logs for non well formed XML files

2 years ago · 27af5122d2
parent b09d7ddc74
commit 27af5122d2
4 changed files with 123 additions and 25 deletions
--- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java
+++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java
@ -22,6 +22,8 @@ import java.util.*;

 import org.apache.commons.lang3.StringUtils;
 import org.dom4j.*;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;

 import com.google.common.collect.Lists;
 import com.google.common.collect.Sets;
@ -77,6 +79,8 @@ public abstract class AbstractMdRecordToOafMapper {

 	protected static final Map<String, String> nsContext = new HashMap<>();

+	private static final Logger log = LoggerFactory.getLogger(AbstractMdRecordToOafMapper.class);
+
 	static {
 		nsContext.put("dr", "http://www.driver-repository.eu/namespace/dr");
 		nsContext.put("dri", "http://www.driver-repository.eu/namespace/dri");
@ -106,37 +110,41 @@ public abstract class AbstractMdRecordToOafMapper {
 	public List<Oaf> processMdRecord(final String xml) throws DocumentException {

 		DocumentFactory.getInstance().setXPathNamespaceURIs(nsContext);
+		try {
+			final Document doc = DocumentHelper
+				.parseText(
+					xml
+						.replaceAll(DATACITE_SCHEMA_KERNEL_4, DATACITE_SCHEMA_KERNEL_3)
+						.replaceAll(DATACITE_SCHEMA_KERNEL_4_SLASH, DATACITE_SCHEMA_KERNEL_3)
+						.replaceAll(DATACITE_SCHEMA_KERNEL_3_SLASH, DATACITE_SCHEMA_KERNEL_3));
+
+			final KeyValue collectedFrom = getProvenanceDatasource(
+				doc, "//oaf:collectedFrom/@id", "//oaf:collectedFrom/@name");
+
+			if (collectedFrom == null) {
+				return Lists.newArrayList();
+			}

-		final Document doc = DocumentHelper
-			.parseText(
-				xml
-					.replaceAll(DATACITE_SCHEMA_KERNEL_4, DATACITE_SCHEMA_KERNEL_3)
-					.replaceAll(DATACITE_SCHEMA_KERNEL_4_SLASH, DATACITE_SCHEMA_KERNEL_3)
-					.replaceAll(DATACITE_SCHEMA_KERNEL_3_SLASH, DATACITE_SCHEMA_KERNEL_3));
-
-		final KeyValue collectedFrom = getProvenanceDatasource(
-			doc, "//oaf:collectedFrom/@id", "//oaf:collectedFrom/@name");
-
-		if (collectedFrom == null) {
-			return Lists.newArrayList();
-		}
-
-		final KeyValue hostedBy = StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id"))
-			? collectedFrom
-			: getProvenanceDatasource(doc, "//oaf:hostedBy/@id", "//oaf:hostedBy/@name");
+			final KeyValue hostedBy = StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id"))
+				? collectedFrom
+				: getProvenanceDatasource(doc, "//oaf:hostedBy/@id", "//oaf:hostedBy/@name");

-		if (hostedBy == null) {
-			return Lists.newArrayList();
-		}
+			if (hostedBy == null) {
+				return Lists.newArrayList();
+			}

-		final DataInfo info = prepareDataInfo(doc, invisible);
-		final long lastUpdateTimestamp = new Date().getTime();
+			final DataInfo info = prepareDataInfo(doc, invisible);
+			final long lastUpdateTimestamp = new Date().getTime();

-		final List<Instance> instances = prepareInstances(doc, info, collectedFrom, hostedBy);
+			final List<Instance> instances = prepareInstances(doc, info, collectedFrom, hostedBy);

-		final String type = getResultType(doc, instances);
+			final String type = getResultType(doc, instances);

-		return createOafs(doc, type, instances, collectedFrom, info, lastUpdateTimestamp);
+			return createOafs(doc, type, instances, collectedFrom, info, lastUpdateTimestamp);
+		} catch (DocumentException e) {
+			log.error("Error with record:\n" + xml);
+			throw e;
+		}
 	}

 	protected String getResultType(final Document doc, final List<Instance> instances) {
--- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java
+++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java
@ -12,6 +12,7 @@ import java.util.Objects;
 import java.util.Optional;
 import java.util.stream.Collectors;

+import kotlin.jvm.Throws;
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.dom4j.DocumentException;
@ -926,6 +927,17 @@ class MappersTest {
 //		assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue()));
 	}

+	@Test
+	void testNotWellFormed() throws IOException, DocumentException {
+		final String xml = IOUtils
+			.toString(Objects.requireNonNull(getClass().getResourceAsStream("oaf_notwellformed.xml")));
+		final DocumentException generalEx = new DocumentException();
+
+		DocumentException exception = assertThrows(DocumentException.class, () -> {
+			new OafToOafMapper(vocs, false, true).processMdRecord(xml);
+		});
+	}
+
 	private void assertValidId(final String id) {
 		// System.out.println(id);

--- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_notwellformed.xml
+++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_notwellformed.xml
@ -0,0 +1,70 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<record xmlns:dc="http://purl.org/dc/elements/1.1/"
+        xmlns:dr="http://www.driver-repository.eu/namespace/dr"
+        xmlns:dri="http://www.driver-repository.eu/namespace/dri"
+        xmlns:oaf="http://namespace.openaire.eu/oaf"
+        xmlns:oai="http://www.openarchives.org/OAI/2.0/"
+        xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+    <header xmlns="http://namespace.openaire.eu/">
+        <dri:objIdentifier>jairo_______::000012e58ed836576ef2a0d38b0f726f</dri:objIdentifier>
+        <dri:recordIdentifier>oai:irdb.nii.ac.jp:01221:0000010198</dri:recordIdentifier>
+        <dri:dateOfCollection/>
+        <dri:mdFormat/>
+        <dri:mdFormatInterpretation/>
+        <dri:repositoryId/>
+        <dr:objectIdentifier/>
+        <dr:dateOfCollection>2021-05-10T11:31:09.424Z</dr:dateOfCollection>
+        <dr:dateOfTransformation>2021-06-03T01:45:42.536Z</dr:dateOfTransformation>
+        <oaf:datasourceprefix>jairo_______</oaf:datasourceprefix>
+    </header>
+    <metadata xmlns="http://namespace.openaire.eu/">
+        <dc:title>多項式GCDを用いた復号法に関する研究<dc:title>
+        <dc:creator>上原, 剛</dc:creator>
+        <dc:creator>甲斐, 博</dc:creator>
+        <dc:creator>野田, 松太郎</dc:creator>
+        <dc:format>application/pdf</dc:format>
+        <dc:identifier>http://hdl.handle.net/2433/25934</dc:identifier>
+        <dc:language>jpn</dc:language>
+        <dc:publisher>京都大学数理解析研究所</dc:publisher>
+        <dc:subject classid="ndc" classname="ndc"
+                    schemeid="dnet:subject_classification_typologies" schemename="dnet:subject_classification_typologies">410</dc:subject>
+        <dc:type>Departmental Bulletin Paper</dc:type>
+        <dr:CobjCategory type="publication">0014</dr:CobjCategory>
+        <oaf:dateAccepted>2004-10-01</oaf:dateAccepted>
+        <oaf:projectid/>
+        <oaf:collectedDatasourceid>openaire____::554c7c2873</oaf:collectedDatasourceid>
+        <oaf:accessrights>OPEN</oaf:accessrights>
+        <oaf:hostedBy id="openaire____::554c7c2873" name="JAIRO"/>
+        <oaf:collectedFrom id="openaire____::554c7c2873" name="JAIRO"/>
+        <oaf:identifier identifierType="handle">2433/25934</oaf:identifier>
+        <oaf:identifier identifierType="ncid">AN00061013</oaf:identifier>
+        <oaf:identifier identifierType="LandingPage">http://hdl.handle.net/2433/25934</oaf:identifier>
+        <oaf:fulltext>http://repository.kulib.kyoto-u.ac.jp/dspace/bitstream/2433/25934/1/1395-16.pdf</oaf:fulltext>
+        <oaf:journal ep="110" iss="" issn="1880-2818" sp="104" vol="1395">数理解析研究所講究録</oaf:journal>
+    </metadata>
+    <about>
+        <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">
+            <originDescription altered="true" harvestDate="2021-05-10T11:31:09.424Z">
+                <baseURL>https%3A%2F%2Firdb.nii.ac.jp%2Foai</baseURL>
+                <identifier>oai:irdb.nii.ac.jp:01221:0000010198</identifier>
+                <datestamp>2021-04-13T13:36:29Z</datestamp>
+                <metadataNamespace/>
+                <originDescription altered="true" harvestDate="2021-04-13T13:36:29Z">
+                    <baseURL>http://repository.kulib.kyoto-u.ac.jp/dspace-oai/request</baseURL>
+                    <identifier>oai:repository.kulib.kyoto-u.ac.jp:2433/25934</identifier>
+                    <datestamp>2012-07-12T14:15:41Z</datestamp>
+                    <metadataNamespace>http://irdb.nii.ac.jp/oai</metadataNamespace>
+                </originDescription>
+            </originDescription>
+        </provenance>
+        <oaf:datainfo>
+            <oaf:inferred>false</oaf:inferred>
+            <oaf:deletedbyinference>false</oaf:deletedbyinference>
+            <oaf:trust>0.9</oaf:trust>
+            <oaf:inferenceprovenance/>
+            <oaf:provenanceaction classid="sysimport:crosswalk:repository"
+                                  classname="sysimport:crosswalk:repository"
+                                  schemeid="dnet:provenanceActions" schemename="dnet:provenanceActions"/>
+        </oaf:datainfo>
+    </about>
+</record>
--- a/dhp-workflows/dhp-graph-mapper/src/test/resources/log4j.properties
+++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/log4j.properties
@ -0,0 +1,8 @@
+# Root logger option
+log4j.rootLogger=DEBUG, stdout
+
+# Direct log messages to stdout
+log4j.appender.stdout=org.apache.log4j.ConsoleAppender
+log4j.appender.stdout.Target=System.out
+log4j.appender.stdout.layout=org.apache.log4j.PatternLayout
+log4j.appender.stdout.layout.ConversionPattern=%d{yyyy-MM-dd HH:mm:ss} %-5p %c{1}:%L - %m%n