From e62018e95d45cb99442d80576527590a19419194 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Wed, 3 Aug 2022 12:26:05 +0200 Subject: [PATCH 01/10] [aggregator graph] added more assertions in test --- .../graph/raw/MigrateDbEntitiesApplicationTest.java | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java index 9048a22ea..408196665 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java @@ -18,6 +18,7 @@ import java.util.Objects; import java.util.Optional; import java.util.stream.Collectors; +import eu.dnetlib.dhp.schema.common.ModelConstants; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; import org.junit.jupiter.api.BeforeEach; @@ -252,6 +253,18 @@ public class MigrateDbEntitiesApplicationTest { assertValidId(r2.getSource()); assertEquals(r1.getSource(), r2.getTarget()); assertEquals(r2.getSource(), r1.getTarget()); + + assertTrue(r1.getSource().startsWith("10|")); + assertTrue(r1.getTarget().startsWith("20|")); + + assertEquals(ModelConstants.DATASOURCE_ORGANIZATION, r1.getRelType()); + assertEquals(ModelConstants.DATASOURCE_ORGANIZATION, r2.getRelType()); + + assertEquals(ModelConstants.PROVISION, r1.getSubRelType()); + assertEquals(ModelConstants.PROVISION, r2.getSubRelType()); + + assertEquals(ModelConstants.IS_PROVIDED_BY, r1.getRelClass()); + assertEquals(ModelConstants.PROVIDES, r2.getRelClass()); } @Test From b09d7ddc74fc13d3d1e7cfefccbfe1e472e88c41 Mon Sep 17 00:00:00 2001 From: Antonis Lempesis Date: Wed, 3 Aug 2022 12:26:59 +0300 Subject: [PATCH 02/10] fixed the datasourceOrganization relations --- .../eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql index 6fa0e6fdf..01bed17cc 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql @@ -93,7 +93,7 @@ where d.datainfo.deletedbyinference=false and d.datainfo.invisible=false; CREATE TABLE ${stats_db_name}.datasource_organizations STORED AS PARQUET AS SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS organization FROM ${openaire_db_name}.relation r -WHERE r.reltype = 'datasourceOrganization' and r.datainfo.deletedbyinference = false and r.target like '20|%' and r.datainfo.invisible=false; +WHERE r.reltype = 'datasourceOrganization' and r.datainfo.deletedbyinference = false and r.source like '20|%' and r.datainfo.invisible=false; -- datasource sources: -- where the datasource info have been collected from. From 27af5122d2d7f7d6d549dc23a5bf79a0c0030d1c Mon Sep 17 00:00:00 2001 From: Alessia Bardi Date: Mon, 12 Sep 2022 14:25:23 +0200 Subject: [PATCH 03/10] logs for non well formed XML files --- .../raw/AbstractMdRecordToOafMapper.java | 62 +++++++++------- .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 12 ++++ .../dhp/oa/graph/raw/oaf_notwellformed.xml | 70 +++++++++++++++++++ .../src/test/resources/log4j.properties | 8 +++ 4 files changed, 125 insertions(+), 27 deletions(-) create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_notwellformed.xml create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/log4j.properties diff --git 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 index a05faab80..e263cffa8 100644 --- 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 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 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 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"); - final KeyValue collectedFrom = getProvenanceDatasource( - doc, "//oaf:collectedFrom/@id", "//oaf:collectedFrom/@name"); + if (collectedFrom == null) { + return Lists.newArrayList(); + } - 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"); + + if (hostedBy == null) { + return Lists.newArrayList(); + } + + final DataInfo info = prepareDataInfo(doc, invisible); + final long lastUpdateTimestamp = new Date().getTime(); + + final List instances = prepareInstances(doc, info, collectedFrom, hostedBy); + + final String type = getResultType(doc, instances); + + return createOafs(doc, type, instances, collectedFrom, info, lastUpdateTimestamp); + } catch (DocumentException e) { + log.error("Error with record:\n" + xml); + throw e; } - - 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(); - } - - final DataInfo info = prepareDataInfo(doc, invisible); - final long lastUpdateTimestamp = new Date().getTime(); - - final List instances = prepareInstances(doc, info, collectedFrom, hostedBy); - - final String type = getResultType(doc, instances); - - return createOafs(doc, type, instances, collectedFrom, info, lastUpdateTimestamp); } protected String getResultType(final Document doc, final List instances) { diff --git 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 index b75f626d6..c4e34a9a8 100644 --- 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); diff --git 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 new file mode 100644 index 000000000..09384054e --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_notwellformed.xml @@ -0,0 +1,70 @@ + + +
