From 2b9d0416eca2b0b1fc5b9a2b7ed19ca0868ddd2c Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 19 Oct 2023 16:26:37 +0200 Subject: [PATCH 1/7] [graph raw] URL Validator to accept double slashes --- .../raw/AbstractMdRecordToOafMapper.java | 2 +- .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 14 ++++ .../dnetlib/dhp/oa/graph/raw/idus_sevilla.xml | 65 +++++++++++++++++++ 3 files changed, 80 insertions(+), 1 deletion(-) create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/idus_sevilla.xml 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 b37e6a755..bca6a2aae 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 @@ -29,7 +29,7 @@ public abstract class AbstractMdRecordToOafMapper { protected final VocabularyGroup vocs; - protected static final UrlValidator URL_VALIDATOR = UrlValidator.getInstance(); + protected static final UrlValidator URL_VALIDATOR = new UrlValidator(UrlValidator.ALLOW_2_SLASHES); private final boolean invisible; 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 b506d3a62..da7a890ee 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 @@ -797,6 +797,20 @@ class MappersTest { assertFalse(p_cleaned.getTitle().isEmpty()); } + @Test + void test_instance_url_validation() throws IOException { + final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("idus_sevilla.xml"))); + final List list = new OafToOafMapper(vocs, false, true).processMdRecord(xml); + + final Publication p = (Publication) list.get(0); + + assertNotNull(p.getInstance()); + assertFalse(p.getInstance().isEmpty()); + assertNotNull(p.getInstance().get(0).getUrl()); + assertFalse(p.getInstance().get(0).getUrl().isEmpty()); + assertEquals("https://idus.us.es/handle//11441/118940", p.getInstance().get(0).getUrl().get(0)); + } + @Test void testZenodo() throws IOException, DocumentException { final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("odf_zenodo.xml"))); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/idus_sevilla.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/idus_sevilla.xml new file mode 100644 index 000000000..1bfa3c7c3 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/idus_sevilla.xml @@ -0,0 +1,65 @@ + + +
+ od______3272::6a4d00217a024a46ce9697ce98b13c2a + oai:idus.us.es:11441/118940 + + + + + + 2021-08-20T12:32:32.826Z + 2023-07-04T15:47:55.397Z + od______3272 +
+ + El museo pictorico y escala optica : tomo I : theorica de la pintura en que se describe su origen ... y se aprueban con demonstraciomes mathematicas y filosoficas, sus mas radicales fundamentos + Palomino de Castro y Velasco, Antonio, 1653-1726 + Rovira y Brocandel, Hipólito, 1693-1765 + Palomino de Castro y Velasco, Antonio, 1653-1726 + 2021-08-12T08:59:53Z + 1715 + A 042(a)/063 + application/pdf + https://idus.us.es/handle//11441/118940 + spa + En Madrid : por Lucas Antonio de Bedmar ... : vendese en casa de Don Joseph de Villar y Villanueva, 1715 + info:eu-repo/semantics/book + info:eu-repo/semantics/publishedVersion + 0002 + 1715-01-01 + + opendoar____::3272 + OPEN + + + https://idus.us.es/handle//11441/118940 + + http://creativecommons.org/licenses/by-nc-nd/4.0/ + + + + + http%3A%2F%2Fidus.us.es%2Foai%2Fdriver + oai:idus.us.es:11441/118940 + 2021-08-12T08:59:54Z + http://www.openarchives.org/OAI/2.0/oai_dc/ + + + + false + false + 0.9 + + + + + \ No newline at end of file From 6b19dcee80cdc19b6acdd95e6b05e5a4093b3ba7 Mon Sep 17 00:00:00 2001 From: Serafeim Chatzopoulos Date: Thu, 19 Oct 2023 19:58:25 +0300 Subject: [PATCH 2/7] Add actionset creation for pubmed affiliations --- .../PrepareAffiliationRelations.java | 32 ++++++++++++------- .../input_actionset_parameter.json | 8 ++++- .../bipaffiliations/job.properties | 1 + .../bipaffiliations/oozie_app/workflow.xml | 7 +++- 4 files changed, 35 insertions(+), 13 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java index 603ad6339..cbfba30c5 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java @@ -12,6 +12,7 @@ import org.apache.hadoop.io.Text; import org.apache.hadoop.io.compress.GzipCodec; import org.apache.hadoop.mapred.SequenceFileOutputFormat; import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaPairRDD; import org.apache.spark.api.java.function.FlatMapFunction; import org.apache.spark.sql.