Revision 48027
Added by Alessia Bardi almost 7 years ago
| modules/dnet-openaireplus-workflows/trunk/src/test/java/leu/dnetlib/msro/openaireplus/workflows/nodes/claims/ApplyClaimRelsJobNodeTest.java | ||
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package leu.dnetlib.msro.openaireplus.workflows.nodes.claims; |
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import com.google.protobuf.InvalidProtocolBufferException; |
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import eu.dnetlib.data.proto.OafProtos.Oaf; |
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import eu.dnetlib.msro.openaireplus.workflows.nodes.claims.ApplyClaimRelsJobNode; |
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import eu.dnetlib.msro.rmi.MSROException; |
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import org.junit.Test; |
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import org.postgresql.util.Base64; |
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/** |
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* Created by Alessia Bardi on 26/06/2017. |
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* |
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* @author Alessia Bardi |
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*/ |
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public class ApplyClaimRelsJobNodeTest {
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private ApplyClaimRelsJobNode applyClaims = new ApplyClaimRelsJobNode(); |
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@Test |
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public void testGetValue() throws MSROException, InvalidProtocolBufferException {
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String sourceId = "40|corda_______::9f752db0b5ec9ca23673ca7f4cb0808e"; |
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String semantics = "resultProject_outcome_produces"; |
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String targetId = "50|userclaim___::6a8f649d968e734a6733c23a351c1859"; |
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long time = System.currentTimeMillis(); |
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//final String sourceId, final String semantics, final String targetId, final long timestamp |
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String res = applyClaims.getValue(sourceId, semantics, targetId, time); |
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Oaf.Builder builder = Oaf.newBuilder().mergeFrom(Base64.decode(res)); |
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System.out.println(builder.build().toString()); |
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} |
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@Test(expected = MSROException.class) |
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public void testGetValueErrSem() throws MSROException {
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String sourceId = "40|corda_______::9f752db0b5ec9ca23673ca7f4cb0808e"; |
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String semantics = "produces"; |
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String targetId = "50|userclaim___::6a8f649d968e734a6733c23a351c1859"; |
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long time = System.currentTimeMillis(); |
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//final String sourceId, final String semantics, final String targetId, final long timestamp |
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String res = applyClaims.getValue(sourceId, semantics, targetId, time); |
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System.out.println(res); |
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} |
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} |
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| modules/dnet-openaireplus-workflows/trunk/src/test/java/eu/dnetlib/msro/openaireplus/workflows/nodes/claims/ApplyClaimRelsJobNodeTest.java | ||
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package eu.dnetlib.msro.openaireplus.workflows.nodes.claims; |
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import com.google.protobuf.InvalidProtocolBufferException; |
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import eu.dnetlib.data.proto.OafProtos.Oaf; |
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import eu.dnetlib.msro.rmi.MSROException; |
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import org.junit.Test; |
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import org.postgresql.util.Base64; |
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/** |
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* Created by Alessia Bardi on 26/06/2017. |
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* |
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* @author Alessia Bardi |
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*/ |
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public class ApplyClaimRelsJobNodeTest {
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private ApplyClaimRelsJobNode applyClaims = new ApplyClaimRelsJobNode(); |
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@Test |
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public void testGetValue() throws MSROException, InvalidProtocolBufferException {
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String sourceId = "40|corda_______::9f752db0b5ec9ca23673ca7f4cb0808e"; |
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String semantics = "resultProject_outcome_produces"; |
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String targetId = "50|userclaim___::6a8f649d968e734a6733c23a351c1859"; |
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System.out.println(getValue(sourceId, semantics, targetId)); |
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} |
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@Test(expected = MSROException.class) |
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public void testGetValueErrSem() throws MSROException, InvalidProtocolBufferException {
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String sourceId = "40|corda_______::9f752db0b5ec9ca23673ca7f4cb0808e"; |
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String semantics = "produces"; |
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String targetId = "50|userclaim___::6a8f649d968e734a6733c23a351c1859"; |
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getValue(sourceId, semantics, targetId); |
