From b2349659cfceca0f749a75a388a012a3939ae1a0 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 5 Jun 2020 18:37:38 +0200 Subject: [PATCH 1/8] WIP: graph property fixing implementation --- .../dhp/oa/graph/fix/FixGraphProperties.java | 210 +++++++++++++ .../dhp/oa/graph/fix/config-default.xml | 18 ++ .../eu/dnetlib/dhp/oa/graph/fix/workflow.xml | 289 ++++++++++++++++++ .../oa/graph/input_fix_graph_parameters.json | 32 ++ 4 files changed, 549 insertions(+) create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/fix/FixGraphProperties.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/fix/config-default.xml create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/fix/workflow.xml create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_fix_graph_parameters.json diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/fix/FixGraphProperties.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/fix/FixGraphProperties.java new file mode 100644 index 000000000..bbcadde59 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/fix/FixGraphProperties.java @@ -0,0 +1,210 @@ +package eu.dnetlib.dhp.oa.graph.fix; + +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils; +import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup; +import eu.dnetlib.dhp.schema.common.EntityType; +import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.oaf.*; +import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Dataset; +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 scala.Tuple2; + +import java.util.List; +import java.util.Objects; +import java.util.Optional; +import java.util.stream.Collectors; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +public class FixGraphProperties { + + private static final Logger log = LoggerFactory.getLogger(FixGraphProperties.class); + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + public static void main(String[] args) throws Exception { + + String jsonConfiguration = IOUtils + .toString( + FixGraphProperties.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/input_fix_graph_parameters.json")); + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); + + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + String inputPath = parser.get("inputPath"); + log.info("inputPath: {}", inputPath); + + String outputPath = parser.get("outputPath"); + log.info("outputPath: {}", outputPath); + + String isLookupUrl = parser.get("isLookupUrl"); + log.info("isLookupUrl: {}", isLookupUrl); + + String graphTableClassName = parser.get("graphTableClassName"); + log.info("graphTableClassName: {}", graphTableClassName); + + Class entityClazz = (Class) Class.forName(graphTableClassName); + + final VocabularyGroup vocs = VocabularyGroup.loadVocsFromIS(isLookupUrl); + + SparkConf conf = new SparkConf(); + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + removeOutputDir(spark, outputPath); + fixGraphTable(spark, vocs, inputPath, entityClazz, outputPath); + }); + } + + private static void fixGraphTable( + SparkSession spark, + VocabularyGroup vocs, + String inputPath, + Class clazz, + String outputPath) { + + MapFunction fixFn = getFixingFunction(vocs, clazz); + + readTableFromPath(spark, inputPath, clazz) + .map(fixFn, Encoders.bean(clazz)) + .write() + .mode(SaveMode.Overwrite) + .parquet(outputPath); + } + + private static MapFunction getFixingFunction(VocabularyGroup vocs, Class clazz) { + + switch (clazz.getCanonicalName()) { + case "eu.dnetlib.dhp.schema.oaf.Publication": + case "eu.dnetlib.dhp.schema.oaf.Dataset": + case "eu.dnetlib.dhp.schema.oaf.OtherResearchProduct": + case "eu.dnetlib.dhp.schema.oaf.Software": + return (MapFunction) value -> { + Result r = (Result) value; + + if (r.getLanguage() != null) { + r.setLanguage(vocs.getTermAsQualifier("dnet:languages", "und")); + } else { + r.setLanguage(vocs.getTermAsQualifier("dnet:languages", r.getLanguage().getClassid())); + } + if (r.getCountry() != null) { + r.setCountry( + r.getCountry() + .stream() + .filter(Objects::nonNull) + .map(c -> { + Qualifier q = vocs.getTermAsQualifier("dnet:countries", c.getClassid()); + Country cn = new Country(); + cn.setDataInfo(c.getDataInfo()); + cn.setClassid(q.getClassid()); + cn.setClassname(cn.getClassname()); + cn.setSchemeid("dnet:countries"); + cn.setSchemename("dnet:countries"); + return cn; + }) + .collect(Collectors.toList())); + } + + if (r.getSubject() != null) { + r.setSubject( + r.getSubject() + .stream() + .filter(Objects::nonNull) + .map(s -> { + if (s.getQualifier() == null || StringUtils.isBlank(s.getQualifier().getClassid())) { + s.setQualifier(vocs.getTermAsQualifier("dnet:subject_classification_typologies", "UNKNOWN")); + } + }) + .collect(Collectors.toList()) + ); + } + + if (r.getPublisher() != null && StringUtils.isBlank(r.getPublisher().getValue())) { + r.setPublisher(null); + } + if (r.getBestaccessright() == null) { + r.setBestaccessright(vocs.getTermAsQualifier("dnet:access_modes", "UNKNOWN")); + } + if (r.getInstance() != null) { + for(Instance i : r.getInstance()) { + if (i.getAccessright() == null) { + i.setAccessright(vocs.getTermAsQualifier("dnet:access_modes", "UNKNOWN")); + } + if (i.getInstancetype() != null) { + i.setInstancetype(vocs.getTermAsQualifier("dnet:publication_resource", i.getInstancetype().getClassid())); + } else { + i.setInstancetype(vocs.getTermAsQualifier("dnet:publication_resource", "0000")); + } + + + } + } + + return clazz.cast(r); + }; + case "eu.dnetlib.dhp.schema.oaf.Datasource": + return (MapFunction) value -> { + return value; + }; + case "eu.dnetlib.dhp.schema.oaf.Organization": + return (MapFunction) value -> { + Organization o = (Organization) value; + + if (o.getCountry() == null) { + o.setCountry(vocs.getTermAsQualifier("dnet:countries", "UNKNOWN")); + } else { + o.setCountry(vocs.getTermAsQualifier("dnet:countries", o.getCountry().getClassid())); + } + + return clazz.cast(o); + }; + case "eu.dnetlib.dhp.schema.oaf.Project": + return (MapFunction) value -> { + return value; + }; + case "eu.dnetlib.dhp.schema.oaf.Relation": + return (MapFunction) value -> { + return value; + }; + default: + throw new RuntimeException("unknown class: " + clazz.getCanonicalName()); + } + + } + + private static Dataset readTableFromPath( + SparkSession spark, String inputEntityPath, Class clazz) { + + log.info("Reading Graph table from: {}", inputEntityPath); + return spark + .read() + .textFile(inputEntityPath) + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, clazz), + Encoders.bean(clazz)); + } + + private static void removeOutputDir(SparkSession spark, String path) { + HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/fix/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/fix/config-default.xml new file mode 100644 index 000000000..2e0ed9aee --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/fix/config-default.xml @@ -0,0 +1,18 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/fix/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/fix/workflow.xml new file mode 100644 index 000000000..e93f58279 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/fix/workflow.xml @@ -0,0 +1,289 @@ + + + + + graphInputPath + the input path to read graph content + + + graphOutputPath + the target path to store fixed graph + + + isLookupUrl + the address of the lookUp service + + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + oozieActionShareLibForSpark2 + oozie action sharelib for spark 2.* + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + spark 2.* extra listeners classname + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + spark 2.* sql query execution listeners classname + + + spark2YarnHistoryServerAddress + spark 2.* yarn history server address + + + spark2EventLogDir + spark 2.* event log dir location + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + + + + + + + + + + + yarn + cluster + Fix publications + eu.dnetlib.dhp.oa.graph.fix.FixGraphProperties + dhp-graph-mapper-${projectVersion}.jar + + --executor-cores=${sparkExecutorCoresForJoining} + --executor-memory=${sparkExecutorMemoryForJoining} + --driver-memory=${sparkDriverMemoryForJoining} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=7680 + --conf spark.network.timeout=${sparkNetworkTimeout} + + --inputPath${graphInputPath}/publication + --outputPath${graphOutputPath}/publication + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Publication + --isLookupUrl${isLookupUrl} + + + + + + + + yarn + cluster + Fix datasets + eu.dnetlib.dhp.oa.graph.fix.FixGraphProperties + dhp-graph-mapper-${projectVersion}.jar + + --executor-cores=${sparkExecutorCoresForJoining} + --executor-memory=${sparkExecutorMemoryForJoining} + --driver-memory=${sparkDriverMemoryForJoining} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=7680 + --conf spark.network.timeout=${sparkNetworkTimeout} + + --inputPath${graphInputPath}/dataset + --outputPath${graphOutputPath}/dataset + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Dataset + --isLookupUrl${isLookupUrl} + + + + + + + + yarn + cluster + Fix otherresearchproducts + eu.dnetlib.dhp.oa.graph.fix.FixGraphProperties + dhp-graph-mapper-${projectVersion}.jar + + --executor-cores=${sparkExecutorCoresForJoining} + --executor-memory=${sparkExecutorMemoryForJoining} + --driver-memory=${sparkDriverMemoryForJoining} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=7680 + --conf spark.network.timeout=${sparkNetworkTimeout} + + --inputPath${graphInputPath}/otherresearchproduct + --outputPath${graphOutputPath}/otherresearchproduct + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct + --isLookupUrl${isLookupUrl} + + + + + + + + yarn + cluster + Fix softwares + eu.dnetlib.dhp.oa.graph.fix.FixGraphProperties + dhp-graph-mapper-${projectVersion}.jar + + --executor-cores=${sparkExecutorCoresForJoining} + --executor-memory=${sparkExecutorMemoryForJoining} + --driver-memory=${sparkDriverMemoryForJoining} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=7680 + --conf spark.network.timeout=${sparkNetworkTimeout} + + --inputPath${graphInputPath}/software + --outputPath${graphOutputPath}/software + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Software + --isLookupUrl${isLookupUrl} + + + + + + + + yarn + cluster + Fix datasources + eu.dnetlib.dhp.oa.graph.fix.FixGraphProperties + dhp-graph-mapper-${projectVersion}.jar + + --executor-cores=${sparkExecutorCoresForJoining} + --executor-memory=${sparkExecutorMemoryForJoining} + --driver-memory=${sparkDriverMemoryForJoining} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=7680 + --conf spark.network.timeout=${sparkNetworkTimeout} + + --inputPath${graphInputPath}/datasource + --outputPath${graphOutputPath}/datasource + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Datasource + --isLookupUrl${isLookupUrl} + + + + + + + + yarn + cluster + Fix organizations + eu.dnetlib.dhp.oa.graph.fix.FixGraphProperties + dhp-graph-mapper-${projectVersion}.jar + + --executor-cores=${sparkExecutorCoresForJoining} + --executor-memory=${sparkExecutorMemoryForJoining} + --driver-memory=${sparkDriverMemoryForJoining} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=7680 + --conf spark.network.timeout=${sparkNetworkTimeout} + + --inputPath${graphInputPath}/organization + --outputPath${graphOutputPath}/organization + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Organization + --isLookupUrl${isLookupUrl} + + + + + + + + yarn + cluster + Fix projects + eu.dnetlib.dhp.oa.graph.fix.FixGraphProperties + dhp-graph-mapper-${projectVersion}.jar + + --executor-cores=${sparkExecutorCoresForJoining} + --executor-memory=${sparkExecutorMemoryForJoining} + --driver-memory=${sparkDriverMemoryForJoining} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=7680 + --conf spark.network.timeout=${sparkNetworkTimeout} + + --inputPath${graphInputPath}/project + --outputPath${graphOutputPath}/project + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Project + --isLookupUrl${isLookupUrl} + + + + + + + + yarn + cluster + Fix relations + eu.dnetlib.dhp.oa.graph.fix.FixGraphProperties + dhp-graph-mapper-${projectVersion}.jar + + --executor-cores=${sparkExecutorCoresForJoining} + --executor-memory=${sparkExecutorMemoryForJoining} + --driver-memory=${sparkDriverMemoryForJoining} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=7680 + --conf spark.network.timeout=${sparkNetworkTimeout} + + --inputPath${graphInputPath}/relation + --outputPath${graphOutputPath}/relation + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Relation + --isLookupUrl${isLookupUrl} + + + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_fix_graph_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_fix_graph_parameters.json new file mode 100644 index 000000000..9cfed1e91 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_fix_graph_parameters.json @@ -0,0 +1,32 @@ +[ + { + "paramName": "issm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "when true will stop SparkSession after job execution", + "paramRequired": false + }, + { + "paramName": "in", + "paramLongName": "inputPath", + "paramDescription": "the path to the graph data dump to read", + "paramRequired": true + }, + { + "paramName": "out", + "paramLongName": "outputPath", + "paramDescription": "the path to store the output graph", + "paramRequired": true + }, + { + "paramName": "isu", + "paramLongName": "isLookupUrl", + "paramDescription": "url to the ISLookup Service", + "paramRequired": true + }, + { + "paramName": "class", + "paramLongName": "graphTableClassName", + "paramDescription": "class name moelling the graph table", + "paramRequired": true + } +] From d9f33582c5cd10f4fc27973f4e62291aa096724b Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 9 Jun 2020 17:20:40 +0200 Subject: [PATCH 2/8] WIP: graph cleaner implementation --- .../oa/graph/clean/CleanGraphProperties.java | 119 ++ .../dhp/oa/graph/clean/CleaningRule.java | 89 ++ .../dhp/oa/graph/fix/FixGraphProperties.java | 210 --- .../raw/GenerateEntitiesApplication.java | 5 +- .../raw/MigrateDbEntitiesApplication.java | 3 +- .../oa/graph/raw/common/OafMapperUtils.java | 4 + .../dhp/oa/graph/raw/common/Vocabulary.java | 45 +- .../oa/graph/raw/common/VocabularyGroup.java | 75 +- .../graph/{fix => clean}/config-default.xml | 0 .../dhp/oa/graph/{fix => clean}/workflow.xml | 90 +- ...json => input_clean_graph_parameters.json} | 0 .../xquery/load_vocabularies_synonyms.xquery | 6 + .../dhp/oa/graph/clean/CleaningRuleTest.java | 71 + .../eu/dnetlib/dhp/oa/graph/clean/result.json | 691 +++++++++ .../dnetlib/dhp/oa/graph/clean/synonyms.txt | 1279 +++++++++++++++++ .../eu/dnetlib/dhp/oa/graph/clean/terms.txt | 1044 ++++++++++++++ 16 files changed, 3454 insertions(+), 277 deletions(-) create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphProperties.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRule.java delete mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/fix/FixGraphProperties.java rename dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/{fix => clean}/config-default.xml (100%) rename dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/{fix => clean}/workflow.xml (85%) rename dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/{input_fix_graph_parameters.json => input_clean_graph_parameters.json} (100%) create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/xquery/load_vocabularies_synonyms.xquery create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRuleTest.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/terms.txt diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphProperties.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphProperties.java new file mode 100644 index 000000000..86dca6d21 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphProperties.java @@ -0,0 +1,119 @@ + +package eu.dnetlib.dhp.oa.graph.clean; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.beans.BeanInfo; +import java.beans.IntrospectionException; +import java.beans.Introspector; +import java.beans.PropertyDescriptor; +import java.lang.reflect.InvocationTargetException; +import java.util.Map; +import java.util.Objects; +import java.util.Optional; +import java.util.TreeMap; +import java.util.stream.Collectors; + +import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Dataset; +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 com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup; +import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.utils.ISLookupClientFactory; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; +import scala.Predef; + +public class CleanGraphProperties { + + private static final Logger log = LoggerFactory.getLogger(CleanGraphProperties.class); + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + public static void main(String[] args) throws Exception { + + String jsonConfiguration = IOUtils + .toString( + CleanGraphProperties.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json")); + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); + + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + String inputPath = parser.get("inputPath"); + log.info("inputPath: {}", inputPath); + + String outputPath = parser.get("outputPath"); + log.info("outputPath: {}", outputPath); + + String isLookupUrl = parser.get("isLookupUrl"); + log.info("isLookupUrl: {}", isLookupUrl); + + String graphTableClassName = parser.get("graphTableClassName"); + log.info("graphTableClassName: {}", graphTableClassName); + + Class entityClazz = (Class) Class.forName(graphTableClassName); + + final ISLookUpService isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl); + final VocabularyGroup vocs = VocabularyGroup.loadVocsFromIS(isLookupService); + + SparkConf conf = new SparkConf(); + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + removeOutputDir(spark, outputPath); + fixGraphTable(spark, vocs, inputPath, entityClazz, outputPath); + }); + } + + private static void fixGraphTable( + SparkSession spark, + VocabularyGroup vocs, + String inputPath, + Class clazz, + String outputPath) { + + CleaningRule rule = new CleaningRule<>(vocs); + + readTableFromPath(spark, inputPath, clazz) + .map(rule, Encoders.bean(clazz)) + .write() + .mode(SaveMode.Overwrite) + .parquet(outputPath); + } + + private static Dataset readTableFromPath( + SparkSession spark, String inputEntityPath, Class clazz) { + + log.info("Reading Graph table from: {}", inputEntityPath); + return spark + .read() + .textFile(inputEntityPath) + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, clazz), + Encoders.bean(clazz)); + } + + private static void removeOutputDir(SparkSession spark, String path) { + HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRule.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRule.java new file mode 100644 index 000000000..c00c7b4d9 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRule.java @@ -0,0 +1,89 @@ + +package eu.dnetlib.dhp.oa.graph.clean; + +import java.beans.BeanInfo; +import java.beans.IntrospectionException; +import java.beans.Introspector; +import java.beans.PropertyDescriptor; +import java.lang.reflect.Field; +import java.lang.reflect.InvocationTargetException; +import java.util.*; + +import org.apache.spark.api.java.function.MapFunction; + +import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup; +import eu.dnetlib.dhp.schema.oaf.Oaf; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.oaf.Qualifier; + +public class CleaningRule implements MapFunction { + + private VocabularyGroup vocabularies; + + public CleaningRule(VocabularyGroup vocabularies) { + this.vocabularies = vocabularies; + } + + @Override + public T call(T value) throws Exception { + + doClean(value); + + return value; + } + + private void doClean(Object o) { + if (Objects.isNull(o)) { + return; + } + + if (o instanceof Iterable) { + for (Object oi : (Iterable) o) { + doClean(oi); + } + } else { + + Class clazz = o.getClass(); + + if (clazz.isPrimitive() + || o instanceof Integer + || o instanceof Double + || o instanceof Float + || o instanceof Long + || o instanceof Boolean + || o instanceof String) { + return; + } else { + try { + for (Field field : getAllFields(new LinkedList<>(), clazz)) { + field.setAccessible(true); + Object value = field.get(o); + if (value instanceof Qualifier) { + Qualifier q = (Qualifier) value; + if (vocabularies.vocabularyExists(q.getSchemeid())) { + + field.set(o, vocabularies.lookup(q.getSchemeid(), q.getClassid())); + } + + } else { + doClean(value); + } + } + } catch (IllegalAccessException | IllegalArgumentException e) { + throw new RuntimeException(e); + } + } + } + } + + private static List getAllFields(List fields, Class clazz) { + fields.addAll(Arrays.asList(clazz.getDeclaredFields())); + + final Class superclass = clazz.getSuperclass(); + if (Objects.nonNull(superclass) && superclass.getPackage().equals(Oaf.class.getPackage())) { + getAllFields(fields, superclass); + } + + return fields; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/fix/FixGraphProperties.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/fix/FixGraphProperties.java deleted file mode 100644 index bbcadde59..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/fix/FixGraphProperties.java +++ /dev/null @@ -1,210 +0,0 @@ -package eu.dnetlib.dhp.oa.graph.fix; - -import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.common.HdfsSupport; -import eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils; -import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup; -import eu.dnetlib.dhp.schema.common.EntityType; -import eu.dnetlib.dhp.schema.common.ModelSupport; -import eu.dnetlib.dhp.schema.oaf.*; -import org.apache.commons.io.IOUtils; -import org.apache.commons.lang3.StringUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.sql.Dataset; -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 scala.Tuple2; - -import java.util.List; -import java.util.Objects; -import java.util.Optional; -import java.util.stream.Collectors; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - -public class FixGraphProperties { - - private static final Logger log = LoggerFactory.getLogger(FixGraphProperties.class); - - private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - - public static void main(String[] args) throws Exception { - - String jsonConfiguration = IOUtils - .toString( - FixGraphProperties.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/input_fix_graph_parameters.json")); - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); - - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - - String inputPath = parser.get("inputPath"); - log.info("inputPath: {}", inputPath); - - String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); - - String isLookupUrl = parser.get("isLookupUrl"); - log.info("isLookupUrl: {}", isLookupUrl); - - String graphTableClassName = parser.get("graphTableClassName"); - log.info("graphTableClassName: {}", graphTableClassName); - - Class entityClazz = (Class) Class.forName(graphTableClassName); - - final VocabularyGroup vocs = VocabularyGroup.loadVocsFromIS(isLookupUrl); - - SparkConf conf = new SparkConf(); - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - removeOutputDir(spark, outputPath); - fixGraphTable(spark, vocs, inputPath, entityClazz, outputPath); - }); - } - - private static void fixGraphTable( - SparkSession spark, - VocabularyGroup vocs, - String inputPath, - Class clazz, - String outputPath) { - - MapFunction fixFn = getFixingFunction(vocs, clazz); - - readTableFromPath(spark, inputPath, clazz) - .map(fixFn, Encoders.bean(clazz)) - .write() - .mode(SaveMode.Overwrite) - .parquet(outputPath); - } - - private static MapFunction getFixingFunction(VocabularyGroup vocs, Class clazz) { - - switch (clazz.getCanonicalName()) { - case "eu.dnetlib.dhp.schema.oaf.Publication": - case "eu.dnetlib.dhp.schema.oaf.Dataset": - case "eu.dnetlib.dhp.schema.oaf.OtherResearchProduct": - case "eu.dnetlib.dhp.schema.oaf.Software": - return (MapFunction) value -> { - Result r = (Result) value; - - if (r.getLanguage() != null) { - r.setLanguage(vocs.getTermAsQualifier("dnet:languages", "und")); - } else { - r.setLanguage(vocs.getTermAsQualifier("dnet:languages", r.getLanguage().getClassid())); - } - if (r.getCountry() != null) { - r.setCountry( - r.getCountry() - .stream() - .filter(Objects::nonNull) - .map(c -> { - Qualifier q = vocs.getTermAsQualifier("dnet:countries", c.getClassid()); - Country cn = new Country(); - cn.setDataInfo(c.getDataInfo()); - cn.setClassid(q.getClassid()); - cn.setClassname(cn.getClassname()); - cn.setSchemeid("dnet:countries"); - cn.setSchemename("dnet:countries"); - return cn; - }) - .collect(Collectors.toList())); - } - - if (r.getSubject() != null) { - r.setSubject( - r.getSubject() - .stream() - .filter(Objects::nonNull) - .map(s -> { - if (s.getQualifier() == null || StringUtils.isBlank(s.getQualifier().getClassid())) { - s.setQualifier(vocs.getTermAsQualifier("dnet:subject_classification_typologies", "UNKNOWN")); - } - }) - .collect(Collectors.toList()) - ); - } - - if (r.getPublisher() != null && StringUtils.isBlank(r.getPublisher().getValue())) { - r.setPublisher(null); - } - if (r.getBestaccessright() == null) { - r.setBestaccessright(vocs.getTermAsQualifier("dnet:access_modes", "UNKNOWN")); - } - if (r.getInstance() != null) { - for(Instance i : r.getInstance()) { - if (i.getAccessright() == null) { - i.setAccessright(vocs.getTermAsQualifier("dnet:access_modes", "UNKNOWN")); - } - if (i.getInstancetype() != null) { - i.setInstancetype(vocs.getTermAsQualifier("dnet:publication_resource", i.getInstancetype().getClassid())); - } else { - i.setInstancetype(vocs.getTermAsQualifier("dnet:publication_resource", "0000")); - } - - - } - } - - return clazz.cast(r); - }; - case "eu.dnetlib.dhp.schema.oaf.Datasource": - return (MapFunction) value -> { - return value; - }; - case "eu.dnetlib.dhp.schema.oaf.Organization": - return (MapFunction) value -> { - Organization o = (Organization) value; - - if (o.getCountry() == null) { - o.setCountry(vocs.getTermAsQualifier("dnet:countries", "UNKNOWN")); - } else { - o.setCountry(vocs.getTermAsQualifier("dnet:countries", o.getCountry().getClassid())); - } - - return clazz.cast(o); - }; - case "eu.dnetlib.dhp.schema.oaf.Project": - return (MapFunction) value -> { - return value; - }; - case "eu.dnetlib.dhp.schema.oaf.Relation": - return (MapFunction) value -> { - return value; - }; - default: - throw new RuntimeException("unknown class: " + clazz.getCanonicalName()); - } - - } - - private static Dataset readTableFromPath( - SparkSession spark, String inputEntityPath, Class clazz) { - - log.info("Reading Graph table from: {}", inputEntityPath); - return spark - .read() - .textFile(inputEntityPath) - .map( - (MapFunction) value -> OBJECT_MAPPER.readValue(value, clazz), - Encoders.bean(clazz)); - } - - private static void removeOutputDir(SparkSession spark, String path) { - HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); - } - -} 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 8e5ba9cd1..704f101ae 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 @@ -39,6 +39,8 @@ import eu.dnetlib.dhp.schema.oaf.Project; import eu.dnetlib.dhp.schema.oaf.Publication; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.Software; +import eu.dnetlib.dhp.utils.ISLookupClientFactory; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import scala.Tuple2; public class GenerateEntitiesApplication { @@ -71,7 +73,8 @@ public class GenerateEntitiesApplication { final String isLookupUrl = parser.get("isLookupUrl"); log.info("isLookupUrl: {}", isLookupUrl); - final VocabularyGroup vocs = VocabularyGroup.loadVocsFromIS(isLookupUrl); + final ISLookUpService isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl); + final VocabularyGroup vocs = VocabularyGroup.loadVocsFromIS(isLookupService); final SparkConf conf = new SparkConf(); runWithSparkSession(conf, isSparkSessionManaged, spark -> { diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java index 653027039..89bf5c379 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java @@ -71,6 +71,7 @@ import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.schema.oaf.Software; import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import eu.dnetlib.dhp.utils.ISLookupClientFactory; public class MigrateDbEntitiesApplication extends AbstractMigrationApplication implements Closeable { @@ -151,7 +152,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i super(hdfsPath); this.dbClient = new DbClient(dbUrl, dbUser, dbPassword); this.lastUpdateTimestamp = new Date().getTime(); - this.vocs = VocabularyGroup.loadVocsFromIS(isLookupUrl); + this.vocs = VocabularyGroup.loadVocsFromIS(ISLookupClientFactory.getLookUpService(isLookupUrl)); } public void execute(final String sqlFile, final Function> producer) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/OafMapperUtils.