*; import org.apache.spark.sql.Dataset; @@ -58,10 +59,13 @@ public class PrepareAffiliationRelations implements Serializable { log.info("isSparkSessionManaged: {}", isSparkSessionManaged); final String inputPath = parser.get("inputPath"); - log.info("inputPath {}: ", inputPath); + log.info("inputPath: {}", inputPath); + + final String pubmedInputPath = parser.get("pubmedInputPath"); + log.info("pubmedInputPath: {}", pubmedInputPath); final String outputPath = parser.get("outputPath"); - log.info("outputPath {}: ", outputPath); + log.info("outputPath: {}", outputPath); SparkConf conf = new SparkConf(); @@ -70,12 +74,22 @@ public class PrepareAffiliationRelations implements Serializable { isSparkSessionManaged, spark -> { Constants.removeOutputDir(spark, outputPath); - prepareAffiliationRelations(spark, inputPath, outputPath); + + List collectedFromCrossref = OafMapperUtils.listKeyValues(ModelConstants.CROSSREF_ID, "Crossref"); + JavaPairRDD crossrefRelations = prepareAffiliationRelations(spark, inputPath, collectedFromCrossref); + + List collectedFromPubmed = OafMapperUtils.listKeyValues(ModelConstants.PUBMED_CENTRAL_ID, "Pubmed"); + JavaPairRDD pubmedRelations = prepareAffiliationRelations(spark, inputPath, collectedFromPubmed); + + crossrefRelations + .union(pubmedRelations) + .saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class); + }); } - private static void prepareAffiliationRelations(SparkSession spark, String inputPath, - String outputPath) { + private static JavaPairRDD prepareAffiliationRelations(SparkSession spark, String inputPath, + List collectedfrom) { // load and parse affiliation relations from HDFS Dataset df = spark @@ -92,7 +106,7 @@ public class PrepareAffiliationRelations implements Serializable { new Column("matching.Confidence").as("confidence")); // prepare action sets for affiliation relations - df + return df .toJavaRDD() .flatMap((FlatMapFunction) row -> { @@ -120,8 +134,6 @@ public class PrepareAffiliationRelations implements Serializable { qualifier, Double.toString(row.getAs("confidence"))); - List collectedfrom = OafMapperUtils.listKeyValues(ModelConstants.CROSSREF_ID, "Crossref"); - // return bi-directional relations return getAffiliationRelationPair(paperId, affId, collectedfrom, dataInfo).iterator(); @@ -129,9 +141,7 @@ public class PrepareAffiliationRelations implements Serializable { .map(p -> new AtomicAction(Relation.class, p)) .mapToPair( aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()), - new Text(OBJECT_MAPPER.writeValueAsString(aa)))) - .saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class); - + new Text(OBJECT_MAPPER.writeValueAsString(aa)))); } private static List getAffiliationRelationPair(String paperId, String affId, List collectedfrom, diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/input_actionset_parameter.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/input_actionset_parameter.json index 7663a454b..96dcc3b32 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/input_actionset_parameter.json +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/input_actionset_parameter.json @@ -8,7 +8,13 @@ { "paramName": "ip", "paramLongName": "inputPath", - "paramDescription": "the URL from where to get the programme file", + "paramDescription": "the path to get the input data from Crossref", + "paramRequired": true + }, + { + "paramName": "pip", + "paramLongName": "pubmedInputPath", + "paramDescription": "the path to get the input data from Pubmed", "paramRequired": true }, { diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/job.properties b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/job.properties index d942e6772..fe3cbb633 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/job.properties +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/job.properties @@ -32,4 +32,5 @@ spark2SqlQueryExecutionListeners=com.cloudera.spark.lineage.NavigatorQueryListen oozie.wf.application.path=${oozieTopWfApplicationPath} inputPath=/data/bip-affiliations/data.json +pubmedInputPath=/data/bip-affiiations/pubmed-data.json outputPath=/tmp/crossref-affiliations-output-v5 diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/oozie_app/workflow.xml index 9930cfe17..c0a6bfc52 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/oozie_app/workflow.xml @@ -3,7 +3,11 @@ inputPath - the path where to find the inferred affiliation relations + the path where to find the inferred affiliation relations from Crossref + + + pubmedInputPath + the path where to find the inferred affiliation relations from Pubmed outputPath @@ -97,6 +101,7 @@ --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} --inputPath${inputPath} + --pubmedInputPath${pubmedInputPath} --outputPath${outputPath} From aad5982bf171d4504de660afa1a4350bd7e761f9 Mon Sep 17 00:00:00 2001 From: Serafeim Chatzopoulos Date: Fri, 20 Oct 2023 12:48:21 +0300 Subject: [PATCH 3/7] Change the description of the workflow --- .../PrepareAffiliationRelations.java | 22 ++++++++++++------- .../bipaffiliations/oozie_app/workflow.xml | 2 +- 2 files changed, 15 insertions(+), 9 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java index cbfba30c5..18d98be54 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java @@ -75,21 +75,27 @@ public class PrepareAffiliationRelations implements Serializable { spark -> { Constants.removeOutputDir(spark, outputPath); - List collectedFromCrossref = OafMapperUtils.listKeyValues(ModelConstants.CROSSREF_ID, "Crossref"); - JavaPairRDD crossrefRelations = prepareAffiliationRelations(spark, inputPath, collectedFromCrossref); + List collectedFromCrossref = OafMapperUtils + .listKeyValues(ModelConstants.CROSSREF_ID, "Crossref"); + JavaPairRDD crossrefRelations = prepareAffiliationRelations( + spark, inputPath, collectedFromCrossref); - List collectedFromPubmed = OafMapperUtils.listKeyValues(ModelConstants.PUBMED_CENTRAL_ID, "Pubmed"); - JavaPairRDD pubmedRelations = prepareAffiliationRelations(spark, inputPath, collectedFromPubmed); + List collectedFromPubmed = OafMapperUtils + .listKeyValues(ModelConstants.PUBMED_CENTRAL_ID, "Pubmed"); + JavaPairRDD pubmedRelations = prepareAffiliationRelations( + spark, inputPath, collectedFromPubmed); crossrefRelations - .union(pubmedRelations) - .saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class); + .union(pubmedRelations) + .saveAsHadoopFile( + outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class); }); } - private static JavaPairRDD prepareAffiliationRelations(SparkSession spark, String inputPath, - List collectedfrom) { + private static JavaPairRDD prepareAffiliationRelations(SparkSession spark, + String inputPath, + List collectedfrom) { // load and parse affiliation relations from HDFS Dataset df = spark diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/oozie_app/workflow.xml index c0a6bfc52..e3fdddfd6 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/oozie_app/workflow.xml @@ -87,7 +87,7 @@ yarn cluster - Produces the atomic action with the inferred by BIP! affiliation relations from Crossref + Produces the atomic action with the inferred by BIP! affiliation relations (from Crossref and Pubmed) eu.dnetlib.dhp.actionmanager.bipaffiliations.PrepareAffiliationRelations dhp-aggregation-${projectVersion}.jar From a82aaf57b219faa880817cf18213b22944cb730b Mon Sep 17 00:00:00 2001 From: Serafeim Chatzopoulos Date: Wed, 25 Oct 2023 12:05:02 -0700 Subject: [PATCH 4/7] Renaming input param for crossref input path --- .../bipaffiliations/PrepareAffiliationRelations.java | 8 ++++---- .../bipaffiliations/input_actionset_parameter.json | 4 ++-- .../dhp/actionmanager/bipaffiliations/job.properties | 4 ++-- .../actionmanager/bipaffiliations/oozie_app/workflow.xml | 4 ++-- 4 files changed, 10 insertions(+), 10 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java index 18d98be54..1bdb06ecc 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java @@ -58,8 +58,8 @@ public class PrepareAffiliationRelations implements Serializable { Boolean isSparkSessionManaged = Constants.isSparkSessionManaged(parser); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - final String