseurl", URLEncoder.encode(ifc.getBaseUrl(), "UTF-8"));
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st.setAttribute("metadatanamespace", getMetadataNamespace(ifc.getAccessParams().get("format")));
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| 55 | 60 |
|
| 56 | 61 |
/* |
| 57 | 62 |
* If namespacePrefix has been already pushed to env by some custom JobNode e.g. ObtainOpenaireDataSourceParamsJobNode then push |
| ... | ... | |
| 61 | 66 |
if (token.getEnv().hasAttribute("namespacePrefix")) {
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| 62 | 67 |
st.setAttribute("namespacePrefix", token.getEnv().getAttribute("namespacePrefix"));
|
| 63 | 68 |
} else {
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List<String> namespacePrefix; |
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String xQuery = "/*[.//RESOURCE_IDENTIFIER/@value='" + datasourceId + "']//EXTRA_FIELDS/FIELD/value[../key='NamespacePrefix']/string()"; |
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namespacePrefix = serviceLocator.getService(ISLookUpService.class).quickSearchProfile(xQuery); |
|
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if (namespacePrefix.size() != 0) {
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st.setAttribute("namespacePrefix", namespacePrefix.get(0));
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| 69 |
} else {
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| 70 |
xQuery = "/*[.//RESOURCE_IDENTIFIER/@value='" + datasourceId + "']//DATASOURCE_ORIGINAL_ID/string()"; |
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| 71 |
namespacePrefix = serviceLocator.getService(ISLookUpService.class).quickSearchProfile(xQuery); |
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| 72 |
if (namespacePrefix.size() != 0) {
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| 73 |
st.setAttribute("namespacePrefix", namespacePrefix.get(0));
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| 74 |
} else {
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| 75 |
st.setAttribute("namespacePrefix", datasourceId);
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| 76 |
} |
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| 77 |
} |
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| 69 |
st.setAttribute("namespacePrefix", ds.getNamespacePrefix());
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| 78 | 70 |
} |
| 79 | 71 |
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| 80 |
final W3CEndpointReference epr = xsltMappedResultSetFactory.createMappedResultSet(new EPRUtils().getEpr(inputEpr), st.toString());
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| 72 |
final ResultSet<String> rs = resultSetFactory.transform(inputRs, new ApplyXslt(st.toString()));
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| 81 | 73 |
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| 82 |
token.getEnv().setAttribute(outputEprParam, epr.toString());
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| 74 |
token.getEnv().setTransientAttribute(outputResultSetParam, rs);
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| 83 | 75 |
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| 84 | 76 |
return Arc.DEFAULT_ARC; |
| 85 |
} catch (ISLookUpException e) {
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| 86 |
throw new ManagerServiceException("Error while initializing mdBuilder template (" + getMdBuilderTemplateXslt().getFilename() + ") for datasource "
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| 87 |
+ datasourceId, e); |
|
| 88 |
} catch (IOException e) {
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| 89 |
throw new ManagerServiceException("Error parsing template: " + getMdBuilderTemplateXslt().getFilename(), e);
|
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| 90 | 77 |
} catch (Exception e) {
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| 91 |
log.error(st.toString()); |
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| 92 |
throw new ManagerServiceException(e); |
|
| 78 |
final String msg = "Error creating mdBuilder (" + getMdBuilderTemplateXslt().getFilename() + ") for datasource " + datasourceId;
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| 79 |
log.error(msg, e); |
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| 80 |
throw new ManagerServiceException(msg, e); |
|
| 93 | 81 |
} |
| 94 | 82 |
} |
| 95 | 83 |
|
| 96 |
private String getBaseUrl() throws ISLookUpException {
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| 97 |
String xQuery = "/*[.//RESOURCE_IDENTIFIER/@value='{datasourceId}']//INTERFACE[@id='{interfaceId}']//BASE_URL/string()";
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| 98 |
xQuery = xQuery.replace("{interfaceId}", datasourceInterface).replace("{datasourceId}", datasourceId);
|
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| 99 |
return serviceLocator.getService(ISLookUpService.class).getResourceProfileByQuery(xQuery); |