+ jairo_______::000012e58ed836576ef2a0d38b0f726f + oai:irdb.nii.ac.jp:01221:0000010198 + + + + + + 2021-05-10T11:31:09.424Z + 2021-06-03T01:45:42.536Z + jairo_______ +
+ + 多項式GCDを用いた復号法に関する研究 + 上原, 剛 + 甲斐, 博 + 野田, 松太郎 + application/pdf + http://hdl.handle.net/2433/25934 + jpn + 京都大学数理解析研究所 + 410 + Departmental Bulletin Paper + 0014 + 2004-10-01 + + openaire____::554c7c2873 + OPEN + + + 2433/25934 + AN00061013 + http://hdl.handle.net/2433/25934 + http://repository.kulib.kyoto-u.ac.jp/dspace/bitstream/2433/25934/1/1395-16.pdf + 数理解析研究所講究録 + + + + + https%3A%2F%2Firdb.nii.ac.jp%2Foai + oai:irdb.nii.ac.jp:01221:0000010198 + 2021-04-13T13:36:29Z + + + http://repository.kulib.kyoto-u.ac.jp/dspace-oai/request + oai:repository.kulib.kyoto-u.ac.jp:2433/25934 + 2012-07-12T14:15:41Z + http://irdb.nii.ac.jp/oai + + + + + false + false + 0.9 + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/log4j.properties b/dhp-workflows/dhp-graph-mapper/src/test/resources/log4j.properties new file mode 100644 index 000000000..71255bb77 --- /dev/null +++ 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 \ No newline at end of file From b99a01134545beb75cf3a4114575be61c9c75486 Mon Sep 17 00:00:00 2001 From: Alessia Bardi Date: Tue, 13 Sep 2022 11:51:55 +0200 Subject: [PATCH 04/10] return empty Oaf list if record cannot be parsed --- .../dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java | 2 +- .../test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java | 5 +---- 2 files changed, 2 insertions(+), 5 deletions(-) diff --git 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 index e263cffa8..984254665 100644 --- 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 @@ -143,7 +143,7 @@ public abstract class AbstractMdRecordToOafMapper { return createOafs(doc, type, instances, collectedFrom, info, lastUpdateTimestamp); } catch (DocumentException e) { log.error("Error with record:\n" + xml); - throw e; + return Lists.newArrayList(); } } diff --git 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 index c4e34a9a8..8165ad757 100644 --- 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 @@ -931,11 +931,8 @@ class MappersTest { void testNotWellFormed() throws IOException, DocumentException { final String xml = IOUtils .toString(Objects.requireNonNull(getClass().getResourceAsStream("oaf_notwellformed.xml"))); - final DocumentException generalEx = new DocumentException(); + assertEquals(0, new OafToOafMapper(vocs, false, true).processMdRecord(xml).size()); - DocumentException exception = assertThrows(DocumentException.class, () -> { - new OafToOafMapper(vocs, false, true).processMdRecord(xml); - }); } private void assertValidId(final String id) { From a0919ed495c61da8d4cecbfa4c322d8f9c95176a Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Wed, 14 Sep 2022 13:27:39 +0200 Subject: [PATCH 05/10] [aggregator graph] save invalid records aside for further inspection --- .../raw/AbstractMdRecordToOafMapper.java | 2 +- .../raw/GenerateEntitiesApplication.java | 37 ++++++++++++++++++- .../graph/generate_entities_parameters.json | 6 +++ .../oa/graph/raw_all/oozie_app/workflow.xml | 2 + .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 2 - .../raw/MigrateDbEntitiesApplicationTest.java | 2 +- 6 files changed, 45 insertions(+), 6 deletions(-) diff --git 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 index 984254665..cdc707084 100644 --- 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 @@ -107,7 +107,7 @@ public abstract class AbstractMdRecordToOafMapper { this.forceOriginalId = false; } - public List processMdRecord(final String xml) throws DocumentException { + public List processMdRecord(final String xml) { DocumentFactory.getInstance().setXPathNamespaceURIs(nsContext); try { diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java index 6bb18c375..e9de43f7f 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java @@ -16,6 +16,9 @@ import org.apache.hadoop.io.compress.GzipCodec; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.rdd.RDD; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; import org.dom4j.DocumentException; import org.slf4j.Logger; @@ -76,6 +79,9 @@ public class GenerateEntitiesApplication { final String targetPath = parser.get("targetPath"); log.info("targetPath: {}", targetPath); + final String invalidPath = parser.get("invalidPath"); + log.info("invalidPath: {}", invalidPath); + final String isLookupUrl = parser.get("isLookupUrl"); log.info("isLookupUrl: {}", isLookupUrl); @@ -97,7 +103,8 @@ public class GenerateEntitiesApplication { final SparkConf conf = new SparkConf(); runWithSparkSession(conf, isSparkSessionManaged, spark -> { HdfsSupport.remove(targetPath, spark.sparkContext().hadoopConfiguration()); - generateEntities(spark, vocs, sourcePaths, targetPath, shouldHashId, mode); + HdfsSupport.remove(invalidPath, spark.sparkContext().hadoopConfiguration()); + generateEntities(spark, vocs, sourcePaths, targetPath, invalidPath, shouldHashId, mode); }); } @@ -106,6 +113,7 @@ public class GenerateEntitiesApplication { final VocabularyGroup vocs, final String sourcePaths, final String targetPath, + final String invalidPath, final boolean shouldHashId, final Mode mode) { @@ -121,6 +129,19 @@ public class GenerateEntitiesApplication { JavaRDD inputRdd = sc.emptyRDD(); for (final String sp : existingSourcePaths) { + RDD invalidRecords = sc + .sequenceFile(sp, Text.class, Text.class) + .map(k -> new Tuple2<>(k._1().toString(), k._2().toString())) + .map(k -> tryApplyMapping(k._1(), k._2(), shouldHashId, vocs)) + .filter(Objects::nonNull) + .rdd(); + spark + .createDataset(invalidRecords, Encoders.STRING()) + .write() + .mode(SaveMode.Append) + .option("compression", "gzip") + .text(invalidPath); + inputRdd = inputRdd .union( sc @@ -159,7 +180,7 @@ public class GenerateEntitiesApplication { final String id, final String s, final boolean shouldHashId, - final VocabularyGroup vocs) throws DocumentException { + final VocabularyGroup vocs) { final String type = StringUtils.substringAfter(id, ":"); switch (type.toLowerCase()) { @@ -196,6 +217,18 @@ public class GenerateEntitiesApplication { } } + private static String tryApplyMapping( + final String id, + final String s, + final boolean shouldHashId, + final VocabularyGroup vocs) { + + if (convertToListOaf(id, s, shouldHashId, vocs).isEmpty()) { + return s; + } + return null; + } + private static Oaf convertFromJson(final String s, final Class clazz) { try { return OBJECT_MAPPER.readValue(s, clazz); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/generate_entities_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/generate_entities_parameters.json index 52cbbf45f..da6730fbb 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/generate_entities_parameters.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/generate_entities_parameters.json @@ -17,6 +17,12 @@ "paramDescription": "the path of the target file", "paramRequired": true }, + { + "paramName": "i", + "paramLongName": "invalidPath", + "paramDescription": "the path of the invalid records file", + "paramRequired": false + }, { "paramName": "isu", "paramLongName": "isLookupUrl", diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml index c6cc46c0f..d00232e9a 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml @@ -468,6 +468,7 @@ --sourcePaths${contentPath}/db_claims,${contentPath}/oaf_claims,${contentPath}/odf_claims --targetPath${workingDir}/entities_claim + --invalidPath${workingDir}/invalid_records_claim --isLookupUrl${isLookupUrl} --shouldHashId${shouldHashId} --modeclaim @@ -517,6 +518,7 @@ --sourcePaths${contentPath}/db_openaire,${contentPath}/db_openorgs,${contentPath}/oaf_records,${contentPath}/odf_records,${contentPath}/oaf_records_hdfs,${contentPath}/odf_records_hdfs,${contentPath}/oaf_records_invisible --targetPath${workingDir}/entities + --invalidPath${workingDir}/invalid_records --isLookupUrl${isLookupUrl} --shouldHashId${shouldHashId} diff --git 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 index 8165ad757..204649633 100644 --- 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 @@ -12,7 +12,6 @@ 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; @@ -22,7 +21,6 @@ import org.junit.jupiter.api.extension.ExtendWith; import org.mockito.Mock; import org.mockito.junit.jupiter.MockitoExtension; -import com.fasterxml.jackson.core.JsonProcessingException; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java index 408196665..11947dbe7 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java @@ -18,7 +18,6 @@ import java.util.Objects; import java.util.Optional; import java.util.stream.Collectors; -import eu.dnetlib.dhp.schema.common.ModelConstants; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; import org.junit.jupiter.api.BeforeEach; @@ -32,6 +31,7 @@ import com.fasterxml.jackson.core.type.TypeReference; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; +import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; From c48f6e9c57c6b1fe549d59e032bc0cad6fa01f66 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Wed, 14 Sep 2022 17:11:26 +0200 Subject: [PATCH 06/10] [aggregator graph] save