inputPath = parser.get("inputPath"); - log.info("inputPath: {}", inputPath); + final String crossrefInputPath = parser.get("crossrefInputPath"); + log.info("crossrefInputPath: {}", crossrefInputPath); final String pubmedInputPath = parser.get("pubmedInputPath"); log.info("pubmedInputPath: {}", pubmedInputPath); @@ -78,12 +78,12 @@ public class PrepareAffiliationRelations implements Serializable { List collectedFromCrossref = OafMapperUtils .listKeyValues(ModelConstants.CROSSREF_ID, "Crossref"); JavaPairRDD crossrefRelations = prepareAffiliationRelations( - spark, inputPath, collectedFromCrossref); + spark, crossrefInputPath, collectedFromCrossref); List collectedFromPubmed = OafMapperUtils .listKeyValues(ModelConstants.PUBMED_CENTRAL_ID, "Pubmed"); JavaPairRDD pubmedRelations = prepareAffiliationRelations( - spark, inputPath, collectedFromPubmed); + spark, pubmedInputPath, collectedFromPubmed); crossrefRelations .union(pubmedRelations) diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/input_actionset_parameter.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/input_actionset_parameter.json index 96dcc3b32..c6f905199 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/input_actionset_parameter.json +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/input_actionset_parameter.json @@ -6,8 +6,8 @@ "paramRequired": false }, { - "paramName": "ip", - "paramLongName": "inputPath", + "paramName": "cip", + "paramLongName": "crossrefInputPath", "paramDescription": "the path to get the input data from Crossref", "paramRequired": true }, diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/job.properties b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/job.properties index fe3cbb633..a3d55ff0c 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/job.properties +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/job.properties @@ -31,6 +31,6 @@ spark2SqlQueryExecutionListeners=com.cloudera.spark.lineage.NavigatorQueryListen # The following is needed as a property of a workflow oozie.wf.application.path=${oozieTopWfApplicationPath} -inputPath=/data/bip-affiliations/data.json -pubmedInputPath=/data/bip-affiiations/pubmed-data.json +crossrefInputPath=/data/bip-affiliations/data.json +pubmedInputPath=/data/bip-affiliations/pubmed-data.json outputPath=/tmp/crossref-affiliations-output-v5 diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/oozie_app/workflow.xml index e3fdddfd6..c5ac6f884 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/oozie_app/workflow.xml @@ -2,7 +2,7 @@ - inputPath + crossrefInputPath the path where to find the inferred affiliation relations from Crossref @@ -100,7 +100,7 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - --inputPath${inputPath} + --crossrefInputPath${crossrefInputPath} --pubmedInputPath${pubmedInputPath} --outputPath${outputPath} From 2090003ea96dee43c3cd6c90f50f6d4a2b39a869 Mon Sep 17 00:00:00 2001 From: Serafeim Chatzopoulos Date: Thu, 26 Oct 2023 13:47:06 -0700 Subject: [PATCH 5/7] Adjust tests to new WF input params --- .../PrepareAffiliationRelationsTest.java | 15 ++++++++++----- 1 file changed, 10 insertions(+), 5 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelationsTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelationsTest.java index ed8e5fe0d..e2639996c 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelationsTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelationsTest.java @@ -74,17 +74,22 @@ public class PrepareAffiliationRelationsTest { @Test void testMatch() throws Exception { - String affiliationRelationsPath = getClass() + String crossrefAffiliationRelationPath = getClass() .getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror.json") .getPath(); + String pubmedAffiliationRelationsPath = getClass() + .getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror.json") + .getPath(); + String outputPath = workingDir.toString() + "/actionSet"; PrepareAffiliationRelations .main( new String[] { "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-inputPath", affiliationRelationsPath, + "-crossrefInputPath", crossrefAffiliationRelationPath, + "-pubmedInputPath", pubmedAffiliationRelationsPath, "-outputPath", outputPath }); @@ -101,7 +106,7 @@ public class PrepareAffiliationRelationsTest { // ); // } // count the number of relations - assertEquals(20, tmp.count()); + assertEquals(40, tmp.count()); Dataset dataset = spark.createDataset(tmp.rdd(), Encoders.bean(Relation.class)); dataset.createOrReplaceTempView("result"); @@ -112,7 +117,7 @@ public class PrepareAffiliationRelationsTest { // verify that we have equal number of bi-directional relations Assertions .assertEquals( - 10, execVerification + 20, execVerification .filter( "relClass='" + ModelConstants.HAS_AUTHOR_INSTITUTION + "'") .collectAsList() @@ -120,7 +125,7 @@ public class PrepareAffiliationRelationsTest { Assertions .assertEquals( - 10, execVerification + 20, execVerification .filter( "relClass='" + ModelConstants.IS_AUTHOR_INSTITUTION_OF + "'") .collectAsList() From 262d7c581b56244cc3eab179bcb3ad82ba6174ae Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 31 Oct 2023 14:34:10 +0100 Subject: [PATCH 6/7] [graph cleaning] implemented further suggestions from https://support.openaire.eu/issues/8898 --- .../oaf/utils/GraphCleaningFunctions.java | 95 +++++++++++++++++-- .../graph/clean/CleanGraphSparkJobTest.java | 15 +++ .../clean/graph/publication/publication.json | 2 +- 3 files changed, 103 insertions(+), 9 deletions(-) diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java index b4402a2fb..e8bada028 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java @@ -3,16 +3,20 @@ package eu.dnetlib.dhp.schema.oaf.utils; import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.getProvenance; +import java.net.MalformedURLException; +import java.net.URL; import java.time.LocalDate; import java.time.ZoneId; import java.time.format.DateTimeFormatter; import java.time.format.DateTimeParseException; import java.util.*; import java.util.function.Function; +import java.util.function.Supplier; import java.util.stream.Collectors; import java.util.stream.Stream; import org.apache.commons.lang3.StringUtils; +import org.apache.cxf.common.util.UrlUtils; import com.github.sisyphsu.dateparser.DateParserUtils; import com.google.common.collect.Lists; @@ -23,6 +27,7 @@ import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.*; import me.xuender.unidecode.Unidecode; +import sun.awt.HKSCS; public class GraphCleaningFunctions extends CleaningFunctions { @@ -36,6 +41,13 @@ public class GraphCleaningFunctions extends CleaningFunctions { public static final int TITLE_FILTER_RESIDUAL_LENGTH = 5; private static final String NAME_CLEANING_REGEX = "[\\r\\n\\t\\s]+"; + + private static final Set INVALID_AUTHOR_NAMES = new HashSet<>(); + + private static final Set INVALID_URLS = new HashSet<>(); + + private static final Set INVALID_URL_HOSTS = new HashSet<>(); + private static final HashSet PEER_REVIEWED_TYPES = new HashSet<>(); static { @@ -48,6 +60,47 @@ public class GraphCleaningFunctions extends CleaningFunctions { PEER_REVIEWED_TYPES.add("Thesis"); PEER_REVIEWED_TYPES.add("Bachelor thesis"); PEER_REVIEWED_TYPES.add("Conference object"); + + INVALID_AUTHOR_NAMES.add("(:null)"); + INVALID_AUTHOR_NAMES.add("(:unap)"); + INVALID_AUTHOR_NAMES.add("(:tba)"); + INVALID_AUTHOR_NAMES.add("(:unas)"); + INVALID_AUTHOR_NAMES.add("(:unav)"); + INVALID_AUTHOR_NAMES.add("(:unkn)"); + INVALID_AUTHOR_NAMES.add("(:unkn) unknown"); + INVALID_AUTHOR_NAMES.add(":none"); + INVALID_AUTHOR_NAMES.add(":null"); + INVALID_AUTHOR_NAMES.add(":unas"); + INVALID_AUTHOR_NAMES.add(":unav"); + INVALID_AUTHOR_NAMES.add(":unkn"); + INVALID_AUTHOR_NAMES.add("[autor desconocido]"); + INVALID_AUTHOR_NAMES.add("[s. n.]"); + INVALID_AUTHOR_NAMES.add("[s.n]"); + INVALID_AUTHOR_NAMES.add("[unknown]"); + INVALID_AUTHOR_NAMES.add("anonymous"); + INVALID_AUTHOR_NAMES.add("n.n."); + INVALID_AUTHOR_NAMES.add("nn"); + INVALID_AUTHOR_NAMES.add("no name supplied"); + INVALID_AUTHOR_NAMES.add("none"); + INVALID_AUTHOR_NAMES.add("none available"); + INVALID_AUTHOR_NAMES.add("not available not available"); + INVALID_AUTHOR_NAMES.add("null &na;"); + INVALID_AUTHOR_NAMES.add("null