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} |
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private String getValue(final String rowKey, final String semantics, final String targetId) throws MSROException, InvalidProtocolBufferException {
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long time = System.currentTimeMillis(); |
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//final String sourceId, final String semantics, final String targetId, final long timestamp |
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String res = applyClaims.getValue(rowKey, semantics, targetId, time); |
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Oaf.Builder builder = Oaf.newBuilder().mergeFrom(Base64.decode(res)); |
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return builder.build().toString(); |
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} |
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} |
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| modules/dnet-openaireplus-workflows/trunk/src/test/java/eu/dnetlib/msro/openaireplus/workflows/nodes/claims/ApplyClaimUpdatesJobNodeTest.java | ||
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package eu.dnetlib.msro.openaireplus.workflows.nodes.claims; |
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import com.google.protobuf.InvalidProtocolBufferException; |
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import eu.dnetlib.data.proto.OafProtos.Oaf; |
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import eu.dnetlib.msro.rmi.MSROException; |
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import org.junit.Test; |
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import org.postgresql.util.Base64; |
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/** |
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* Created by Alessia Bardi on 26/06/2017. |
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* |
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* @author Alessia Bardi |
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*/ |
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public class ApplyClaimUpdatesJobNodeTest {
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private ApplyClaimUpdatesJobNode applyClaims = new ApplyClaimUpdatesJobNode(); |
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@Test |
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public void testGetValueEGI() throws MSROException, InvalidProtocolBufferException {
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String context = "egi"; |
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String rowkey = "50|userclaim___::6a8f649d968e734a6733c23a351c1859"; |
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System.out.println(getValue(context, rowkey)); |
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} |
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@Test |
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public void testGetValueEGILongId() throws MSROException, InvalidProtocolBufferException {
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String context = "egi::classification::natsc::earths::other"; |
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String rowkey = "50|userclaim___::6a8f649d968e734a6733c23a351c1859"; |
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System.out.println(getValue(context, rowkey)); |
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} |
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private String getValue(final String context, final String rowkey) throws MSROException, InvalidProtocolBufferException {
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String semantics = "relatedTo"; |
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long time = System.currentTimeMillis(); |
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//final String sourceId, final String semantics, final String targetId, final long timestamp |
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String res = applyClaims.getValue(context, semantics, rowkey, time); |
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Oaf.Builder builder = Oaf.newBuilder().mergeFrom(Base64.decode(res)); |
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return builder.build().toString(); |
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} |
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} |
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| modules/dnet-openaireplus-workflows/trunk/src/main/java/eu/dnetlib/msro/openaireplus/workflows/nodes/claims/AbstractClaimsToHBASE.java | ||
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package eu.dnetlib.msro.openaireplus.workflows.nodes.claims; |
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import eu.dnetlib.data.mapreduce.util.OafRowKeyDecoder; |
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import eu.dnetlib.data.proto.FieldTypeProtos.DataInfo; |
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import eu.dnetlib.data.proto.FieldTypeProtos.Qualifier; |
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import eu.dnetlib.data.transform.xml.AbstractDNetXsltFunctions; |
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import eu.dnetlib.enabling.locators.UniqueServiceLocator; |
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import eu.dnetlib.msro.workflows.nodes.ProgressJobNode; |
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import eu.dnetlib.msro.workflows.nodes.SimpleJobNode; |
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import eu.dnetlib.msro.workflows.util.ProgressProvider; |
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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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/** |
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* Created by Alessia Bardi on 28/06/2017. |
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* |
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* @author Alessia Bardi |
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*/ |
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public abstract class AbstractClaimsToHBASE extends SimpleJobNode implements ProgressJobNode {
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private static final Log log = LogFactory.getLog(AbstractClaimsToHBASE.class); |
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private String sql; |
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private String countQuery; |
