forked from D-Net/dnet-hadoop
logs for non well formed XML files
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parent
b09d7ddc74
commit
27af5122d2
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@ -22,6 +22,8 @@ import java.util.*;
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import org.apache.commons.lang3.StringUtils;
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import org.dom4j.*;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import com.google.common.collect.Lists;
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import com.google.common.collect.Sets;
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@ -77,6 +79,8 @@ public abstract class AbstractMdRecordToOafMapper {
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protected static final Map<String, String> nsContext = new HashMap<>();
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private static final Logger log = LoggerFactory.getLogger(AbstractMdRecordToOafMapper.class);
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static {
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nsContext.put("dr", "http://www.driver-repository.eu/namespace/dr");
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nsContext.put("dri", "http://www.driver-repository.eu/namespace/dri");
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@ -106,37 +110,41 @@ public abstract class AbstractMdRecordToOafMapper {
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public List<Oaf> processMdRecord(final String xml) throws DocumentException {
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DocumentFactory.getInstance().setXPathNamespaceURIs(nsContext);
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try {
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final Document doc = DocumentHelper
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.parseText(
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xml
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.replaceAll(DATACITE_SCHEMA_KERNEL_4, DATACITE_SCHEMA_KERNEL_3)
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.replaceAll(DATACITE_SCHEMA_KERNEL_4_SLASH, DATACITE_SCHEMA_KERNEL_3)
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.replaceAll(DATACITE_SCHEMA_KERNEL_3_SLASH, DATACITE_SCHEMA_KERNEL_3));
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final Document doc = DocumentHelper
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.parseText(
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xml
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.replaceAll(DATACITE_SCHEMA_KERNEL_4, DATACITE_SCHEMA_KERNEL_3)
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.replaceAll(DATACITE_SCHEMA_KERNEL_4_SLASH, DATACITE_SCHEMA_KERNEL_3)
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.replaceAll(DATACITE_SCHEMA_KERNEL_3_SLASH, DATACITE_SCHEMA_KERNEL_3));
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final KeyValue collectedFrom = getProvenanceDatasource(
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doc, "//oaf:collectedFrom/@id", "//oaf:collectedFrom/@name");
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final KeyValue collectedFrom = getProvenanceDatasource(
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doc, "//oaf:collectedFrom/@id", "//oaf:collectedFrom/@name");
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if (collectedFrom == null) {
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return Lists.newArrayList();
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}
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if (collectedFrom == null) {
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return Lists.newArrayList();
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final KeyValue hostedBy = StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id"))
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? collectedFrom
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: getProvenanceDatasource(doc, "//oaf:hostedBy/@id", "//oaf:hostedBy/@name");
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if (hostedBy == null) {
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return Lists.newArrayList();
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}
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final DataInfo info = prepareDataInfo(doc, invisible);
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final long lastUpdateTimestamp = new Date().getTime();
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final List<Instance> instances = prepareInstances(doc, info, collectedFrom, hostedBy);
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final String type = getResultType(doc, instances);
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return createOafs(doc, type, instances, collectedFrom, info, lastUpdateTimestamp);
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} catch (DocumentException e) {
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log.error("Error with record:\n" + xml);
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throw e;
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}
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final KeyValue hostedBy = StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id"))
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? collectedFrom
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: getProvenanceDatasource(doc, "//oaf:hostedBy/@id", "//oaf:hostedBy/@name");
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if (hostedBy == null) {
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return Lists.newArrayList();
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}
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final DataInfo info = prepareDataInfo(doc, invisible);
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final long lastUpdateTimestamp = new Date().getTime();
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final List<Instance> instances = prepareInstances(doc, info, collectedFrom, hostedBy);
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final String type = getResultType(doc, instances);
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return createOafs(doc, type, instances, collectedFrom, info, lastUpdateTimestamp);
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}
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protected String getResultType(final Document doc, final List<Instance> instances) {
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@ -12,6 +12,7 @@ import java.util.Objects;
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import java.util.Optional;
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import java.util.stream.Collectors;
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import kotlin.jvm.Throws;
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import org.apache.commons.io.IOUtils;
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import org.apache.commons.lang3.StringUtils;
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import org.dom4j.DocumentException;
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@ -926,6 +927,17 @@ class MappersTest {
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// assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue()));
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}
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@Test
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void testNotWellFormed() throws IOException, DocumentException {
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final String xml = IOUtils
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.toString(Objects.requireNonNull(getClass().getResourceAsStream("oaf_notwellformed.xml")));
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final DocumentException generalEx = new DocumentException();
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DocumentException exception = assertThrows(DocumentException.class, () -> {
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new OafToOafMapper(vocs, false, true).processMdRecord(xml);
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});