invalid records aside for further inspection --- .../dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java | 2 +- .../dhp/oa/graph/raw/GenerateEntitiesApplication.java | 8 +++++--- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git 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 index cdc707084..0a32766c9 100644 --- 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 @@ -143,7 +143,7 @@ public abstract class AbstractMdRecordToOafMapper { return createOafs(doc, type, instances, collectedFrom, info, lastUpdateTimestamp); } catch (DocumentException e) { log.error("Error with record:\n" + xml); - return Lists.newArrayList(); + return null; } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java index e9de43f7f..290a22656 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java @@ -126,8 +126,6 @@ public class GenerateEntitiesApplication { log.info("Generate entities from files:"); existingSourcePaths.forEach(log::info); - JavaRDD inputRdd = sc.emptyRDD(); - for (final String sp : existingSourcePaths) { RDD invalidRecords = sc .sequenceFile(sp, Text.class, Text.class) @@ -141,7 +139,11 @@ public class GenerateEntitiesApplication { .mode(SaveMode.Append) .option("compression", "gzip") .text(invalidPath); + } + JavaRDD inputRdd = sc.emptyRDD(); + + for (final String sp : existingSourcePaths) { inputRdd = inputRdd .union( sc @@ -223,7 +225,7 @@ public class GenerateEntitiesApplication { final boolean shouldHashId, final VocabularyGroup vocs) { - if (convertToListOaf(id, s, shouldHashId, vocs).isEmpty()) { + if (Objects.isNull(convertToListOaf(id, s, shouldHashId, vocs))) { return s; } return null; From 9e7ec4198fb99514b2f5e5f1c7817ffa7d0c1f8e Mon Sep 17 00:00:00 2001 From: Alessia Bardi Date: Wed, 14 Sep 2022 18:08:56 +0200 Subject: [PATCH 07/10] fixed test --- .../src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git 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 index 204649633..390920027 100644 --- 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 @@ -929,7 +929,7 @@ class MappersTest { void testNotWellFormed() throws IOException, DocumentException { final String xml = IOUtils .toString(Objects.requireNonNull(getClass().getResourceAsStream("oaf_notwellformed.xml"))); - assertEquals(0, new OafToOafMapper(vocs, false, true).processMdRecord(xml).size()); + assertEquals(null, new OafToOafMapper(vocs, false, true).processMdRecord(xml)); } From 1e42d984e1ead5e1e7519d69f8150f44060f9565 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 15 Sep 2022 10:49:42 +0200 Subject: [PATCH 08/10] [aggregator graph] save invalid records aside for further inspection --- .../dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java | 2 +- .../dhp/oa/graph/raw/GenerateEntitiesApplication.java | 10 +++++----- .../java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java | 7 ++++--- 3 files changed, 10 insertions(+), 9 deletions(-) diff --git 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 index 0a32766c9..cdc707084 100644 --- 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 @@ -143,7 +143,7 @@ public abstract class AbstractMdRecordToOafMapper { return createOafs(doc, type, instances, collectedFrom, info, lastUpdateTimestamp); } catch (DocumentException e) { log.error("Error with record:\n" + xml); - return null; + return Lists.newArrayList(); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java index 290a22656..06d5e9acb 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java @@ -150,8 +150,8 @@ public class GenerateEntitiesApplication { .sequenceFile(sp, Text.class, Text.class) .map(k -> new Tuple2<>(k._1().toString(), k._2().toString())) .map(k -> convertToListOaf(k._1(), k._2(), shouldHashId, vocs)) - .filter(Objects::nonNull) - .flatMap(List::iterator)); + .flatMap(List::iterator) + .filter(Objects::nonNull)); } switch (mode) { @@ -225,7 +225,8 @@ public class GenerateEntitiesApplication { final boolean shouldHashId, final VocabularyGroup vocs) { - if (Objects.isNull(convertToListOaf(id, s, shouldHashId, vocs))) { + final List oaf = convertToListOaf(id, s, shouldHashId, vocs); + if (Optional.ofNullable(oaf).map(List::isEmpty).orElse(false)) { return s; } return null; @@ -235,8 +236,7 @@ public class GenerateEntitiesApplication { try { return OBJECT_MAPPER.readValue(s, clazz); } catch (final Exception e) { - log.error("Error parsing object of class: {}", clazz); - log.error(s); + log.error("Error parsing object of class: {}:\n{}", clazz, s); throw new IllegalArgumentException(e); } } diff --git 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 index 390920027..506a69012 100644 --- 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 @@ -926,11 +926,12 @@ class MappersTest { } @Test - void testNotWellFormed() throws IOException, DocumentException { + void testNotWellFormed() throws IOException { final String xml = IOUtils .toString(Objects.requireNonNull(getClass().getResourceAsStream("oaf_notwellformed.xml"))); - assertEquals(null, new OafToOafMapper(vocs, false, true).processMdRecord(xml)); - + final List actual = new OafToOafMapper(vocs, false, true).processMdRecord(xml); + assertNotNull(actual); + assertTrue(actual.isEmpty()); } private void assertValidId(final String id) { From e370e940d871b5b9772eff48300ad8d9074641c3 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 16 Sep 2022 14:06:28 +0200 Subject: [PATCH 09/10] [aggregator graph] save invalid records aside for further inspection --- .../raw/GenerateEntitiesApplication.java | 37 +----- .../graph/raw/VerifyRecordsApplication.java | 108 ++++++++++++++++++ .../common/AbstractMigrationApplication.java | 6 +- .../graph/generate_entities_parameters.json | 6 - .../oa/graph/raw_all/oozie_app/workflow.xml | 54 ++++++++- .../oa/graph/verify_records_parameters.json | 26 +++++ 6 files changed, 191 insertions(+), 46 deletions(-) create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/VerifyRecordsApplication.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/verify_records_parameters.json diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java index 06d5e9acb..5f9d98073 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java @@ -79,9 +79,6 @@ public class GenerateEntitiesApplication { final String targetPath = parser.get("targetPath"); log.info("targetPath: {}", targetPath); - final String invalidPath = parser.get("invalidPath"); - log.info("invalidPath: {}", invalidPath); - final String isLookupUrl = parser.get("isLookupUrl"); log.info("isLookupUrl: {}", isLookupUrl); @@ -103,8 +100,7 @@ public class GenerateEntitiesApplication { final SparkConf conf = new SparkConf(); runWithSparkSession(conf, isSparkSessionManaged, spark -> { HdfsSupport.remove(targetPath, spark.sparkContext().hadoopConfiguration()); - HdfsSupport.remove(invalidPath, spark.sparkContext().hadoopConfiguration()); - generateEntities(spark, vocs, sourcePaths, targetPath, invalidPath, shouldHashId, mode); + generateEntities(spark, vocs, sourcePaths, targetPath, shouldHashId, mode); }); } @@ -113,7 +109,6 @@ public class GenerateEntitiesApplication { final VocabularyGroup vocs, final String sourcePaths, final String targetPath, - final String invalidPath, final boolean shouldHashId, final Mode mode) { @@ -126,21 +121,6 @@ public class GenerateEntitiesApplication { log.info("Generate entities from files:"); existingSourcePaths.forEach(log::info); - for (final String sp : existingSourcePaths) { - RDD invalidRecords = sc - .sequenceFile(sp, Text.class, Text.class) - .map(k -> new Tuple2<>(k._1().toString(), k._2().toString())) - .map(k -> tryApplyMapping(k._1(), k._2(), shouldHashId, vocs)) - .filter(Objects::nonNull) - .rdd(); - spark - .createDataset(invalidRecords, Encoders.STRING()) - .write() - .mode(SaveMode.Append) - .option("compression", "gzip") - .text(invalidPath); - } - JavaRDD inputRdd = sc.emptyRDD(); for (final String sp : existingSourcePaths) { @@ -178,7 +158,7 @@ public class GenerateEntitiesApplication { .saveAsTextFile(targetPath, GzipCodec.class); } - private static List convertToListOaf( + public static List convertToListOaf( final String id, final String s, final boolean shouldHashId, @@ -219,19 +199,6 @@ public class GenerateEntitiesApplication { } } - private static String tryApplyMapping( - final String id, - final String s, - final boolean shouldHashId, - final VocabularyGroup vocs) { - - final List oaf = convertToListOaf(id, s, shouldHashId, vocs); - if (Optional.ofNullable(oaf).map(List::isEmpty).orElse(false)) { - return s; - } - return null; - } - private static Oaf convertFromJson(final String s, final Class clazz) { try { return OBJECT_MAPPER.readValue(s, clazz); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/VerifyRecordsApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/VerifyRecordsApplication.java new file mode 100644 index 000000000..a8eb871c8 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/VerifyRecordsApplication.java @@ -0,0 +1,108 @@ + +package eu.dnetlib.dhp.oa.graph.raw; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.util.Arrays; +import java.util.List; +import java.util.Objects; +import java.util.Optional; +import java.util.stream.Collectors; + +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.io.Text; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.rdd.RDD; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.sql.SparkSession; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; +import