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private int total = 0; |
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private int processed = 0; |
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private String clusterName; |
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private String tableName; |
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@Autowired |
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private UniqueServiceLocator serviceLocator; |
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@Autowired |
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private ClaimDatabaseUtils claimDatabaseUtils; |
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@Override |
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public ProgressProvider getProgressProvider() {
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return new ProgressProvider() {
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@Override |
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public boolean isInaccurate() {
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return false; |
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} |
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@Override |
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public int getTotalValue() {
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return total; |
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} |
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@Override |
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public int getCurrentValue() {
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return processed; |
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} |
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}; |
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} |
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protected String getOpenAIREType(final String type){
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switch(type){
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case "publication": |
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case "dataset": |
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return "result"; |
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default: |
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return type; |
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} |
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} |
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protected String getFullId(final String type, final String id) {
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final String fullId = AbstractDNetXsltFunctions.oafSimpleId(type, id); |
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return OafRowKeyDecoder.decode(fullId).getKey(); |
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} |
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protected static DataInfo getDataInfo(){
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return DataInfo.newBuilder().setTrust("0.91").setInferred(false)
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.setProvenanceaction( |
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Qualifier.newBuilder() |
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.setClassid("user:claim")
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.setClassname("user:claim")
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.setSchemeid("dnet:provenanceActions")
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.setSchemename("dnet:provenanceActions")).build();
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} |
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public String getSql() {
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return sql; |
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} |
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public void setSql(final String sql) {
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this.sql = sql; |
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} |
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public String getCountQuery() {
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return countQuery; |
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} |
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public void setCountQuery(final String countQuery) {
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this.countQuery = countQuery; |
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} |
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public int getTotal() {
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return total; |
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} |
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public void setTotal(final int total) {
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this.total = total; |
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} |
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public int getProcessed() {
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return processed; |
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} |
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public void setProcessed(final int processed) {
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this.processed = processed; |
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} |
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public void incrementProcessed(){
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processed++; |
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} |
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public String getClusterName() {
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return clusterName; |
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} |
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public void setClusterName(final String clusterName) {
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this.clusterName = clusterName; |
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} |
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public String getTableName() {
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return tableName; |
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} |
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public void setTableName(final String tableName) {
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this.tableName = tableName; |
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} |