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/OafMapperUtils.java index 9beed2837..58f068943 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/OafMapperUtils.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/OafMapperUtils.java @@ -60,6 +60,10 @@ public class OafMapperUtils { .collect(Collectors.toList()); } + public static Qualifier unknown(final String schemeid, final String schemename) { + return qualifier("UNKNOWN", "Unknown", schemeid, schemename); + } + public static Qualifier qualifier( final String classid, final String classname, diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/Vocabulary.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/Vocabulary.java index c955ee640..ffa64861c 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/Vocabulary.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/Vocabulary.java @@ -4,14 +4,29 @@ package eu.dnetlib.dhp.oa.graph.raw.common; import java.io.Serializable; import java.util.HashMap; import java.util.Map; +import java.util.Optional; + +import org.apache.commons.lang3.StringUtils; + +import com.google.common.collect.Maps; + +import eu.dnetlib.dhp.schema.oaf.Qualifier; public class Vocabulary implements Serializable { private final String id; private final String name; + /** + * Code to Term mappings for this Vocabulary. + */ private final Map terms = new HashMap<>(); + /** + * Synonym to Code mappings for this Vocabulary. + */ + private final Map synonyms = Maps.newHashMap(); + public Vocabulary(final String id, final String name) { this.id = id; this.name = name; @@ -30,7 +45,7 @@ public class Vocabulary implements Serializable { } public VocabularyTerm getTerm(final String id) { - return terms.get(id.toLowerCase()); + return Optional.ofNullable(id).map(s -> s.toLowerCase()).map(s -> terms.get(s)).orElse(null); } protected void addTerm(final String id, final String name) { @@ -40,4 +55,32 @@ public class Vocabulary implements Serializable { protected boolean termExists(final String id) { return terms.containsKey(id.toLowerCase()); } + + protected void addSynonym(final String syn, final String termCode) { + synonyms.put(syn, termCode.toLowerCase()); + } + + public VocabularyTerm getTermBySynonym(final String syn) { + return getTerm(synonyms.get(syn)); + } + + public Qualifier getTermAsQualifier(final String termId) { + if (StringUtils.isBlank(termId)) { + return OafMapperUtils.unknown(getId(), getName()); + } else if (termExists(termId)) { + final VocabularyTerm t = getTerm(termId); + return OafMapperUtils.qualifier(t.getId(), t.getName(), getId(), getName()); + } else { + return OafMapperUtils.qualifier(termId, termId, getId(), getName()); + } + } + + public Qualifier getSynonymAsQualifier(final String syn) { + return Optional + .ofNullable(getTermBySynonym(syn)) + .map(term -> getTermAsQualifier(term.getId())) + .orElse(null); + // .orElse(OafMapperUtils.unknown(getId(), getName())); + } + } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/VocabularyGroup.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/VocabularyGroup.java index 43ed7f2d9..6af80683e 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/VocabularyGroup.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/VocabularyGroup.java @@ -1,33 +1,40 @@ package eu.dnetlib.dhp.oa.graph.raw.common; -import java.io.IOException; import java.io.Serializable; import java.util.HashMap; import java.util.Map; +import java.util.Optional; +import java.util.function.Supplier; -import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; -import eu.dnetlib.dhp.oa.graph.raw.GenerateEntitiesApplication; import eu.dnetlib.dhp.schema.oaf.Qualifier; -import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; public class VocabularyGroup implements Serializable { - public static VocabularyGroup loadVocsFromIS(final String isLookupUrl) throws IOException, ISLookUpException { - final ISLookUpService isLookUpService = ISLookupClientFactory.getLookUpService(isLookupUrl); + public static final String VOCABULARIES_XQUERY = "for $x in collection(' /db/DRIVER/VocabularyDSResources/VocabularyDSResourceType') \n" + + + "let $vocid := $x//VOCABULARY_NAME/@code\n" + + "let $vocname := $x//VOCABULARY_NAME/text()\n" + + "for $term in ($x//TERM)\n" + + "return concat($vocid,' @=@ ',$vocname,' @=@ ',$term/@code,' @=@ ',$term/@english_name)"; - final String xquery = IOUtils - .toString( - GenerateEntitiesApplication.class - .getResourceAsStream("/eu/dnetlib/dhp/oa/graph/xquery/load_vocabularies.xquery")); + public static final String VOCABULARY_SYNONYMS_XQUERY = "for $x in collection('/db/DRIVER/VocabularyDSResources/VocabularyDSResourceType')\n" + + + "let $vocid := $x//VOCABULARY_NAME/@code\n" + + "let $vocname := $x//VOCABULARY_NAME/text()\n" + + "for $term in ($x//TERM)\n" + + "for $syn in ($term//SYNONYM/@term)\n" + + "return concat($vocid,' @=@ ',$term/@code,' @=@ ', $syn)\n"; + + public static VocabularyGroup loadVocsFromIS(ISLookUpService isLookUpService) throws ISLookUpException { final VocabularyGroup vocs = new VocabularyGroup(); - for (final String s : isLookUpService.quickSearchProfile(xquery)) { + for (final String s : isLookUpService.quickSearchProfile(VOCABULARIES_XQUERY)) { final String[] arr = s.split("@=@"); if (arr.length == 4) { final String vocId = arr[0].trim(); @@ -40,6 +47,19 @@ public class VocabularyGroup implements Serializable { } vocs.addTerm(vocId, termId, termName); + vocs.addSynonyms(vocId, termId, termId); + } + } + + for (final String s : isLookUpService.quickSearchProfile(VOCABULARY_SYNONYMS_XQUERY)) { + final String[] arr = s.split("@=@"); + if (arr.length == 3) { + final String vocId = arr[0].trim(); + final String termId = arr[1].trim(); + final String syn = arr[2].trim(); + + vocs.addSynonyms(vocId, termId, syn); + vocs.addSynonyms(vocId, termId, termId); } } @@ -66,16 +86,21 @@ public class VocabularyGroup implements Serializable { } } + public Qualifier lookup(String vocId, String id) { + return Optional + .ofNullable(getSynonymAsQualifier(vocId, id)) + .orElse(getTermAsQualifier(vocId, id)); + } + public Qualifier getTermAsQualifier(final String vocId, final String id) { - if (StringUtils.isBlank(id)) { - return OafMapperUtils.qualifier("UNKNOWN", "UNKNOWN", vocId, vocId); - } else if (termExists(vocId, id)) { - final Vocabulary v = vocs.get(vocId.toLowerCase()); - final VocabularyTerm t = v.getTerm(id); - return OafMapperUtils.qualifier(t.getId(), t.getName(), v.getId(), v.getName()); - } else { - return OafMapperUtils.qualifier(id, id, vocId, vocId); + return vocs.get(vocId.toLowerCase()).getTermAsQualifier(id); + } + + public Qualifier getSynonymAsQualifier(final String vocId, final String syn) { + if (StringUtils.isBlank(vocId)) { + return OafMapperUtils.unknown("", ""); } + return vocs.get(vocId.toLowerCase()).getSynonymAsQualifier(syn); } public boolean termExists(final String vocId, final String id) { @@ -86,4 +111,16 @@ public class VocabularyGroup implements Serializable { return vocs.containsKey(vocId.toLowerCase()); } + private void addSynonyms(final String vocId, final String termId, final String syn) { + String id = Optional + .ofNullable(vocId) + .map(s -> s.toLowerCase()) + .orElseThrow( + () -> new IllegalArgumentException(String.format("empty vocabulary id for [term:%s, synonym:%s]"))); + Optional + .ofNullable(vocs.get(id)) + .orElseThrow(() -> new IllegalArgumentException("missing vocabulary id: " + vocId)) + .addSynonym(syn, termId); + } + } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/fix/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/config-default.xml similarity index 100% rename from dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/fix/config-default.xml rename to dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/config-default.xml diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/fix/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/workflow.xml similarity index 85% rename from dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/fix/workflow.xml rename to dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/workflow.xml index e93f58279..d152448af 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/fix/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/workflow.xml @@ -1,4 +1,4 @@ - + @@ -7,7 +7,7 @@ graphOutputPath - the target path to store fixed graph + the target path to store cleaned graph isLookupUrl @@ -50,29 +50,29 @@ - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - - - - - + + + + + + + + + - + yarn cluster - Fix publications - eu.dnetlib.dhp.oa.graph.fix.FixGraphProperties + Clean publications + eu.dnetlib.dhp.oa.graph.clean.CleanGraphProperties dhp-graph-mapper-${projectVersion}.jar --executor-cores=${sparkExecutorCoresForJoining} @@ -90,16 +90,16 @@ --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Publication --isLookupUrl${isLookupUrl} - + - + yarn cluster - Fix datasets - eu.dnetlib.dhp.oa.graph.fix.FixGraphProperties + Clean datasets + eu.dnetlib.dhp.oa.graph.clean.CleanGraphProperties dhp-graph-mapper-${projectVersion}.jar --executor-cores=${sparkExecutorCoresForJoining} @@ -117,16 +117,16 @@ --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Dataset --isLookupUrl${isLookupUrl} - + - + yarn cluster - Fix otherresearchproducts - eu.dnetlib.dhp.oa.graph.fix.FixGraphProperties + Clean otherresearchproducts + eu.dnetlib.dhp.oa.graph.clean.CleanGraphProperties dhp-graph-mapper-${projectVersion}.jar --executor-cores=${sparkExecutorCoresForJoining} @@ -144,16 +144,16 @@ --graphTableClassNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct --isLookupUrl${isLookupUrl} - + - + yarn cluster - Fix softwares - eu.dnetlib.dhp.oa.graph.fix.FixGraphProperties + Clean softwares + eu.dnetlib.dhp.oa.graph.clean.CleanGraphProperties dhp-graph-mapper-${projectVersion}.jar --executor-cores=${sparkExecutorCoresForJoining} @@ -171,16 +171,16 @@ --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Software --isLookupUrl${isLookupUrl} - + - + yarn cluster - Fix datasources - eu.dnetlib.dhp.oa.graph.fix.FixGraphProperties + Clean datasources + eu.dnetlib.dhp.oa.graph.clean.CleanGraphProperties dhp-graph-mapper-${projectVersion}.jar --executor-cores=${sparkExecutorCoresForJoining} @@ -198,16 +198,16 @@ --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Datasource --isLookupUrl${isLookupUrl} - + - + yarn cluster - Fix organizations - eu.dnetlib.dhp.oa.graph.fix.FixGraphProperties + Clean organizations + eu.dnetlib.dhp.oa.graph.clean.CleanGraphProperties dhp-graph-mapper-${projectVersion}.jar --executor-cores=${sparkExecutorCoresForJoining} @@ -225,16 +225,16 @@ --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Organization --isLookupUrl${isLookupUrl} - + - + yarn cluster - Fix projects - eu.dnetlib.dhp.oa.graph.fix.FixGraphProperties + Clean projects + eu.dnetlib.dhp.oa.graph.clean.CleanGraphProperties dhp-graph-mapper-${projectVersion}.jar --executor-cores=${sparkExecutorCoresForJoining} @@ -252,16 +252,16 @@ --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Project --isLookupUrl${isLookupUrl} - + - + yarn cluster - Fix relations - eu.dnetlib.dhp.oa.graph.fix.FixGraphProperties + Clean relations + eu.dnetlib.dhp.oa.graph.clean.CleanGraphProperties dhp-graph-mapper-${projectVersion}.jar --executor-cores=${sparkExecutorCoresForJoining} @@ -279,11 +279,11 @@ --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Relation --isLookupUrl${isLookupUrl} - + - + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_fix_graph_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json similarity index 100% rename from dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_fix_graph_parameters.json rename to dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/xquery/load_vocabularies_synonyms.xquery b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/xquery/load_vocabularies_synonyms.xquery new file mode 100644 index 000000000..f4f8cb45d --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/xquery/load_vocabularies_synonyms.xquery @@ -0,0 +1,6 @@ +for $x in collection('/db/DRIVER/VocabularyDSResources/VocabularyDSResourceType') +let $vocid := $x//VOCABULARY_NAME/@code +let $vocname := $x//VOCABULARY_NAME/text() + for $term in ($x//TERM) + for $syn in ($term//SYNONYM/@term) + return concat($vocid,' @=@ ',$term/@code,' @=@ ', $syn) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRuleTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRuleTest.java new file mode 100644 index 000000000..fab3c0c01 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRuleTest.java @@ -0,0 +1,71 @@ + +package eu.dnetlib.dhp.oa.graph.clean; + +import static org.mockito.Mockito.lenient; + +import java.io.IOException; +import java.util.List; + +import org.apache.commons.io.IOUtils; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.junit.jupiter.api.extension.ExtendWith; +import org.mockito.Mock; +import org.mockito.junit.jupiter.MockitoExtension; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; + +@ExtendWith(MockitoExtension.class) +public class CleaningRuleTest { + + public static final ObjectMapper MAPPER = new ObjectMapper(); + @Mock + private ISLookUpService isLookUpService; + + private VocabularyGroup vocabularies; + + private CleaningRule cleaningRule; + + @BeforeEach + public void setUp() throws ISLookUpException, IOException { + lenient().when(isLookUpService.quickSearchProfile(VocabularyGroup.VOCABULARIES_XQUERY)).thenReturn(vocs()); + lenient() + .when(isLookUpService.quickSearchProfile(VocabularyGroup.VOCABULARY_SYNONYMS_XQUERY)) + .thenReturn(synonyms()); + + vocabularies = VocabularyGroup.loadVocsFromIS(isLookUpService); + cleaningRule = new CleaningRule(vocabularies); + } + + @Test + public void testCleaning() throws Exception { + + String json = IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/result.json")); + Publication p_in = MAPPER.readValue(json, Publication.class); + + Publication p_out = cleaningRule.call(p_in); + + Assertions.assertNotNull(p_out); + + // TODO add more assertions to verity the cleaned values + System.out.println(MAPPER.writeValueAsString(p_out)); + + } + + private List vocs() throws IOException { + return IOUtils + .readLines(CleaningRuleTest.class.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/terms.txt")); + } + + private List synonyms() throws IOException { + return IOUtils + .readLines(CleaningRuleTest.class.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt")); + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json new file mode 100644 index 000000000..c45544b40 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json @@ -0,0 +1,691 @@ +{ + "author": [ + { + "affiliation": [ + ], + "fullname": "Brien, Tom", + "name": "Tom", + "pid": [ + ], + "rank": 1, + "surname": "Brien" + }, + { + "affiliation": [ + ], + "fullname": "Ade, Peter", + "name": "Peter", + "pid": [ + ], + "rank": 2, + "surname": "Ade" + }, + { + "affiliation": [ + ], + "fullname": "Barry, Peter S.", + "name": "Peter S.", + "pid": [ + ], + "rank": 3, + "surname": "Barry" + }, + { + "affiliation": [ + ], + "fullname": "Dunscombe, Chris 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], + "title": [ + { + "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": "main title", + "classname": "main title", + "schemeid": "dnet:dataCite_title", + "schemename": "dnet:dataCite_title" + }, + "value": "Optical response of strained- and unstrained-silicon cold-electron bolometers" + } + ] +} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt new file mode 100644 index 000000000..10eba3e86 --- /dev/null +++ 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+dnet:subject_classification_typologies @=@ dnet:subject_classification_typologies @=@ gok @=@ Göttingen Online Classification +dnet:subject_classification_typologies @=@ dnet:subject_classification_typologies @=@ ec:h2020topics @=@ Horizon 2020 Topics +dnet:subject_classification_typologies @=@ dnet:subject_classification_typologies @=@ jel @=@ JEL Classification +dnet:subject_classification_typologies @=@ dnet:subject_classification_typologies @=@ lcsh @=@ Library of Congress Subject Headings +dnet:subject_classification_typologies @=@ dnet:subject_classification_typologies @=@ msc @=@ Mathematics Subject Classification +dnet:subject_classification_typologies @=@ dnet:subject_classification_typologies @=@ mesheuropmc @=@ Medical Subject Headings +dnet:subject_classification_typologies @=@ dnet:subject_classification_typologies @=@ mesh @=@ Medical Subject Headings +dnet:subject_classification_typologies @=@ dnet:subject_classification_typologies @=@ bk @=@ Nederlandse basisclassificatie +dnet:subject_classification_typologies @=@ dnet:subject_classification_typologies @=@ dnet:od_subjects @=@ OpenDOAR subjects +dnet:subject_classification_typologies @=@ dnet:subject_classification_typologies @=@ ocis @=@ Optics Classification and Indexing Scheme +dnet:subject_classification_typologies @=@ dnet:subject_classification_typologies @=@ pacs @=@ Physics and Astronomy Classification Scheme +dnet:subject_classification_typologies @=@ dnet:subject_classification_typologies @=@ rvk @=@ Regensburger Verbundklassifikation +dnet:subject_classification_typologies @=@ dnet:subject_classification_typologies @=@ UNKNOWN @=@ UNKNOWN +dnet:subject_classification_typologies @=@ dnet:subject_classification_typologies @=@ wos @=@ Web of Science Subject Areas +dnet:subject_classification_typologies @=@ dnet:subject_classification_typologies @=@ arxiv @=@ arXiv +dnet:subject_classification_typologies @=@ dnet:subject_classification_typologies @=@ keyword @=@ keyword +dnet:subject_classification_typologies @=@ dnet:subject_classification_typologies @=@ udc @=@ Universal Decimal Classification +dnet:protocols @=@ dnet:protocols @=@ HTTPWithFileName @=@ HTTPWithFileName +dnet:protocols @=@ dnet:protocols @=@ NetCDF @=@ NetCDF +dnet:protocols @=@ dnet:protocols @=@ OpenDAP @=@ OpenDAP +dnet:protocols @=@ dnet:protocols @=@ schemaorg @=@ Schema.org +dnet:protocols @=@ dnet:protocols @=@ UNKNOWN @=@ UNKNOWN +dnet:protocols @=@ dnet:protocols @=@ api @=@ api +dnet:protocols @=@ dnet:protocols @=@ dataciteESPlugin @=@ dataciteESPlugin +dnet:protocols @=@ dnet:protocols @=@ datasetsbyjournal @=@ datasetsbyjournal +dnet:protocols @=@ dnet:protocols @=@ datasetsbyproject @=@ datasetsbyproject +dnet:protocols @=@ dnet:protocols @=@ excelFile @=@ excelFile +dnet:protocols @=@ dnet:protocols @=@ file @=@ file +dnet:protocols @=@ dnet:protocols @=@ fileCSV @=@ fileCSV +dnet:protocols @=@ dnet:protocols @=@ fileGzip @=@ fileGzip +dnet:protocols @=@ dnet:protocols @=@ files_by_rpc @=@ files_by_rpc +dnet:protocols @=@ dnet:protocols @=@ files_from_mdstore @=@ files_from_mdstore +dnet:protocols @=@ dnet:protocols @=@ files_from_metadata @=@ files_from_metadata +dnet:protocols @=@ dnet:protocols @=@ filesystem @=@ filesystem +dnet:protocols @=@ dnet:protocols @=@ ftp @=@ ftp +dnet:protocols @=@ dnet:protocols @=@ gristProjects @=@ gristProjects +dnet:protocols @=@ dnet:protocols @=@ gtr2Projects @=@ gtr2Projects +dnet:protocols @=@ dnet:protocols @=@ http @=@ http +dnet:protocols @=@ dnet:protocols @=@ httpCSV @=@ httpCSV +dnet:protocols @=@ dnet:protocols @=@ httpList @=@ httpList +dnet:protocols @=@ dnet:protocols @=@ jdbc @=@ jdbc +dnet:protocols @=@ dnet:protocols @=@ oai @=@ oai +dnet:protocols @=@ dnet:protocols @=@ oai_sets @=@ oai_sets +dnet:protocols @=@ dnet:protocols @=@ other @=@ other +dnet:protocols @=@ dnet:protocols @=@ re3data @=@ re3data +dnet:protocols @=@ dnet:protocols @=@ rest @=@ rest +dnet:protocols @=@ dnet:protocols @=@ rest_json2xml @=@ rest_json2xml +dnet:protocols @=@ dnet:protocols @=@ sftp @=@ sftp +dnet:protocols @=@ dnet:protocols @=@ soap @=@ soap +dnet:protocols @=@ dnet:protocols @=@ sparql @=@ sparql +dnet:protocols @=@ dnet:protocols @=@ sword @=@ sword +dnet:protocols @=@ dnet:protocols @=@ targz @=@ targz +dnet:protocols @=@ dnet:protocols @=@ remoteMdstore @=@ remoteMdstore +ec:funding_typologies @=@ ec:funding_typologies @=@ ec:frameworkprogram @=@ frameworkprogram +ec:funding_typologies @=@ ec:funding_typologies @=@ ec:program @=@ program +ec:funding_typologies @=@ ec:funding_typologies @=@ ec:specificprogram @=@ specificprogram +fct:contractTypes @=@ fct:contractTypes @=@ UNKNOWN @=@ UNKNOWN +wt:contractTypes @=@ wt:contractTypes @=@ UNKNOWN @=@ UNKNOWN +dnet:dataCite_resource @=@ dnet:dataCite_resource @=@ UNKNOWN @=@ UNKNOWN +dnet:dataCite_resource @=@ dnet:dataCite_resource @=@ collection @=@ collection +dnet:dataCite_resource @=@ dnet:dataCite_resource @=@ dataset @=@ dataset +dnet:dataCite_resource @=@ dnet:dataCite_resource @=@ event @=@ event +dnet:dataCite_resource @=@ dnet:dataCite_resource @=@ film @=@ film +dnet:dataCite_resource @=@ dnet:dataCite_resource @=@ image @=@ image +dnet:dataCite_resource @=@ dnet:dataCite_resource @=@ interactiveResource @=@ interactiveResource +dnet:dataCite_resource @=@ dnet:dataCite_resource @=@ model @=@ model +dnet:dataCite_resource @=@ dnet:dataCite_resource @=@ physicalObject @=@ physicalObject +dnet:dataCite_resource @=@ dnet:dataCite_resource @=@ service @=@ service +dnet:dataCite_resource @=@ dnet:dataCite_resource @=@ software @=@ software +dnet:dataCite_resource @=@ dnet:dataCite_resource @=@ sound @=@ sound +dnet:dataCite_resource @=@ dnet:dataCite_resource @=@ text @=@ text +dnet:dataCite_resource @=@ dnet:dataCite_resource @=@ clinicalTrial @=@ clinical trial +dnet:compatibilityLevel @=@ dnet:compatibilityLevel @=@ openaire2.0 @=@ OpenAIRE 2.0 (EC funding) +dnet:compatibilityLevel @=@ dnet:compatibilityLevel @=@ openaire3.0 @=@ OpenAIRE 3.0 (OA, funding) +dnet:compatibilityLevel @=@ dnet:compatibilityLevel @=@ openaire4.0 @=@ OpenAIRE 4.0 (inst.&thematic. repo.) +dnet:compatibilityLevel @=@ dnet:compatibilityLevel @=@ driver @=@ OpenAIRE Basic (DRIVER OA) +dnet:compatibilityLevel @=@ dnet:compatibilityLevel @=@ openaire2.0_data @=@ OpenAIRE Data (funded, referenced datasets) +dnet:compatibilityLevel @=@ dnet:compatibilityLevel @=@ hostedBy @=@ collected from a compatible aggregator +dnet:compatibilityLevel @=@ dnet:compatibilityLevel @=@ files @=@ files +dnet:compatibilityLevel @=@ dnet:compatibilityLevel @=@ native @=@ native +dnet:compatibilityLevel @=@ dnet:compatibilityLevel @=@ UNKNOWN @=@ not available +dnet:compatibilityLevel @=@ dnet:compatibilityLevel @=@ notCompatible @=@ under validation +dnet:compatibilityLevel @=@ dnet:compatibilityLevel @=@ openaire-cris_1.1 @=@ OpenAIRE CRIS v1.1 +dnet:publication_resource @=@ dnet:publication_resource @=@ 0018 @=@ Annotation +dnet:publication_resource @=@ dnet:publication_resource @=@ 0001 @=@ Article +dnet:publication_resource @=@ dnet:publication_resource @=@ 0033 @=@ Audiovisual +dnet:publication_resource @=@ dnet:publication_resource @=@ 0008 @=@ Bachelor thesis +dnet:publication_resource @=@ dnet:publication_resource @=@ 0002 @=@ Book +dnet:publication_resource @=@ dnet:publication_resource @=@ 0037 @=@ Clinical Trial +dnet:publication_resource @=@ dnet:publication_resource @=@ 0022 @=@ Collection +dnet:publication_resource @=@ dnet:publication_resource @=@ 0004 @=@ Conference object +dnet:publication_resource @=@ dnet:publication_resource @=@ 0005 @=@ Contribution for newspaper or weekly magazine +dnet:publication_resource @=@ dnet:publication_resource @=@ 0045 @=@ Data Management Plan +dnet:publication_resource @=@ dnet:publication_resource @=@ 0031 @=@ Data Paper +dnet:publication_resource @=@ dnet:publication_resource @=@ 0021 @=@ Dataset +dnet:publication_resource @=@ dnet:publication_resource @=@ 0006 @=@ Doctoral thesis +dnet:publication_resource @=@ dnet:publication_resource @=@ 0023 @=@ Event +dnet:publication_resource @=@ dnet:publication_resource @=@ 0009 @=@ External research report +dnet:publication_resource @=@ dnet:publication_resource @=@ 0024 @=@ Film +dnet:publication_resource @=@ dnet:publication_resource @=@ 0025 @=@ Image +dnet:publication_resource @=@ dnet:publication_resource @=@ 0026 @=@ InteractiveResource +dnet:publication_resource @=@ dnet:publication_resource @=@ 0011 @=@ Internal report +dnet:publication_resource @=@ dnet:publication_resource @=@ 0043 @=@ Journal +dnet:publication_resource @=@ dnet:publication_resource @=@ 0010 @=@ Lecture +dnet:publication_resource @=@ dnet:publication_resource @=@ 0007 @=@ Master thesis +dnet:publication_resource @=@ dnet:publication_resource @=@ 0027 @=@ Model +dnet:publication_resource @=@ dnet:publication_resource @=@ 0012 @=@ Newsletter +dnet:publication_resource @=@ dnet:publication_resource @=@ 0020 @=@ Other ORP type +dnet:publication_resource @=@ dnet:publication_resource @=@ 0039 @=@ Other dataset type +dnet:publication_resource @=@ dnet:publication_resource @=@ 0038 @=@ Other literature type +dnet:publication_resource @=@ dnet:publication_resource @=@ 0040 @=@ Other software type +dnet:publication_resource @=@ dnet:publication_resource @=@ 0013 @=@ Part of book or chapter of book +dnet:publication_resource @=@ dnet:publication_resource @=@ 0019 @=@ Patent +dnet:publication_resource @=@ dnet:publication_resource @=@ 0028 @=@ PhysicalObject +dnet:publication_resource @=@ dnet:publication_resource @=@ 0016 @=@ Preprint +dnet:publication_resource @=@ dnet:publication_resource @=@ 0034 @=@ Project deliverable +dnet:publication_resource @=@ dnet:publication_resource @=@ 0035 @=@ Project milestone +dnet:publication_resource @=@ dnet:publication_resource @=@ 0036 @=@ Project proposal +dnet:publication_resource @=@ dnet:publication_resource @=@ 0017 @=@ Report +dnet:publication_resource @=@ dnet:publication_resource @=@ 0014 @=@ Research +dnet:publication_resource @=@ dnet:publication_resource @=@ 0015 @=@ Review +dnet:publication_resource @=@ dnet:publication_resource @=@ 0029 @=@ Software +dnet:publication_resource @=@ dnet:publication_resource @=@ 0032 @=@ Software Paper +dnet:publication_resource @=@ dnet:publication_resource @=@ 0030 @=@ Sound +dnet:publication_resource @=@ dnet:publication_resource @=@ 0044 @=@ Thesis +dnet:publication_resource @=@ dnet:publication_resource @=@ 0000 @=@ UNKNOWN +dnet:provenanceActions @=@ dnet:provenanceActions @=@ sysimport:crosswalk:aggregator @=@ Harvested +dnet:provenanceActions @=@ dnet:provenanceActions @=@ sysimport:crosswalk:cris @=@ Harvested +dnet:provenanceActions @=@ dnet:provenanceActions @=@ sysimport:crosswalk:datasetarchive @=@ Harvested +dnet:provenanceActions @=@ dnet:provenanceActions @=@ sysimport:crosswalk:entityregistry @=@ Harvested +dnet:provenanceActions @=@ dnet:provenanceActions @=@ sysimport:crosswalk:infospace @=@ Harvested +dnet:provenanceActions @=@ dnet:provenanceActions @=@ sysimport:crosswalk:repository @=@ Harvested +dnet:provenanceActions @=@ dnet:provenanceActions @=@ sysimport:mining:aggregator @=@ Inferred