eu.dnetlib.dhp.schema.oaf.Oaf; +import eu.dnetlib.dhp.utils.ISLookupClientFactory; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; +import scala.Tuple2; + +public class VerifyRecordsApplication { + + private static final Logger log = LoggerFactory.getLogger(VerifyRecordsApplication.class); + + public static void main(final String[] args) throws Exception { + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + VerifyRecordsApplication.class + .getResourceAsStream("/eu/dnetlib/dhp/oa/graph/verify_records_parameters.json"))); + + parser.parseArgument(args); + + final Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + final String sourcePaths = parser.get("sourcePaths"); + log.info("sourcePaths: {}", sourcePaths); + + final String invalidPath = parser.get("invalidPath"); + log.info("invalidPath: {}", invalidPath); + + final String isLookupUrl = parser.get("isLookupUrl"); + log.info("isLookupUrl: {}", isLookupUrl); + + final ISLookUpService isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl); + final VocabularyGroup vocs = VocabularyGroup.loadVocsFromIS(isLookupService); + + final SparkConf conf = new SparkConf(); + runWithSparkSession(conf, isSparkSessionManaged, spark -> { + HdfsSupport.remove(invalidPath, spark.sparkContext().hadoopConfiguration()); + validateRecords(spark, sourcePaths, invalidPath, vocs); + }); + } + + private static void validateRecords(SparkSession spark, String sourcePaths, String invalidPath, + VocabularyGroup vocs) { + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + final List existingSourcePaths = Arrays + .stream(sourcePaths.split(",")) + .filter(p -> HdfsSupport.exists(p, sc.hadoopConfiguration())) + .collect(Collectors.toList()); + + log.info("Verify records in files:"); + existingSourcePaths.forEach(log::info); + + for (final String sp : existingSourcePaths) { + RDD invalidRecords = sc + .sequenceFile(sp, Text.class, Text.class) + .map(k -> tryApplyMapping(k._1().toString(), k._2().toString(), true, vocs)) + .filter(Objects::nonNull) + .rdd(); + spark + .createDataset(invalidRecords, Encoders.STRING()) + .write() + .mode(SaveMode.Append) + .option("compression", "gzip") + .text(invalidPath); + } + } + + private static String tryApplyMapping( + final String id, + final String xmlRecord, + final boolean shouldHashId, + final VocabularyGroup vocs) { + + final List oaf = GenerateEntitiesApplication.convertToListOaf(id, xmlRecord, shouldHashId, vocs); + if (Optional.ofNullable(oaf).map(List::isEmpty).orElse(false)) { + return xmlRecord; + } + return null; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/AbstractMigrationApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/AbstractMigrationApplication.java index cba64899b..6f63e9327 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/AbstractMigrationApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/AbstractMigrationApplication.java @@ -4,6 +4,7 @@ package eu.dnetlib.dhp.oa.graph.raw.common; import java.io.Closeable; import java.io.IOException; import java.util.Arrays; +import java.util.List; import java.util.Set; import java.util.concurrent.atomic.AtomicInteger; import java.util.stream.Collectors; @@ -24,8 +25,11 @@ import org.apache.http.impl.client.HttpClients; import com.fasterxml.jackson.core.JsonProcessingException; import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; +import eu.dnetlib.dhp.oa.graph.raw.OafToOafMapper; +import eu.dnetlib.dhp.oa.graph.raw.OdfToOafMapper; import eu.dnetlib.dhp.schema.mdstore.MDStoreWithInfo; -import eu.dnetlib.dhp.schema.oaf.Oaf; +import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.utils.DHPUtils; public class AbstractMigrationApplication implements Closeable { diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/generate_entities_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/generate_entities_parameters.json index da6730fbb..52cbbf45f 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/generate_entities_parameters.