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public UniqueServiceLocator getServiceLocator() {
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return serviceLocator; |
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} |
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public void setServiceLocator(final UniqueServiceLocator serviceLocator) {
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this.serviceLocator = serviceLocator; |
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} |
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public ClaimDatabaseUtils getClaimDatabaseUtils() {
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return claimDatabaseUtils; |
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} |
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public void setClaimDatabaseUtils(final ClaimDatabaseUtils claimDatabaseUtils) {
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this.claimDatabaseUtils = claimDatabaseUtils; |
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} |
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} |
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| modules/dnet-openaireplus-workflows/trunk/src/main/java/eu/dnetlib/msro/openaireplus/workflows/nodes/claims/ApplyClaimRelsJobNode.java | ||
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import com.googlecode.sarasvati.Arc; |
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import com.googlecode.sarasvati.NodeToken; |
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import eu.dnetlib.data.hadoop.rmi.HadoopService; |
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import eu.dnetlib.data.mapreduce.util.OafRowKeyDecoder; |
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import eu.dnetlib.data.proto.FieldTypeProtos.DataInfo; |
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import eu.dnetlib.data.proto.FieldTypeProtos.Qualifier; |
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import eu.dnetlib.data.proto.KindProtos.Kind; |
| ... | ... | |
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import eu.dnetlib.data.proto.ResultProjectProtos.ResultProject.Outcome; |
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import eu.dnetlib.data.proto.ResultResultProtos.ResultResult; |
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import eu.dnetlib.data.proto.ResultResultProtos.ResultResult.PublicationDataset; |
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import eu.dnetlib.data.transform.xml.AbstractDNetXsltFunctions; |
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import eu.dnetlib.enabling.locators.UniqueServiceLocator; |
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import eu.dnetlib.msro.rmi.MSROException; |
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import eu.dnetlib.msro.workflows.nodes.ProgressJobNode; |
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import eu.dnetlib.msro.workflows.nodes.SimpleJobNode; |
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import eu.dnetlib.msro.workflows.util.ProgressProvider; |
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import eu.dnetlib.utils.ontologies.OntologyLoader; |
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import org.apache.commons.codec.binary.Base64; |
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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.apache.hadoop.util.StringUtils; |
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import org.springframework.beans.factory.annotation.Autowired; |
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/** |
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* Created by alessia on 23/10/15. |
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*/ |
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public class ApplyClaimRelsJobNode extends SimpleJobNode implements ProgressJobNode {
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public class ApplyClaimRelsJobNode extends AbstractClaimsToHBASE {
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private static final Log log = LogFactory.getLog(ApplyClaimRelsJobNode.class); |
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private final String SEPARATOR = "_"; |
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@Autowired |
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private UniqueServiceLocator serviceLocator; |
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@Autowired |
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private ClaimDatabaseUtils claimDatabaseUtils; |
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private String sql; |
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private String countQuery; |
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private int total = 0; |
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private int processed = 0; |
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private String clusterName; |
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private String tableName; |
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// private String fetchSqlAsText(final String path) throws IOException {
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// return IOUtils.toString(getClass().getResourceAsStream(path)); |
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// } |
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@Override |
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protected String execute(NodeToken token) throws Exception {
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//TODO: use claim.claim_date from the claim db |
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long timestamp = System.currentTimeMillis(); |
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total = this.claimDatabaseUtils.count(countQuery);
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List<Claim> claimRels = this.claimDatabaseUtils.query(sql);
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setTotal(getClaimDatabaseUtils().count(getCountQuery()));
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List<Claim> claimRels = getClaimDatabaseUtils().query(getSql());
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int totalWrites = 0; |
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int valid = 0; |
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int discardedClaims = 0; |
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HadoopService hadoopService = serviceLocator.getService(HadoopService.class);
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HadoopService hadoopService = getServiceLocator().getService(HadoopService.class);