by OpenAIRE +dnet:provenanceActions @=@ dnet:provenanceActions @=@ sysimport:mining:cris @=@ Inferred by OpenAIRE +dnet:provenanceActions @=@ dnet:provenanceActions @=@ sysimport:mining:datasetarchive @=@ Inferred by OpenAIRE +dnet:provenanceActions @=@ dnet:provenanceActions @=@ sysimport:mining:entityregistry @=@ Inferred by OpenAIRE +dnet:provenanceActions @=@ dnet:provenanceActions @=@ sysimport:mining:infospace @=@ Inferred by OpenAIRE +dnet:provenanceActions @=@ dnet:provenanceActions @=@ sysimport:mining:repository @=@ Inferred by OpenAIRE +dnet:provenanceActions @=@ dnet:provenanceActions @=@ UNKNOWN @=@ UNKNOWN +dnet:provenanceActions @=@ dnet:provenanceActions @=@ user:claim:pid @=@ Linked by user +dnet:provenanceActions @=@ dnet:provenanceActions @=@ user:claim:search @=@ Linked by user +dnet:provenanceActions @=@ dnet:provenanceActions @=@ user:insert @=@ Linked by user +dnet:provenanceActions @=@ dnet:provenanceActions @=@ user:claim @=@ Linked by user +dnet:provenanceActions @=@ dnet:provenanceActions @=@ sysimport:actionset @=@ Harvested +dnet:provenanceActions @=@ dnet:provenanceActions @=@ iis @=@ Inferred by OpenAIRE +dnet:provenanceActions @=@ dnet:provenanceActions @=@ propagation:project:semrel @=@ Inferred by OpenAIRE +dnet:provenanceActions @=@ dnet:provenanceActions @=@ sysimport:actionset:orcidworks-no-doi @=@ Harvested +dnet:provenanceActions @=@ dnet:provenanceActions @=@ sysimport:dedup @=@ Inferred by OpenAIRE +dnet:provenanceActions @=@ dnet:provenanceActions @=@ sysimport:crosswalk @=@ Harvested +dnet:datasource_typologies @=@ dnet:datasource_typologies @=@ crissystem @=@ CRIS System +dnet:datasource_typologies @=@ dnet:datasource_typologies @=@ datarepository::unknown @=@ Data Repository +dnet:datasource_typologies @=@ dnet:datasource_typologies @=@ aggregator::datarepository @=@ Data Repository Aggregator +dnet:datasource_typologies @=@ dnet:datasource_typologies @=@ infospace @=@ Information Space +dnet:datasource_typologies @=@ dnet:datasource_typologies @=@ pubsrepository::institutional @=@ Institutional Repository +dnet:datasource_typologies @=@ dnet:datasource_typologies @=@ aggregator::pubsrepository::institutional @=@ Institutional Repository Aggregator +dnet:datasource_typologies @=@ dnet:datasource_typologies @=@ pubsrepository::journal @=@ Journal +dnet:datasource_typologies @=@ dnet:datasource_typologies @=@ aggregator::pubsrepository::journals @=@ Journal Aggregator/Publisher +dnet:datasource_typologies @=@ dnet:datasource_typologies @=@ pubsrepository::mock @=@ Other +dnet:datasource_typologies @=@ dnet:datasource_typologies @=@ pubscatalogue::unknown @=@ Publication Catalogue +dnet:datasource_typologies @=@ dnet:datasource_typologies @=@ pubsrepository::unknown @=@ Publication Repository +dnet:datasource_typologies @=@ dnet:datasource_typologies @=@ aggregator::pubsrepository::unknown @=@ Publication Repository Aggregator +dnet:datasource_typologies @=@ dnet:datasource_typologies @=@ entityregistry @=@ Registry +dnet:datasource_typologies @=@ dnet:datasource_typologies @=@ scholarcomminfra @=@ Scholarly Comm. Infrastructure +dnet:datasource_typologies @=@ dnet:datasource_typologies @=@ pubsrepository::thematic @=@ Thematic Repository +dnet:datasource_typologies @=@ dnet:datasource_typologies @=@ websource @=@ Web Source +dnet:datasource_typologies @=@ dnet:datasource_typologies @=@ entityregistry::projects @=@ Funder database +dnet:datasource_typologies @=@ dnet:datasource_typologies @=@ entityregistry::repositories @=@ Registry of repositories +dnet:datasource_typologies @=@ dnet:datasource_typologies @=@ softwarerepository @=@ Software Repository +dnet:datasource_typologies @=@ dnet:datasource_typologies @=@ aggregator::softwarerepository @=@ Software Repository Aggregator +dnet:datasource_typologies @=@ dnet:datasource_typologies @=@ orprepository @=@ Repository +dnet:datasource_typologies @=@ dnet:datasource_typologies @=@ researchgraph @=@ Research Graph +dnet:datasource_typologies @=@ dnet:datasource_typologies @=@ entityregistry::products @=@ Registry of research products +dnet:datasource_typologies @=@ dnet:datasource_typologies @=@ entityregistry::researchers @=@ Registry of researchers +dnet:datasource_typologies @=@ dnet:datasource_typologies @=@ entityregistry::organizations @=@ Registry of organizations +wt:funding_typologies @=@ Wellcome Trust: Funding Typologies @=@ wt:fundingStream @=@ Wellcome Trust: Funding Stream +dnet:review_levels @=@ dnet:review_levels @=@ 0000 @=@ UNKNOWN +dnet:review_levels @=@ dnet:review_levels @=@ 0002 @=@ nonPeerReviewed +dnet:review_levels @=@ dnet:review_levels @=@ 0001 @=@ peerReviewed \ No newline at end of file From a2fdf85ba1bacef38c43d94c8f62e7e05ecb265d Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 9 Jun 2020 19:52:53 +0200 Subject: [PATCH 3/8] WIP: graph cleaner implementation --- .../dhp/schema/common/ModelConstants.java | 1 + .../eu/dnetlib/dhp/schema/oaf/Instance.java | 6 +-- .../migration/ProtoConverter.java | 11 ++++- .../DnetCollectorWorkerApplicationTests.java | 2 + .../doiboost/crossref/Crossref2Oaf.scala | 6 ++- .../dhp/oa/graph/clean/CleaningRule.java | 16 +++---- .../dhp/oa/graph/raw/OafToOafMapper.java | 10 +--- .../dhp/oa/graph/raw/OdfToOafMapper.java | 16 +------ .../oa/graph/raw/common/VocabularyGroup.java | 18 ++++++-- .../dhp/oa/graph/clean/CleaningRuleTest.java | 40 ++++++++++++++-- .../eu/dnetlib/dhp/oa/graph/clean/result.json | 46 ++++++++++++++++++- .../oa/provision/utils/XmlRecordFactory.java | 4 +- 12 files changed, 131 insertions(+), 45 deletions(-) diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelConstants.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelConstants.java index e32dd10fa..fba20dda1 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelConstants.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelConstants.java @@ -14,6 +14,7 @@ public class ModelConstants { public static final String DNET_DATA_CITE_RESOURCE = "dnet:dataCite_resource"; public static final String DNET_PROVENANCE_ACTIONS = "dnet:provenanceActions"; public static final String DNET_COUNTRY_TYPE = "dnet:countries"; + public static final String DNET_REVIEW_LEVELS = "dnet:review_levels"; public static final String SYSIMPORT_CROSSWALK_REPOSITORY = "sysimport:crosswalk:repository"; public static final String SYSIMPORT_CROSSWALK_ENTITYREGISTRY = "sysimport:crosswalk:entityregistry"; diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Instance.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Instance.java index 2b7d3846c..29d495261 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Instance.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Instance.java @@ -31,7 +31,7 @@ public class Instance implements Serializable { // typed results private Field processingchargecurrency; - private Field refereed; // peer-review status + private Qualifier refereed; // peer-review status public Field getLicense() { return license; @@ -113,11 +113,11 @@ public class Instance implements Serializable { this.processingchargecurrency = processingchargecurrency; } - public Field getRefereed() { + public Qualifier getRefereed() { return refereed; } - public void setRefereed(Field refereed) { + public void setRefereed(Qualifier refereed) { this.refereed = refereed; } diff --git a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/ProtoConverter.java b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/ProtoConverter.java index e55c0eb7b..8ea877aec 100644 --- a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/ProtoConverter.java +++ b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/ProtoConverter.java @@ -96,12 +96,21 @@ public class ProtoConverter implements Serializable { .stream() .distinct() .collect(Collectors.toCollection(ArrayList::new)) : null); - i.setRefereed(mapStringField(ri.getRefereed())); + i.setRefereed(mapRefereed(ri.getRefereed())); i.setProcessingchargeamount(mapStringField(ri.getProcessingchargeamount())); i.setProcessingchargecurrency(mapStringField(ri.getProcessingchargecurrency())); return i; } + private static Qualifier mapRefereed(FieldTypeProtos.StringField refereed) { + Qualifier q = new Qualifier(); + q.setClassid(refereed.getValue()); + q.setSchemename(refereed.getValue()); + q.setSchemeid("dnet:review_levels"); + q.setSchemename("dnet:review_levels"); + return q; + } + private static List convertExternalRefs(OafProtos.Oaf oaf) { ResultProtos.Result r = oaf.getEntity().getResult(); if (r.getExternalReferenceCount() > 0) { diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collector/worker/DnetCollectorWorkerApplicationTests.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collector/worker/DnetCollectorWorkerApplicationTests.java index 87bd3be3d..c745219fe 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collector/worker/DnetCollectorWorkerApplicationTests.