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/generate_entities_parameters.json @@ -17,12 +17,6 @@ "paramDescription": "the path of the target file", "paramRequired": true }, - { - "paramName": "i", - "paramLongName": "invalidPath", - "paramDescription": "the path of the invalid records file", - "paramRequired": false - }, { "paramName": "isu", "paramLongName": "isLookupUrl", diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml index d00232e9a..8262c6923 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml @@ -446,10 +446,34 @@ - - + + + + + yarn + cluster + VerifyRecords_claim + eu.dnetlib.dhp.oa.graph.raw.VerifyRecordsApplication + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory ${sparkExecutorMemory} + --executor-cores ${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --sourcePaths${contentPath}/db_claims,${contentPath}/oaf_claims,${contentPath}/odf_claims + --invalidPath${workingDir}/invalid_records_claim + --isLookupUrl${isLookupUrl} + + + + + yarn @@ -468,7 +492,6 @@ --sourcePaths${contentPath}/db_claims,${contentPath}/oaf_claims,${contentPath}/odf_claims --targetPath${workingDir}/entities_claim - --invalidPath${workingDir}/invalid_records_claim --isLookupUrl${isLookupUrl} --shouldHashId${shouldHashId} --modeclaim @@ -500,6 +523,30 @@ + + + yarn + cluster + VerifyRecords + eu.dnetlib.dhp.oa.graph.raw.VerifyRecordsApplication + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory ${sparkExecutorMemory} + --executor-cores ${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --sourcePaths${contentPath}/db_openaire,${contentPath}/db_openorgs,${contentPath}/oaf_records,${contentPath}/odf_records,${contentPath}/oaf_records_hdfs,${contentPath}/odf_records_hdfs,${contentPath}/oaf_records_invisible + --invalidPath${workingDir}/invalid_records + --isLookupUrl${isLookupUrl} + + + + + yarn @@ -518,7 +565,6 @@ --sourcePaths${contentPath}/db_openaire,${contentPath}/db_openorgs,${contentPath}/oaf_records,${contentPath}/odf_records,${contentPath}/oaf_records_hdfs,${contentPath}/odf_records_hdfs,${contentPath}/oaf_records_invisible --targetPath${workingDir}/entities - --invalidPath${workingDir}/invalid_records --isLookupUrl${isLookupUrl} --shouldHashId${shouldHashId} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/verify_records_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/verify_records_parameters.json new file mode 100644 index 000000000..eb00e7609 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/verify_records_parameters.json @@ -0,0 +1,26 @@ +[ + { + "paramName": "issm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "when true will stop SparkSession after job execution", + "paramRequired": false + }, + { + "paramName": "s", + "paramLongName": "sourcePaths", + "paramDescription": "the HDFS source paths which contains the sequential file (comma separated)", + "paramRequired": true + }, + { + "paramName": "i", + "paramLongName": "invalidPath", + "paramDescription": "the path of the invalid records file", + "paramRequired": false + }, + { + "paramName": "isu", + "paramLongName": "isLookupUrl", + "paramDescription": "the url of the ISLookupService", + "paramRequired": true + } +] \ No newline at end of file From 26e1baddedc95ee93ba7577ef34b29e9b09940ed Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 19 Sep 2022 11:19:10 +0200 Subject: [PATCH 10/10] added instance.url syntactical validation, avoid creating multiple duplicated URLs --- dhp-workflows/dhp-graph-mapper/pom.xml | 5 +++ .../raw/AbstractMdRecordToOafMapper.java | 15 +++++++ .../dhp/oa/graph/raw/OafToOafMapper.java | 35 +++++++++-------- .../dhp/oa/graph/raw/OdfToOafMapper.java | 39 ++++++++++++------- .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 2 +- pom.xml | 6 +++ 6 files changed, 71 insertions(+), 31 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/pom.xml b/dhp-workflows/dhp-graph-mapper/pom.xml index 687f0de66..f579a7d2b 100644 --- a/dhp-workflows/dhp-graph-mapper/pom.xml +++ b/dhp-workflows/dhp-graph-mapper/pom.xml @@ -57,6 +57,11 @@ commons-io + + commons-validator + commons-validator + + org.apache.spark spark-core_2.11 diff --git 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 index 5cfb22cb9..a8d09e4a7 100644 --- 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 @@ -10,9 +10,13 @@ import static eu.dnetlib.dhp.schema.common.ModelConstants.RESULT_PROJECT; import static eu.dnetlib.dhp.schema.common.ModelConstants.UNKNOWN; import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.*; +import java.net.MalformedURLException; +import java.net.URL; import java.util.*; +import java.util.stream.Collectors; import org.apache.commons.lang3.StringUtils; +import org.apache.commons.validator.routines.UrlValidator; import org.dom4j.*; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -617,4 +621,15 @@ public abstract class AbstractMdRecordToOafMapper { return res; } + protected Set validateUrl(Collection url) { + UrlValidator urlValidator = UrlValidator.getInstance(); + if (Objects.isNull(url)) { + return new HashSet<>(); + } + return url + .stream() + .filter(u -> urlValidator.isValid(u)) + .collect(Collectors.toCollection(HashSet::new)); + } + } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java index 9225e174d..30f3935f5 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java @@ -159,22 +159,25 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper { .setProcessingchargecurrency(field(doc.valueOf("//oaf:processingchargeamount/@currency"), info)); final List nodes = Lists.newArrayList(doc.selectNodes("//dc:identifier")); - instance - .setUrl( - nodes - .stream() - .filter(n -> StringUtils.isNotBlank(n.getText())) - .map(n -> n.getText().trim()) - .filter(u -> u.startsWith("http")) - .map(s -> { - try { - return URLDecoder.decode(s, "UTF-8"); - } catch (Throwable t) { - return s; - } - }) - .distinct() - .collect(Collectors.toCollection(ArrayList::new))); + final List url = nodes + .stream() + .filter(n -> StringUtils.isNotBlank(n.getText())) + .map(n -> n.getText().trim()) + .filter(u -> u.startsWith("http")) + .map(s -> { + try { + return URLDecoder.decode(s, "UTF-8"); + } catch (Throwable t) { + return s; + } + }) + .distinct() + .collect(Collectors.toCollection(ArrayList::new)); + final Set validUrl = validateUrl(url); + if (!validUrl.isEmpty()) { + instance.setUrl(new ArrayList<>()); + instance.getUrl().addAll(validUrl); + } return Lists.newArrayList(instance); } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java index d6bfe6714..5781988e6 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java @@ -6,11 +6,14 @@ import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.*; import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.structuredProperty; import java.io.UnsupportedEncodingException; +import java.net.MalformedURLException; +import java.net.URL; import java.net.URLDecoder; import java.util.*; import java.util.stream.Collectors; import org.apache.commons.lang3.StringUtils; +import org.apache.commons.validator.routines.UrlValidator; import org.dom4j.Document; import org.dom4j.Element; import org.dom4j.Node; @@ -171,23 +174,31 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { for (final Object o : doc.selectNodes("//*[local-name()='identifier' and ./@identifierType='landingPage']")) { url.add(trimAndDecodeUrl(((Node) o).getText().trim())); } - for (final Object o : doc - .selectNodes("//*[local-name()='alternateIdentifier' and ./@alternateIdentifierType='DOI']")) { - url.add(HTTP_DOI_PREIFX + ((Node) o).getText().trim()); + + Set validUrl = validateUrl(url); + + if (validUrl.stream().noneMatch(s -> s.contains("doi.org"))) { + for (final Object o : doc + .selectNodes("//*[local-name()='alternateIdentifier' and ./@alternateIdentifierType='DOI']")) { + validUrl.add(HTTP_DOI_PREIFX + ((Node) o).getText().trim()); + } + for (final Object o : doc.selectNodes("//*[local-name()='identifier' and ./@identifierType='DOI']")) { + validUrl.add(HTTP_DOI_PREIFX + ((Node) o).getText().trim()); + } } - for (final Object o : doc.selectNodes("//*[local-name()='identifier' and ./@identifierType='DOI']")) { - url.add(HTTP_DOI_PREIFX + ((Node) o).getText().trim()); + if (validUrl.stream().noneMatch(s -> s.contains("hdl.handle.net"))) { + for (final Object o : doc + .selectNodes("//*[local-name()='alternateIdentifier' and ./@alternateIdentifierType='Handle']")) { + validUrl.add(HTTP_HANDLE_PREIFX + ((Node) o).getText().trim()); + } + for (final Object o : doc.selectNodes("//*[local-name()='identifier' and ./@identifierType='Handle']")) { + validUrl.add(HTTP_HANDLE_PREIFX + ((Node) o).getText().trim()); + } } - for (final Object o : doc - .selectNodes("//*[local-name()='alternateIdentifier' and ./@alternateIdentifierType='Handle']")) { - url.add(HTTP_HANDLE_PREIFX + ((Node) o).getText().trim()); - } - for (final Object o : doc.selectNodes("//*[local-name()='identifier' and ./@identifierType='Handle']")) { - url.add(HTTP_HANDLE_PREIFX + ((Node) o).getText().trim()); - } - if (!url.isEmpty()) { + + if (!validUrl.isEmpty()) { instance.setUrl(new ArrayList<>()); - instance.getUrl().addAll(url); + instance.getUrl().addAll(validUrl); } return Arrays.asList(instance); } diff --git 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 index 231d5b0ac..64b68e6af 100644 --- 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 @@ -950,7 +950,7 @@ class MappersTest { @Test void testNotWellFormed() throws IOException { final String xml = IOUtils - .toString(Objects.requireNonNull(getClass().getResourceAsStream("oaf_notwellformed.xml"))); + .toString(Objects.requireNonNull(getClass().getResourceAsStream("oaf_notwellformed.xml"))); final List actual = new OafToOafMapper(vocs, false, true).processMdRecord(xml); assertNotNull(actual); assertTrue(actual.isEmpty()); diff --git a/pom.xml b/pom.xml index ab59e7be3..a1b26966e 100644 --- a/pom.xml +++ b/pom.xml @@ -200,6 +200,12 @@ ${dhp.commons.lang.version} + + commons-validator + commons-validator + 1.7 + + com.github.sisyphsu dateparser