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for (Claim claim : claimRels) {
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log.debug(claim); |
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try {
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String sourceId = fullId(getOpenAIREType(claim.getSourceType()), claim.getSource());
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String targetId = fullId(getOpenAIREType(claim.getTargetType()), claim.getTarget());
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String sourceId = getFullId(getOpenAIREType(claim.getSourceType()), claim.getSource());
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String targetId = getFullId(getOpenAIREType(claim.getTargetType()), claim.getTarget());
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String value = getValue(sourceId, claim.getSemantics(), targetId, timestamp); |
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/* |
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public void addHBaseColumn(final String clusterName, |
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final String tableName, |
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final String rowKey, |
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final String columnFamily, |
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final String qualifier, |
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final String value) |
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*/ |
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hadoopService.addHBaseColumn(clusterName, tableName, sourceId, claim.getSemantics(), targetId, value); |
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processed++; |
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// adding relationship |
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hadoopService.addHBaseColumn(getClusterName(), getTableName(), sourceId, claim.getSemantics(), targetId, value); |
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totalWrites++; |
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String inverseSemantics = OntologyLoader.fetchInverse(claim.getSemantics()); |
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String inverseValue = getValue(targetId, inverseSemantics, sourceId, timestamp); |
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hadoopService.addHBaseColumn(clusterName, tableName, targetId, inverseSemantics, sourceId, inverseValue); |
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//adding inverse relationship |
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hadoopService.addHBaseColumn(getClusterName(), getTableName(), targetId, inverseSemantics, sourceId, inverseValue); |
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totalWrites++; |
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}catch(IllegalArgumentException e){
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log.error("Discarding claim "+claim+". Cause: "+e.getMessage());
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incrementProcessed(); |
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} catch (IllegalArgumentException e) {
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log.error("Discarding claim " + claim + ". Cause: " + e.getMessage());
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discardedClaims++; |
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} |
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} |
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log.info("totalClaims: " + total);
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token.getEnv().setAttribute("claimSize", total);
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log.info("writeOps: " + totalWrites);
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token.getEnv().setAttribute("writeOps", totalWrites);
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log.info("validClaims: " + valid);
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| 108 |
token.getEnv().setAttribute("validClaims", valid);
|
|
| 109 |
log.info("discardedClaims: " + discardedClaims);
|
|
| 110 |
token.getEnv().setAttribute("discardedClaims", discardedClaims);
|
|
| 71 |
log.info("totalClaimRels: " + getTotal());
|
|
| 72 |
token.getEnv().setAttribute("claimRelsSize", getTotal());
|
|
| 73 |
log.info("claim rels writeOps: " + totalWrites);
|
|
| 74 |
token.getEnv().setAttribute("claimRelsWriteOps", totalWrites);
|
|
| 75 |
log.info("validClaimRels: " + valid);
|
|
| 76 |
token.getEnv().setAttribute("validClaimRels", valid);
|
|
| 77 |
log.info("discardedClaimRels: " + discardedClaims);
|
|
| 78 |
token.getEnv().setAttribute("discardedClaimRels", discardedClaims);
|
|
| 111 | 79 |
|
| 112 | 80 |
return Arc.DEFAULT_ARC; |
| 113 | 81 |
} |
| 114 | 82 |
|
| 115 |
protected String getOpenAIREType(final String type){
|
|
| 116 |
switch(type){
|
|
| 117 |
case "publication": |
|
| 118 |
case "dataset": |
|
| 119 |
return "result"; |
|
| 120 |
default: |
|
| 121 |
return type; |
|
| 122 |
} |
|
| 123 |
} |
|
| 124 |
|
|
| 125 |
|
|
| 126 |
public String getValue(final String sourceId, final String semantics, final String targetId, final long timestamp) throws MSROException{
|
|
| 83 |
protected String getValue(final String sourceId, final String semantics, final String targetId, final long timestamp) throws MSROException {
|
|
| 127 | 84 |
log.debug(StringUtils.format("%s -- %s -- %s", sourceId, semantics, targetId));
|
| 128 | 85 |
String[] relInfo = semantics.split(SEPARATOR); |
| 129 |
if(relInfo.length < 3){
|
|
| 130 |
throw new MSROException("Semantics "+semantics+" not supported: must be splittable in 3 by '_'");
|
|
| 86 |
if (relInfo.length < 3) {
|
|
| 87 |
throw new MSROException("Semantics " + semantics + " not supported: must be splittable in 3 by '_'");
|
|
| 131 | 88 |
} |
| 132 | 89 |
Qualifier.Builder semanticsBuilder = Qualifier.newBuilder().setClassid(relInfo[2]).setClassname(relInfo[2]); |
| 133 | 90 |
|
| ... | ... | |
| 171 | 128 |
)))); |
| 172 | 129 |
break; |
| 173 | 130 |
default: |
| 174 |
throw new MSROException("Semantics "+relInfo[0]+" not supported");
|
|
| 131 |
throw new MSROException("Semantics " + relInfo[0] + " not supported");
|
|
| 175 | 132 |
} |
| 176 | 133 |
|
| 177 | 134 |
builder.setRel(relBuilder); |
| 178 | 135 |
return Base64.encodeBase64String(builder.build().toByteArray()); |
| 179 | 136 |
} |
| 180 |
|
|
| 181 |
private String fullId(final String type, final String id) {
|
|
| 182 |