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| 84 |
private IfaceDesc findIface(final Datasource ds, final String ifaceId) throws ManagerServiceException {
|
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| 85 |
for (IfaceDesc ifc : ds.getInterfaces()) {
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| 86 |
if (ifaceId.equals(ifc.getId())) { return ifc; }
|
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| 87 |
} |
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| 88 |
throw new ManagerServiceException("Missing ds interface: " + ifaceId);
|
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| 100 | 89 |
} |
| 101 | 90 |
|
| 102 |
private String getMetadataIdentifierPath() throws ISLookUpException {
|
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| 103 |
String xQuery = "for $x in collection('/db/DRIVER/RepositoryServiceResources/RepositoryServiceResourceType') "
|
|
| 104 |
+ "return $x//INTERFACE[@id='{interfaceId}']/INTERFACE_EXTRA_FIELD[@name='metadata_identifier_path']/string()";
|
|
| 105 |
xQuery = xQuery.replace("{interfaceId}", datasourceInterface);
|
|
| 106 |
return serviceLocator.getService(ISLookUpService.class).getResourceProfileByQuery(xQuery); |
|
| 107 |
} |
|
| 91 |
private String getMetadataNamespace(final String format) {
|
|
| 92 |
// TODO |
|
| 108 | 93 |
|
| 109 |
private String getMetadataNamespace() {
|
|
| 110 |
try {
|
|
| 111 |
String xQuery = "let $x := /*[.//RESOURCE_IDENTIFIER/@value='{datasourceId}']//INTERFACE[@id='{interfaceId}']/ACCESS_PROTOCOL/@format/string() "
|
|
| 112 |
+ "return /*[.//RESOURCE_TYPE/@value='MetadataFormatDSResourceType']//METADATAFORMAT[@Prefix=$x]/@NameSpace/string()"; |
|
| 113 |
xQuery = xQuery.replace("{interfaceId}", datasourceInterface).replace("{datasourceId}", datasourceId);
|
|
| 114 |
return serviceLocator.getService(ISLookUpService.class).getResourceProfileByQuery(xQuery); |
|
| 115 |
} catch (ISLookUpException e) {
|
|
| 116 |
log.error("The interface is not OAI or the format is not found in the MetadataFormatDSResourceType, thus metadata format in the <about> section "
|
|
| 117 |
+ "cannot managed here and it will be leaved empty (for the time being)"); |
|
| 118 |
return ""; |
|
| 119 |
} |
|
| 94 |
return "http://aaa"; |
|
| 120 | 95 |
} |
| 121 | 96 |
|
| 122 |
public String getInputEprParam() {
|
|
| 123 |
return inputEprParam;
|
|
| 97 |
public String getInputResultSetParam() {
|
|
| 98 |
return inputResultSetParam;
|
|
| 124 | 99 |
} |
| 125 | 100 |
|
| 126 |
public void setInputEprParam(final String inputEprParam) {
|
|
| 127 |
this.inputEprParam = inputEprParam;
|
|
| 101 |
public void setInputResultSetParam(final String inputResultSetParam) {
|
|
| 102 |
this.inputResultSetParam = inputResultSetParam;
|
|
| 128 | 103 |
} |
| 129 | 104 |
|
| 130 |
public String getOutputEprParam() {
|
|
| 131 |
return outputEprParam;
|
|
| 105 |
public String getOutputResultSetParam() {
|
|
| 106 |
return outputResultSetParam;
|
|
| 132 | 107 |
} |
| 133 | 108 |
|
| 134 |
public void setOutputEprParam(final String outputEprParam) {
|
|
| 135 |
this.outputEprParam = outputEprParam;
|
|
| 109 |
public void setOutputResultSetParam(final String outputResultSetParam) {
|
|
| 110 |
this.outputResultSetParam = outputResultSetParam;
|
|
| 136 | 111 |
} |
| 137 | 112 |
|
| 138 |
public XSLTMappedResultSetFactory getXsltMappedResultSetFactory() {
|
|
| 139 |
return xsltMappedResultSetFactory; |
|
| 140 |
} |
|
| 141 |
|
|
| 142 | 113 |
public String getDatasourceId() {
|
| 143 | 114 |
return datasourceId; |
| 144 | 115 |
} |
| ... | ... | |
| 155 | 126 |
this.datasourceInterface = datasourceInterface; |
| 156 | 127 |
} |
| 157 | 128 |
|
| 158 |
@Required |
|
| 159 |
public void setXsltMappedResultSetFactory(final XSLTMappedResultSetFactory xsltMappedResultSetFactory) {
|
|
| 160 |
this.xsltMappedResultSetFactory = xsltMappedResultSetFactory; |
|
| 161 |
} |
|
| 162 |
|
|
| 163 | 129 |
public Resource getMdBuilderTemplateXslt() {
|
| 164 | 130 |
return mdBuilderTemplateXslt; |
| 165 | 131 |
} |
| modules/dnet-node-services/trunk/src/main/java/eu/dnetlib/msro/worker/nodes/transform/TransformJobNode.java | ||
|---|---|---|
| 32 | 32 |
protected String execute(final NodeToken token) throws Exception {
|
| 33 | 33 |
@SuppressWarnings("unchecked")
|
| 34 | 34 |
final ResultSet<String> inputRs = (ResultSet<String>) token.getEnv().getTransientAttribute(inputResultSetParam); |
| 35 |
if (inputRs == null) { throw new ManagerServiceException("InputEprParam (" + inputResultSetParam + ") not found in ENV"); }
|
|
| 35 |
if (inputRs == null) { throw new ManagerServiceException("InputResultSetParam (" + inputResultSetParam + ") not found in ENV"); }
|
|
| 36 | 36 |
|
| 37 | 37 |
final TransformationRule rule = isClient.getResourceByCode(ruleId, TransformationRule.class); |
| 38 | 38 |
|
Also available in: Unified diff
Transformation wf nodes