anonymous"); + INVALID_AUTHOR_NAMES.add("unbekannt"); + INVALID_AUTHOR_NAMES.add("unknown"); + + INVALID_URL_HOSTS.add("creativecommons.org"); + INVALID_URL_HOSTS.add("www.academia.edu"); + INVALID_URL_HOSTS.add("academia.edu"); + INVALID_URL_HOSTS.add("researchgate.net"); + INVALID_URL_HOSTS.add("www.researchgate.net"); + + INVALID_URLS.add("http://repo.scoap3.org/api"); + INVALID_URLS.add("http://ora.ox.ac.uk/objects/uuid:"); + INVALID_URLS.add("http://ntur.lib.ntu.edu.tw/news/agent_contract.pdf"); + INVALID_URLS.add("https://media.springer.com/full/springer-instructions-for-authors-assets/pdf/SN_BPF_EN.pdf"); + INVALID_URLS.add("http://www.tobaccoinduceddiseases.org/dl/61aad426c96519bea4040a374c6a6110/"); + INVALID_URLS.add("https://www.bilboard.nl/verenigingsbladen/bestuurskundige-berichten"); } public static T cleanContext(T value, String contextId, String verifyParam) { @@ -558,6 +611,15 @@ public class GraphCleaningFunctions extends CleaningFunctions { ModelConstants.DATASET_RESULTTYPE_CLASSID.equals(r.getResulttype().getClassid()))) { i.setFulltext(null); } + if (Objects.nonNull(i.getUrl())) { + i + .setUrl( + i + .getUrl() + .stream() + .filter(GraphCleaningFunctions::urlFilter) + .collect(Collectors.toList())); + } } } if (Objects.isNull(r.getBestaccessright()) @@ -580,8 +642,7 @@ public class GraphCleaningFunctions extends CleaningFunctions { .getAuthor() .stream() .filter(Objects::nonNull) - .filter(a -> StringUtils.isNotBlank(a.getFullname())) - .filter(a -> StringUtils.isNotBlank(a.getFullname().replaceAll("[\\W]", ""))) + .filter(GraphCleaningFunctions::isValidAuthorName) .map(GraphCleaningFunctions::cleanupAuthor) .collect(Collectors.toList())); @@ -739,12 +800,30 @@ public class GraphCleaningFunctions extends CleaningFunctions { // HELPERS private static boolean isValidAuthorName(Author a) { - return !Stream - .of(a.getFullname(), a.getName(), a.getSurname()) - .filter(s -> s != null && !s.isEmpty()) - .collect(Collectors.joining("")) - .toLowerCase() - .matches(INVALID_AUTHOR_REGEX); + return StringUtils.isNotBlank(a.getFullname()) && + StringUtils.isNotBlank(a.getFullname().replaceAll("[\\W]", "")) && + !INVALID_AUTHOR_NAMES.contains(StringUtils.lowerCase(a.getFullname()).trim()) && + !Stream + .of(a.getFullname(), a.getName(), a.getSurname()) + .filter(StringUtils::isNotBlank) + .collect(Collectors.joining("")) + .toLowerCase() + .matches(INVALID_AUTHOR_REGEX); + } + + private static boolean urlFilter(String u) { + try { + final URL url = new URL(u); + if (StringUtils.isBlank(url.getPath()) || "/".equals(url.getPath())) { + return false; + } + if (INVALID_URL_HOSTS.contains(url.getHost())) { + return false; + } + return !INVALID_URLS.contains(url.toString()); + } catch (MalformedURLException ex) { + return false; + } } private static List processPidCleaning(List pids) { diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJobTest.java index 65182108e..a1a4c29cd 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJobTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJobTest.java @@ -251,9 +251,19 @@ public class CleanGraphSparkJobTest { .filter(String.format("id = '%s'", id)) .first(); + final Set invalidURLs = new HashSet<>(); + invalidURLs.add("http://academia.edu/abcd"); + invalidURLs.add("http://repo.scoap3.org/api"); + invalidURLs.add("http://hdl.handle.net/"); + assertNull(p_in.getBestaccessright()); assertTrue(p_in instanceof Result); assertTrue(p_in instanceof Publication); + assertNotNull(p_in.getAuthor()); + assertEquals(14, p_in.getAuthor().size()); + assertNotNull(p_in.getInstance()); + assertNotNull(p_in.getInstance().get(0)); + assertEquals(3, p_in.getInstance().get(0).getUrl().stream().filter(invalidURLs::contains).count()); new CleanGraphSparkJob( args( @@ -273,6 +283,9 @@ public class CleanGraphSparkJobTest { assertNull(p.getPublisher()); + assertNotNull(p.getAuthor()); + assertEquals(12, p.getAuthor().size()); + assertEquals("und", p.getLanguage().getClassid()); assertEquals("Undetermined", p.getLanguage().getClassname()); @@ -364,6 +377,8 @@ public class CleanGraphSparkJobTest { .stream() .anyMatch(s -> s.getValue().equals("10.1009/qwerty"))); + assertTrue(p.getInstance().get(0).getUrl().stream().noneMatch(invalidURLs::contains)); + assertNotNull(p.getSubject()); List fos_subjects = p diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/graph/publication/publication.