final String fullId = AbstractDNetXsltFunctions.oafSimpleId(type, id); |
|
| 183 |
return OafRowKeyDecoder.decode(fullId).getKey(); |
|
| 184 |
} |
|
| 185 |
|
|
| 186 |
public String getClusterName() {
|
|
| 187 |
return clusterName; |
|
| 188 |
} |
|
| 189 |
|
|
| 190 |
public void setClusterName(final String clusterName) {
|
|
| 191 |
this.clusterName = clusterName; |
|
| 192 |
} |
|
| 193 |
|
|
| 194 |
public String getTableName() {
|
|
| 195 |
return tableName; |
|
| 196 |
} |
|
| 197 |
|
|
| 198 |
public void setTableName(final String tableName) {
|
|
| 199 |
this.tableName = tableName; |
|
| 200 |
} |
|
| 201 |
|
|
| 202 |
public UniqueServiceLocator getServiceLocator() {
|
|
| 203 |
return serviceLocator; |
|
| 204 |
} |
|
| 205 |
|
|
| 206 |
public void setServiceLocator(final UniqueServiceLocator serviceLocator) {
|
|
| 207 |
this.serviceLocator = serviceLocator; |
|
| 208 |
} |
|
| 209 |
|
|
| 210 |
public ClaimDatabaseUtils getClaimDatabaseUtils() {
|
|
| 211 |
return claimDatabaseUtils; |
|
| 212 |
} |
|
| 213 |
|
|
| 214 |
public void setClaimDatabaseUtils(final ClaimDatabaseUtils claimDatabaseUtils) {
|
|
| 215 |
this.claimDatabaseUtils = claimDatabaseUtils; |
|
| 216 |
} |
|
| 217 |
|
|
| 218 |
public String getSql() {
|
|
| 219 |
return sql; |
|
| 220 |
} |
|
| 221 |
|
|
| 222 |
public void setSql(final String sql) {
|
|
| 223 |
this.sql = sql; |
|
| 224 |
} |
|
| 225 |
|
|
| 226 |
public String getCountQuery() {
|
|
| 227 |
return countQuery; |
|
| 228 |
} |
|
| 229 |
|
|
| 230 |
public void setCountQuery(final String countQuery) {
|
|
| 231 |
this.countQuery = countQuery; |
|
| 232 |
} |
|
| 233 |
|
|
| 234 |
@Override |
|
| 235 |
public ProgressProvider getProgressProvider() {
|
|
| 236 |
return new ProgressProvider() {
|
|
| 237 |
|
|
| 238 |
@Override |
|
| 239 |
public boolean isInaccurate() {
|
|
| 240 |
return false; |
|
| 241 |
} |
|
| 242 |
|
|
| 243 |
@Override |
|
| 244 |
public int getTotalValue() {
|
|
| 245 |
return total; |
|
| 246 |
} |
|
| 247 |
|
|
| 248 |
@Override |
|
| 249 |
public int getCurrentValue() {
|
|
| 250 |
return processed; |
|
| 251 |
} |
|
| 252 |
}; |
|
| 253 |
} |
|
| 254 | 137 |
} |
| modules/dnet-openaireplus-workflows/trunk/src/main/java/eu/dnetlib/msro/openaireplus/workflows/nodes/claims/ApplyClaimUpdatesJobNode.java | ||
|---|---|---|
| 1 | 1 |
package eu.dnetlib.msro.openaireplus.workflows.nodes.claims; |
| 2 | 2 |
|
| 3 |
import java.io.IOException; |
|
| 4 | 3 |
import java.util.List; |
| 5 | 4 |
|
| 6 | 5 |
import com.googlecode.sarasvati.Arc; |
| 7 | 6 |
import com.googlecode.sarasvati.NodeToken; |
| 8 | 7 |
import eu.dnetlib.data.hadoop.rmi.HadoopService; |
| 9 |
import eu.dnetlib.data.mapreduce.util.OafRowKeyDecoder; |
|
| 10 |
import eu.dnetlib.data.proto.FieldTypeProtos.DataInfo; |
|
| 11 |
import eu.dnetlib.data.proto.FieldTypeProtos.Qualifier; |
|
| 12 | 8 |
import eu.dnetlib.data.proto.KindProtos.Kind; |
| 13 | 9 |
import eu.dnetlib.data.proto.OafProtos.Oaf; |
| 14 |
import eu.dnetlib.data.proto.OafProtos.OafRel; |
|
| 15 |
import eu.dnetlib.data.proto.RelMetadataProtos.RelMetadata; |
|
| 16 |
import eu.dnetlib.data.proto.RelTypeProtos.RelType; |
|
| 17 |
import eu.dnetlib.data.proto.RelTypeProtos.SubRelType; |
|
| 18 |
import eu.dnetlib.data.proto.ResultProjectProtos.ResultProject; |
|
| 19 |
import eu.dnetlib.data.proto.ResultProjectProtos.ResultProject.Outcome; |
|
| 20 |
import eu.dnetlib.data.proto.ResultResultProtos.ResultResult; |
|
| 21 |
import eu.dnetlib.data.proto.ResultResultProtos.ResultResult.PublicationDataset; |
|
| 22 |
import eu.dnetlib.data.transform.xml.AbstractDNetXsltFunctions; |
|
| 23 |
import eu.dnetlib.enabling.locators.UniqueServiceLocator; |
|
| 10 |
import eu.dnetlib.data.proto.OafProtos.OafEntity; |
|
| 11 |
import eu.dnetlib.data.proto.ResultProtos.Result; |
|
| 12 |
import eu.dnetlib.data.proto.ResultProtos.Result.Context; |
|
| 13 |
import eu.dnetlib.data.proto.TypeProtos.Type; |
|
| 24 | 14 |
import eu.dnetlib.msro.rmi.MSROException; |
| 25 |
import eu.dnetlib.msro.workflows.nodes.SimpleJobNode; |
|
| 26 |
import eu.dnetlib.utils.ontologies.OntologyLoader; |
|
| 27 | 15 |
import org.apache.commons.codec.binary.Base64; |
| 28 |
import org.apache.commons.io.IOUtils; |
|
| 29 | 16 |
import org.apache.commons.logging.Log; |
| 30 | 17 |
import org.apache.commons.logging.LogFactory; |
| 31 | 18 |
import org.apache.hadoop.util.StringUtils; |
| 32 |
import org.springframework.beans.factory.annotation.Autowired; |
|
| 33 | 19 |
|
| 34 | 20 |
/** |
| 35 | 21 |
* Created by alessia on 23/10/15. |
| 36 | 22 |
*/ |
| 37 |
public class ApplyClaimUpdatesJobNode extends SimpleJobNode {
|
|
| 23 |
public class ApplyClaimUpdatesJobNode extends AbstractClaimsToHBASE {
|
|
| 38 | 24 |
|
| 39 | 25 |
private static final Log log = LogFactory.getLog(ApplyClaimUpdatesJobNode.class); |
| 40 | 26 |
|
| 41 |
private final String SEPARATOR = "_"; |
|
| 42 |
|
|
| 43 |
@Autowired |
|
| 44 |
private UniqueServiceLocator serviceLocator; |
|
| 45 |
|
|
| 46 |
@Autowired |
|
| 47 |
private ClaimDatabaseUtils claimDatabaseUtils; |
|
| 48 |
|
|
| 49 |
private String sql; |
|
| 50 |
|
|
| 51 |
private String clusterName; |
|
| 52 |
|
|
| 53 |
private String tableName; |
|
| 54 |
|
|
| 55 |
private String fetchSqlAsText(final String path) throws IOException {
|
|
| 56 |
return IOUtils.toString(getClass().getResourceAsStream(path)); |
|
| 57 |
} |
|
| 58 |
|
|
| 59 | 27 |
@Override |
| 60 | 28 |
protected String execute(NodeToken token) throws Exception {
|
| 61 | 29 |
//TODO: use claim.claim_date from the claim db |
| 62 | 30 |
long timestamp = System.currentTimeMillis(); |
| 63 | 31 |
|
| 64 |
List<Claim> claimRels = this.claimDatabaseUtils.query(sql);
|
|
| 32 |
List<Claim> claimUpdates = this.getClaimDatabaseUtils().query(getSql());
|
|
| 65 | 33 |
int totalClaims = 0; |
| 66 | 34 |
int totalWrites = 0; |
| 35 |
int discardedClaims = 0; |
|
| 67 | 36 |
|
| 68 |
HadoopService hadoopService = serviceLocator.getService(HadoopService.class);
|
|
| 37 |
HadoopService hadoopService = getServiceLocator().getService(HadoopService.class);
|
|
| 69 | 38 |
|
| 70 |
for (Claim claim : claimRels) {
|
|
| 39 |
for (Claim claim : claimUpdates) {
|
|
| 40 |
try{
|
|
| 71 | 41 |
log.debug(claim); |
| 72 | 42 |
totalClaims++; |
| 73 | 43 |
String contextId = claim.getSource(); |
| 74 |
String targetId = fullId(claim.getTargetType(), claim.getTarget());
|
|
| 44 |
String rowKey = getFullId(getOpenAIREType(claim.getTargetType()), claim.getTarget());
|
|
| 75 | 45 |
|
| 76 |