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}
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private void assertValidId(final String id) {
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// System.out.println(id);
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@ -0,0 +1,70 @@
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<?xml version="1.0" encoding="UTF-8"?>
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<record xmlns:dc="http://purl.org/dc/elements/1.1/"
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xmlns:dr="http://www.driver-repository.eu/namespace/dr"
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xmlns:dri="http://www.driver-repository.eu/namespace/dri"
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xmlns:oaf="http://namespace.openaire.eu/oaf"
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xmlns:oai="http://www.openarchives.org/OAI/2.0/"
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
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<header xmlns="http://namespace.openaire.eu/">
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<dri:objIdentifier>jairo_______::000012e58ed836576ef2a0d38b0f726f</dri:objIdentifier>
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<dri:recordIdentifier>oai:irdb.nii.ac.jp:01221:0000010198</dri:recordIdentifier>
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<dri:dateOfCollection/>
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<dri:mdFormat/>
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<dri:mdFormatInterpretation/>
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<dri:repositoryId/>
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<dr:objectIdentifier/>
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<dr:dateOfCollection>2021-05-10T11:31:09.424Z</dr:dateOfCollection>
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<dr:dateOfTransformation>2021-06-03T01:45:42.536Z</dr:dateOfTransformation>
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<oaf:datasourceprefix>jairo_______</oaf:datasourceprefix>
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</header>
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<metadata xmlns="http://namespace.openaire.eu/">
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<dc:title>多項式GCDを用いた復号法に関する研究<dc:title>
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<dc:creator>上原, 剛</dc:creator>
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<dc:creator>甲斐, 博</dc:creator>
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<dc:creator>野田, 松太郎</dc:creator>
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<dc:format>application/pdf</dc:format>
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<dc:identifier>http://hdl.handle.net/2433/25934</dc:identifier>
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<dc:language>jpn</dc:language>
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<dc:publisher>京都大学数理解析研究所</dc:publisher>
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<dc:subject classid="ndc" classname="ndc"
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schemeid="dnet:subject_classification_typologies" schemename="dnet:subject_classification_typologies">410</dc:subject>
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<dc:type>Departmental Bulletin Paper</dc:type>
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<dr:CobjCategory type="publication">0014</dr:CobjCategory>
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<oaf:dateAccepted>2004-10-01</oaf:dateAccepted>
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<oaf:projectid/>
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<oaf:collectedDatasourceid>openaire____::554c7c2873</oaf:collectedDatasourceid>
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<oaf:accessrights>OPEN</oaf:accessrights>
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<oaf:hostedBy id="openaire____::554c7c2873" name="JAIRO"/>
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<oaf:collectedFrom id="openaire____::554c7c2873" name="JAIRO"/>
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<oaf:identifier identifierType="handle">2433/25934</oaf:identifier>
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<oaf:identifier identifierType="ncid">AN00061013</oaf:identifier>
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<oaf:identifier identifierType="LandingPage">http://hdl.handle.net/2433/25934</oaf:identifier>
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<oaf:fulltext>http://repository.kulib.kyoto-u.ac.jp/dspace/bitstream/2433/25934/1/1395-16.pdf</oaf:fulltext>
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<oaf:journal ep="110" iss="" issn="1880-2818" sp="104" vol="1395">数理解析研究所講究録</oaf:journal>
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</metadata>
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<about>
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<provenance xmlns="http://www.openarchives.org/OAI/2.0/provenance" xsi:schemaLocation="http://www.openarchives.org/OAI/2.0/provenance http://www.openarchives.org/OAI/2.0/provenance.xsd">
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<originDescription altered="true" harvestDate="2021-05-10T11:31:09.424Z">
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<baseURL>https%3A%2F%2Firdb.nii.ac.jp%2Foai</baseURL>
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<identifier>oai:irdb.nii.ac.jp:01221:0000010198</identifier>
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<datestamp>2021-04-13T13:36:29Z</datestamp>
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<metadataNamespace/>
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<originDescription altered="true" harvestDate="2021-04-13T13:36:29Z">
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<baseURL>http://repository.kulib.kyoto-u.ac.jp/dspace-oai/request</baseURL>
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<identifier>oai:repository.kulib.kyoto-u.ac.jp:2433/25934</identifier>
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<datestamp>2012-07-12T14:15:41Z</datestamp>
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<metadataNamespace>http://irdb.nii.ac.jp/oai</metadataNamespace>
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</originDescription>
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</originDescription>
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</provenance>
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<oaf:datainfo>
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<oaf:inferred>false</oaf:inferred>
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<oaf:deletedbyinference>false</oaf:deletedbyinference>
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<oaf:trust>0.9</oaf:trust>
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<oaf:inferenceprovenance/>
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<oaf:provenanceaction classid="sysimport:crosswalk:repository"
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classname="sysimport:crosswalk:repository"
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schemeid="dnet:provenanceActions" schemename="dnet:provenanceActions"/>
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</oaf:datainfo>
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</about>
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</record>
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@ -0,0 +1,8 @@
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# Root logger option
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log4j.rootLogger=DEBUG, stdout
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# Direct log messages to stdout
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log4j.appender.stdout=org.apache.log4j.ConsoleAppender
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log4j.appender.stdout.Target=System.out
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log4j.appender.stdout.layout=org.apache.log4j.PatternLayout
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log4j.appender.stdout.layout.ConversionPattern=%d{yyyy-MM-dd HH:mm:ss} %-5p %c{1}:%L - %m%n
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