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/graph/publication/publication.json index e5d7c88db..e2a2b9449 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/graph/publication/publication.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/graph/publication/publication.json @@ -1,4 +1,4 @@ -{"id":"50|CSC_________::2250a70c903c6ac6e4c01438259e9375","author":[{"affiliation":[],"fullname":"Brien, Tom","name":"Tom","pid":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:datasetarchive","classname":"sysimport:crosswalk:datasetarchive","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"ORCID12","classname":"ORCID12","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"value":"0000-0001-9613-6639"},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:datasetarchive","classname":"sysimport:crosswalk:datasetarchive","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"ORCID12","classname":"ORCID12","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"value":"https://orcid.org/0000-0001-9613-6639"},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"orcid","classname":"ORCID12","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"value":"0000-0001-9613-6639"}],"rank":1,"surname":"Brien"},{"affiliation":[],"fullname":"Ade, Peter","name":"Peter","pid":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:datasetarchive","classname":"sysimport:crosswalk:datasetarchive","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"xyz","classname":"XYZ","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"value":"qwerty"},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:datasetarchive","classname":"sysimport:crosswalk:datasetarchive","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"ORCID","classname":"ORCID","schemeid":"","schemename":""},"value":"asdasd"}],"rank":2,"surname":"Ade"},{"affiliation":[],"fullname":"Barry, Peter S.","name":"Peter S.","pid":null,"rank":3,"surname":"Barry"},{"affiliation":[],"fullname":"Dunscombe, Chris J.","name":"Chris J.","pid":[],"rank":4,"surname":"Dunscombe"},{"affiliation":[],"fullname":"Leadley, David R.","name":"David R.","pid":[],"rank":5,"surname":"Leadley"},{"affiliation":[],"fullname":"Morozov, Dmitry V.","name":"Dmitry V.","pid":[],"rank":6,"surname":"Morozov"},{"affiliation":[],"fullname":"Myronov, Maksym","name":"Maksym","pid":[],"rank":7,"surname":"Myronov"},{"affiliation":[],"fullname":"Parker, Evan","name":"Evan","pid":[],"rank":8,"surname":"Parker"},{"affiliation":[],"fullname":"Prest, Martin J.","name":"Martin J.","pid":[],"rank":9,"surname":"Prest"},{"affiliation":[],"fullname":"Prunnila, Mika","name":"Mika","pid":[],"rank":10,"surname":"Prunnila"},{"affiliation":[],"fullname":"Sudiwala, Rashmi V.","name":"Rashmi V.","pid":[],"rank":11,"surname":"Sudiwala"},{"affiliation":[],"fullname":"Whall, Terry E.","name":"Terry E.","pid":[],"rank":12,"surname":"Whall"},{"affiliation":[],"fullname":"Mauskopf","name":"","pid":[],"rank":13,"surname":""},{"affiliation":[],"fullname":" P. 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deletions(-) diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java index e8bada028..7a8acbd36 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java @@ -11,12 +11,10 @@ import java.time.format.DateTimeFormatter; import java.time.format.DateTimeParseException; import java.util.*; import java.util.function.Function; -import java.util.function.Supplier; import java.util.stream.Collectors; import java.util.stream.Stream; import org.apache.commons.lang3.StringUtils; -import org.apache.cxf.common.util.UrlUtils; import com.github.sisyphsu.dateparser.DateParserUtils; import com.google.common.collect.Lists; @@ -27,7 +25,6 @@ import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.*; import me.xuender.unidecode.Unidecode; -import sun.awt.HKSCS; public class GraphCleaningFunctions extends CleaningFunctions {