String value = getValue(contextId, targetId, claim.getSemantics(), timestamp); |
|
| 77 |
/* |
|
| 78 |
public void addHBaseColumn(final String clusterName, |
|
| 79 |
final String tableName, |
|
| 80 |
final String rowKey, |
|
| 81 |
final String columnFamily, |
|
| 82 |
final String qualifier, |
|
| 83 |
final String value) |
|
| 84 |
*/ |
|
| 85 |
hadoopService.addHBaseColumn(clusterName, tableName, contextId, claim.getSemantics(), targetId, value); |
|
| 46 |
String value = getValue(contextId, rowKey, claim.getSemantics(), timestamp); |
|
| 47 |
hadoopService.addHBaseColumn(getClusterName(), getTableName(), rowKey, "result", "update_" + System.nanoTime(), value); |
|
| 86 | 48 |
totalWrites++; |
| 87 |
|
|
| 88 |
String inverseSemantics = OntologyLoader.fetchInverse(claim.getSemantics()); |
|
| 89 |
String inverseValue = getValue(targetId, contextId, inverseSemantics, timestamp); |
|
| 90 |
hadoopService.addHBaseColumn(clusterName, tableName, targetId, inverseSemantics, contextId, inverseValue); |
|
| 91 |
totalWrites++; |
|
| 92 |
|
|
| 49 |
incrementProcessed(); |
|
| 50 |
} catch (IllegalArgumentException e) {
|
|
| 51 |
log.error("Discarding claim " + claim + ". Cause: " + e.getMessage());
|
|
| 52 |
discardedClaims++; |
|
| 53 |
} |
|
| 93 | 54 |
} |
| 94 | 55 |
|
| 95 |
log.info("totalClaims: " + totalClaims);
|
|
| 96 |
token.getEnv().setAttribute("claimSize", totalClaims);
|
|
| 97 |
log.info("writeOps: " + totalWrites);
|
|
| 98 |
token.getEnv().setAttribute("writeOps", totalWrites);
|
|
| 56 |
log.info("Total Claim Updates: " + totalClaims);
|
|
| 57 |
token.getEnv().setAttribute("claimUpdatesSize", totalClaims);
|
|
| 58 |
log.info("Claim updates writeOps: " + totalWrites);
|
|
| 59 |
token.getEnv().setAttribute("claimUpdatesWriteOps", totalWrites);
|
|
| 60 |
log.info("Discarded Claim Updates: " + discardedClaims);
|
|
| 61 |
token.getEnv().setAttribute("discardedClaimUpdates", discardedClaims);
|
|
| 99 | 62 |
|
| 100 | 63 |
return Arc.DEFAULT_ARC; |
| 101 | 64 |
} |
| 102 | 65 |
|
| 103 |
|
|
| 104 |
private String getValue(final String sourceId, final String semantics, final String targetId, final long timestamp) throws MSROException{
|
|
| 66 |
protected String getValue(final String sourceId, final String semantics, final String targetId, final long timestamp) throws MSROException {
|
|
| 105 | 67 |
log.debug(StringUtils.format("%s -- %s -- %s", sourceId, semantics, targetId));
|
| 106 |
String[] relInfo = semantics.split(SEPARATOR); |
|
| 107 |
Qualifier.Builder semanticsBuilder = Qualifier.newBuilder().setClassid(relInfo[2]).setClassname(relInfo[2]); |
|
| 108 | 68 |
|
| 109 |
Oaf.Builder builder = Oaf.newBuilder().setKind(Kind.relation).setLastupdatetimestamp(timestamp); |
|
| 110 |
builder.setDataInfo(DataInfo.newBuilder().setTrust("0.91").setInferred(false)
|
|
| 111 |
.setProvenanceaction( |
|
| 112 |
Qualifier.newBuilder() |
|
| 113 |
.setClassid("user:claim")
|
|
| 114 |
.setClassname("user:claim")
|
|
| 115 |
.setSchemeid("dnet:provenanceActions")
|
|
| 116 |
.setSchemename("dnet:provenanceActions")
|
|
| 117 |
)); |
|
| 69 |
Result.Builder resultBuilder = Result.newBuilder().setMetadata(Result.Metadata.newBuilder().addContext(getContext(sourceId))); |
|
| 70 |
OafEntity.Builder entityBuilder = OafEntity.newBuilder().setId(targetId).setType(Type.result).setResult(resultBuilder); |
|
| 71 |
Oaf.Builder builder = Oaf.newBuilder().setKind(Kind.entity).setLastupdatetimestamp(timestamp).setEntity(entityBuilder); |
|
| 118 | 72 |
|
| 119 |
final SubRelType subRelType = SubRelType.valueOf(relInfo[1]); |
|
| 120 |
final OafRel.Builder relBuilder = OafRel.newBuilder() |
|
| 121 |
.setSubRelType(subRelType) |
|
| 122 |
.setRelClass(relInfo[2]) |
|
| 123 |
.setRelType(RelType.valueOf(relInfo[0])) |
|
| 124 |
.setSource(sourceId).setTarget(targetId).setChild(false); |
|
| 125 |
|
|
| 126 |
switch (relInfo[0]) {
|
|
| 127 |
case "resultProject": |
|
| 128 |
|
|
| 129 |
relBuilder.setResultProject(ResultProject.newBuilder() |
|
| 130 |
.setOutcome(Outcome.newBuilder().setRelMetadata( |
|
| 131 |
RelMetadata.newBuilder().setSemantics( |
|
| 132 |
semanticsBuilder |
|
| 133 |
.setSchemeid("dnet:result_project_relations")
|
|
| 134 |
.setSchemename("dnet:result_project_relations")
|
|
| 135 |
.build() |
|
| 136 |
)))); |
|
| 137 |
break; |
|
| 138 |
case "resultResult_publicationDataset_isRelatedTo": |
|
| 139 |
relBuilder.setResultResult(ResultResult.newBuilder() |
|
| 140 |
.setPublicationDataset(PublicationDataset.newBuilder().setRelMetadata( |
|
| 141 |
RelMetadata.newBuilder().setSemantics( |
|
| 142 |
semanticsBuilder |
|
| 143 |
.setSchemeid("dnet:result_result_relations")
|
|
| 144 |
.setSchemename("dnet:result_result_relations")
|
|
| 145 |
.build() |
|
| 146 |
)))); |
|
| 147 |
break; |
|
| 148 |
default: |
|
| 149 |
throw new MSROException("Semantics "+relInfo[0]+" not supported");
|
|
| 150 |
} |
|
| 151 |
|
|
| 152 |
builder.setRel(relBuilder); |
|
| 153 | 73 |
return Base64.encodeBase64String(builder.build().toByteArray()); |
| 154 | 74 |
} |
| 155 | 75 |
|
| 156 |
private String fullId(final String type, final String id) {
|
|
| 157 |
final String fullId = AbstractDNetXsltFunctions.oafSimpleId(type, id); |
|
| 158 |
return OafRowKeyDecoder.decode(fullId).getKey(); |
|
| 76 |
private Context getContext(final String sourceId) {
|
|
| 77 |
return Context.newBuilder().setDataInfo(getDataInfo()).setId(sourceId).build(); |
|
| 159 | 78 |
} |
| 160 |
|
|
| 161 |
public String getClusterName() {
|
|
| 162 |
return clusterName; |
|
| 163 |
} |
|
| 164 |
|
|
| 165 |
public void setClusterName(final String clusterName) {
|
|
| 166 |
this.clusterName = clusterName; |
|
| 167 |
} |
|
| 168 |
|
|
| 169 |
public String getTableName() {
|
|
| 170 |
return tableName; |
|
| 171 |
} |
|
| 172 |
|
|
| 173 |
public void setTableName(final String tableName) {
|
|
| 174 |
this.tableName = tableName; |
|
| 175 |
} |
|
| 176 |
|
|
| 177 |
public UniqueServiceLocator getServiceLocator() {
|
|
| 178 |
return serviceLocator; |
|
| 179 |
} |
|
| 180 |
|
|
| 181 |
public void setServiceLocator(final UniqueServiceLocator serviceLocator) {
|
|
| 182 |
this.serviceLocator = serviceLocator; |
|
| 183 |
} |
|
| 184 |
|
|
| 185 |
public ClaimDatabaseUtils getClaimDatabaseUtils() {
|
|
| 186 |
return claimDatabaseUtils; |
|
| 187 |
} |
|
| 188 |
|
|
| 189 |
public void setClaimDatabaseUtils(final ClaimDatabaseUtils claimDatabaseUtils) {
|
|
| 190 |
this.claimDatabaseUtils = claimDatabaseUtils; |
|
| 191 |
} |
|
| 192 |
|
|
| 193 |
public String getSql() {
|
|
| 194 |
return sql; |
|
| 195 |
} |
|
| 196 |
|
|
| 197 |
public void setSql(final String sql) {
|
|
| 198 |
this.sql = sql; |
|
| 199 |
} |
|
| 200 | 79 |
} |
| modules/dnet-openaireplus-workflows/trunk/src/main/java/eu/dnetlib/msro/openaireplus/workflows/nodes/claims/ClaimDatabaseUtils.java | ||
|---|---|---|
| 2 | 2 |
|
| 3 | 3 |
import java.util.List; |
| 4 | 4 |
|
| 5 |
import eu.dnetlib.data.mapreduce.util.OafRowKeyDecoder; |
|
| 6 |
import eu.dnetlib.data.proto.FieldTypeProtos.DataInfo; |
|
| 7 |
import eu.dnetlib.data.proto.FieldTypeProtos.Qualifier; |
|
| 8 |
import eu.dnetlib.data.transform.xml.AbstractDNetXsltFunctions; |
|
| 5 | 9 |
import eu.dnetlib.enabling.database.DataSourceFactory; |
| 6 | 10 |
import eu.dnetlib.enabling.database.utils.JdbcTemplateFactory; |
| 7 | 11 |
import org.springframework.beans.factory.annotation.Autowired; |
| ... | ... | |
| 38 | 42 |
return this.claimsJdbcTemplateFactory.createJdbcTemplate(dbName).queryForObject(sqlCountQuery, Integer.class); |
| 39 | 43 |
} |
| 40 | 44 |
|
| 41 |
|
|
| 42 | 45 |
} |
| modules/dnet-openaireplus-workflows/trunk/src/main/resources/eu/dnetlib/test/profiles/openaireplus/workflows/hbase/tmp_claims2hbase.xml | ||
|---|---|---|
| 11 | 11 |
<WORKFLOW_TYPE>Data Load</WORKFLOW_TYPE> |
| 12 | 12 |
<WORKFLOW_PRIORITY>30</WORKFLOW_PRIORITY> |
| 13 | 13 |
<CONFIGURATION start="manual"> |
| 14 |
<NODE isStart="true" name="start"> |
|
| 15 |
<DESCRIPTION>start</DESCRIPTION> |
|
| 16 |
<PARAMETERS/> |
|
| 17 |
<ARCS> |
|
| 18 |
<ARC to="queryClaimRels"/> |
|
| 19 |
</ARCS> |
|
| 20 |
</NODE> |
|
| 21 |
<NODE name="applyClaimRels" type="ApplyClaimRels"> |
|
| 14 |
<NODE name="applyClaimRels" type="ApplyClaimRels" isStart="true"> |
|
| 22 | 15 |
<DESCRIPTION>Apply Claim Rels</DESCRIPTION> |
| 23 | 16 |
<PARAMETERS> |
| 24 | 17 |
<PARAM managedBy="system" name="clusterName" required="true" type="string">DM</PARAM> |
| 25 | 18 |
<PARAM managedBy="user" name="tableName" required="true" type="string"></PARAM> |
| 26 | 19 |
<PARAM managedBy="user" name="sql" required="true" type="string">SELECT source_type, source_id, target_type, target_id, semantics FROM claim WHERE approved=TRUE AND source_type !='context'</PARAM> |
| 27 |
<PARAM managedBy="user" name="countSql" required="true" type="string">SELECT count(*) FROM claim WHERE approved=TRUE AND source_type !='context'</PARAM>
|
|
| 20 |
<PARAM managedBy="user" name="countQuery" required="true" type="string">SELECT count(*) FROM claim WHERE approved=TRUE AND source_type !='context'</PARAM>
|
|
| 28 | 21 |
</PARAMETERS> |
| 29 | 22 |
<ARCS> |
| 30 | 23 |
<ARC to="applyClaimUpdates"/> |
| ... | ... | |
| 36 | 29 |
<PARAM managedBy="system" name="clusterName" required="true" type="string">DM</PARAM> |
| 37 | 30 |
<PARAM managedBy="user" name="tableName" required="true" type="string"></PARAM> |
| 38 | 31 |
<PARAM managedBy="user" name="sql" required="true" type="string">SELECT source_type, source_id, target_type, target_id, semantics FROM claim WHERE approved=TRUE AND source_type ='context'</PARAM> |
| 39 |
<PARAM managedBy="user" name="countSql" required="true" type="string">SELECT count(*) FROM claim WHERE approved=TRUE AND source_type ='context'</PARAM>
|
|
| 32 |
<PARAM managedBy="user" name="countQuery" required="true" type="string">SELECT count(*) FROM claim WHERE approved=TRUE AND source_type ='context'</PARAM>
|
|
| 40 | 33 |
</PARAMETERS> |
| 41 | 34 |
<ARCS> |
| 42 | 35 |
<ARC to="success"/> |
| modules/dnet-openaireplus-workflows/trunk/src/main/resources/eu/dnetlib/msro/openaireplus/workflows/nodes/claims/applicationContext-claims.xml | ||
|---|---|---|
| 1 | 1 |
<?xml version="1.0" encoding="UTF-8"?> |
| 2 | 2 |
<beans xmlns="http://www.springframework.org/schema/beans" |
| 3 |
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:context="http://www.springframework.org/schema/context" |
|
| 4 |
xmlns:p="http://www.springframework.org/schema/p" xmlns:util="http://www.springframework.org/schema/util" |
|
| 5 |
xsi:schemaLocation="http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans.xsd |
|
| 6 |
http://www.springframework.org/schema/context http://www.springframework.org/schema/context/spring-context.xsd |
|
| 7 |
http://www.springframework.org/schema/util http://www.springframework.org/schema/util/spring-util.xsd"> |
|
| 8 |
|
|
| 9 |
<!--<bean id="claimsJdbcTemplate" class="org.springframework.jdbc.core.JdbcTemplate"--> |
|
| 10 |
<!--p:dataSource-ref="claimsDatasource"/>--> |
|
| 3 |
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" |
|
| 4 |
xmlns:p="http://www.springframework.org/schema/p" |
|
| 5 |
xsi:schemaLocation="http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans.xsd"> |
|
| 6 |
|
|
| 11 | 7 |
<bean id="claimsJdbcTemplateFactory" |
| 12 | 8 |
class="eu.dnetlib.enabling.database.utils.JdbcTemplateFactory" |
| 13 | 9 |
p:dataSourceFactory-ref="claimsDataSourceFactory" /> |
| 14 | 10 |
|
| 15 |
<!--<bean id="claimsDatasource" class="org.apache.commons.dbcp2.BasicDataSource" destroy-method="close">--> |
|
| 16 |
<!--<property name="driverClassName" value="org.postgresql.Driver"/>--> |
|
| 17 |
<!--<property name="url" value="${dnet.openaire.claims.db.url}"/>-->
|
|
| 18 |
<!--<property name="username" value="${dnet.openaire.claims.db.username}"/>-->
|
|
| 19 |
<!--<property name="password" value="${dnet.openaire.claims.db.password}"/>-->
|
|
| 20 |
<!--</bean>--> |
|
| 21 | 11 |
<bean id="claimsDataSourceFactory" |
| 22 | 12 |
class="eu.dnetlib.enabling.database.DataSourceFactoryImpl" |
| 23 | 13 |
p:driverClassName="org.postgresql.Driver" |
| ... | ... | |
| 25 | 15 |
p:username="${dnet.openaire.claims.db.username}"
|
| 26 | 16 |
p:password="${dnet.openaire.claims.db.password}" />
|
| 27 | 17 |
|
| 18 |
<bean id="claimDatabaseUtils" class="eu.dnetlib.msro.openaireplus.workflows.nodes.claims.ClaimDatabaseUtils" /> |
|
| 28 | 19 |
|
| 29 |
<bean id="claimDatabaseUtils" class="eu.dnetlib.msro.openaireplus.workflows.nodes.claims.ClaimDatabaseUtils" /> |
|
| 30 | 20 |
</beans> |
| modules/dnet-openaireplus-workflows/trunk/src/main/resources/eu/dnetlib/msro/openaireplus/workflows/applicationContext-msro-openaire-nodes.xml | ||
|---|---|---|
| 313 | 313 |
class="eu.dnetlib.msro.openaireplus.workflows.nodes.claims.ApplyClaimRelsJobNode" |
| 314 | 314 |
scope="prototype"/> |
| 315 | 315 |
|
| 316 |
<bean id="wfNodeApplyClaimUpdates" |
|
| 317 |
class="eu.dnetlib.msro.openaireplus.workflows.nodes.claims.ApplyClaimUpdatesJobNode" |
|
| 318 |
scope="prototype"/> |
|
| 319 |
|
|
| 316 | 320 |
</beans> |
Also available in: Unified diff
Node for writing context updates on hbase and refactoring