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collector/worker/DnetCollectorWorkerApplicationTests.java @@ -8,6 +8,7 @@ import java.io.File; import org.junit.jupiter.api.AfterEach; import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Disabled; import org.junit.jupiter.api.Test; import com.fasterxml.jackson.databind.ObjectMapper; @@ -19,6 +20,7 @@ import eu.dnetlib.dhp.collection.worker.utils.CollectorPluginFactory; import eu.dnetlib.message.Message; import eu.dnetlib.message.MessageManager; +@Disabled public class DnetCollectorWorkerApplicationTests { private final ArgumentApplicationParser argumentParser = mock(ArgumentApplicationParser.class); diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala index cc2c9d586..ec8aca55c 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala @@ -166,8 +166,10 @@ case object Crossref2Oaf { val has_review = (json \ "relation" \"has-review" \ "id") - if(has_review != JNothing) - instance.setRefereed(asField("peerReviewed")) + if(has_review != JNothing) { + instance.setRefereed( + createQualifier("0001", "peerReviewed", "dnet:review_levels", "dnet:review_levels")) + } instance.setAccessright(getRestrictedQualifier()) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRule.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRule.java index c00c7b4d9..51b930962 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRule.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRule.java @@ -1,19 +1,16 @@ package eu.dnetlib.dhp.oa.graph.clean; -import java.beans.BeanInfo; -import java.beans.IntrospectionException; -import java.beans.Introspector; -import java.beans.PropertyDescriptor; import java.lang.reflect.Field; -import java.lang.reflect.InvocationTargetException; -import java.util.*; +import java.util.Arrays; +import java.util.LinkedList; +import java.util.List; +import java.util.Objects; import org.apache.spark.api.java.function.MapFunction; import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup; import eu.dnetlib.dhp.schema.oaf.Oaf; -import eu.dnetlib.dhp.schema.oaf.Publication; import eu.dnetlib.dhp.schema.oaf.Qualifier; public class CleaningRule implements MapFunction { @@ -61,7 +58,6 @@ public class CleaningRule implements MapFunction { if (value instanceof Qualifier) { Qualifier q = (Qualifier) value; if (vocabularies.vocabularyExists(q.getSchemeid())) { - field.set(o, vocabularies.lookup(q.getSchemeid(), q.getClassid())); } @@ -86,4 +82,8 @@ public class CleaningRule implements MapFunction { return fields; } + + public VocabularyGroup getVocabularies() { + return vocabularies; + } } 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 6f91ce733..2ea8bba4a 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 @@ -4,13 +4,7 @@ package eu.dnetlib.dhp.oa.graph.raw; import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.createOpenaireId; import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.field; import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.structuredProperty; -import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_ACCESS_MODES; -import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_LANGUAGES; -import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PID_TYPES; -import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PUBLICATION_RESOURCE; -import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_RELATED_TO; -import static eu.dnetlib.dhp.schema.common.ModelConstants.PUBLICATION_DATASET; -import static eu.dnetlib.dhp.schema.common.ModelConstants.RESULT_RESULT; +import static eu.dnetlib.dhp.schema.common.ModelConstants.*; import java.util.ArrayList; import java.util.List; @@ -139,7 +133,7 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper { instance .setAccessright(prepareQualifier(doc, "//oaf:accessrights", DNET_ACCESS_MODES)); instance.setLicense(field(doc.valueOf("//oaf:license"), info)); - instance.setRefereed(field(doc.valueOf("//oaf:refereed"), info)); + instance.setRefereed(prepareQualifier(doc, "//oaf:refereed", DNET_REVIEW_LEVELS)); instance .setProcessingchargeamount(field(doc.valueOf("//oaf:processingchargeamount"), info)); 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 bbd9442e1..a2019e959 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 @@ -4,19 +4,7 @@ package eu.dnetlib.dhp.oa.graph.raw; import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.createOpenaireId; import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.field; import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.structuredProperty; -import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_ACCESS_MODES; -import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_DATA_CITE_DATE; -import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_DATA_CITE_RESOURCE; -import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_LANGUAGES; -import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PID_TYPES; -import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PUBLICATION_RESOURCE; -import static eu.dnetlib.dhp.schema.common.ModelConstants.HAS_PARTS; -import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_PART_OF; -import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_SUPPLEMENTED_BY; -import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_SUPPLEMENT_TO; -import static eu.dnetlib.dhp.schema.common.ModelConstants.PART; -import static eu.dnetlib.dhp.schema.common.ModelConstants.RESULT_RESULT; -import static eu.dnetlib.dhp.schema.common.ModelConstants.SUPPLEMENT; +import static eu.dnetlib.dhp.schema.common.ModelConstants.*; import java.util.ArrayList; import java.util.Arrays; @@ -129,7 +117,7 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { instance .setAccessright(prepareQualifier(doc, "//oaf:accessrights", DNET_ACCESS_MODES)); instance.setLicense(field(doc.valueOf("//oaf:license"), info)); - instance.setRefereed(field(doc.valueOf("//oaf:refereed"), info)); + instance.setRefereed(prepareQualifier(doc, "//oaf:refereed", DNET_REVIEW_LEVELS)); instance.setProcessingchargeamount(field(doc.valueOf("//oaf:processingchargeamount"), info)); instance .setProcessingchargecurrency(field(doc.valueOf("//oaf:processingchargeamount/@currency"), info)); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/VocabularyGroup.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/VocabularyGroup.java index 6af80683e..ec95ade00 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/VocabularyGroup.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/VocabularyGroup.java @@ -2,10 +2,9 @@ package eu.dnetlib.dhp.oa.graph.raw.common; import java.io.Serializable; -import java.util.HashMap; -import java.util.Map; -import java.util.Optional; +import java.util.*; import java.util.function.Supplier; +import java.util.stream.Collectors; import org.apache.commons.lang3.StringUtils; @@ -86,6 +85,19 @@ public class VocabularyGroup implements Serializable { } } + public Set getTerms(String vocId) { + if (!vocabularyExists(vocId)) { + return new HashSet<>(); + } + return vocs + .get(vocId.toLowerCase()) + .getTerms() + .values() + .stream() + .map(t -> t.getId()) + .collect(Collectors.toCollection(HashSet::new)); + } + public Qualifier lookup(String vocId, String id) { return Optional .ofNullable(getSynonymAsQualifier(vocId, id)) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRuleTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRuleTest.java index fab3c0c01..019285cc3 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRuleTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRuleTest.java @@ -1,14 +1,17 @@ package eu.dnetlib.dhp.oa.graph.clean; +import static org.junit.jupiter.api.Assertions.*; import static org.mockito.Mockito.lenient; import java.io.IOException; +import java.util.HashSet; import java.util.List; +import java.util.Set; +import java.util.stream.Collectors; +import java.util.stream.Stream; import org.apache.commons.io.IOUtils; -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.BeforeAll; import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.Test; import org.junit.jupiter.api.extension.ExtendWith; @@ -18,7 +21,9 @@ import org.mockito.junit.jupiter.MockitoExtension; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup; +import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyTerm; import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.oaf.Qualifier; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; @@ -26,6 +31,7 @@ import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; public class CleaningRuleTest { public static final ObjectMapper MAPPER = new ObjectMapper(); + @Mock private ISLookUpService isLookUpService; @@ -47,18 +53,46 @@ public class CleaningRuleTest { @Test public void testCleaning() throws Exception { + assertNotNull(cleaningRule.getVocabularies()); + String json = IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/result.json")); Publication p_in = MAPPER.readValue(json, Publication.class); Publication p_out = cleaningRule.call(p_in); - Assertions.assertNotNull(p_out); + assertNotNull(p_out); + + assertEquals("eng", p_out.getLanguage().getClassid()); + assertEquals("English", p_out.getLanguage().getClassname()); + + assertEquals("0018", p_out.getInstance().get(0).getInstancetype().getClassid()); + assertEquals("Annotation", p_out.getInstance().get(0).getInstancetype().getClassname()); + + assertEquals("CLOSED", p_out.getInstance().get(0).getAccessright().getClassid()); + assertEquals("Closed Access", p_out.getInstance().get(0).getAccessright().getClassname()); + + Set pidTerms = vocabularies.getTerms("dnet:pid_types"); + assertTrue( + p_out + .getPid() + .stream() + .map(p -> p.getQualifier()) + .allMatch(q -> pidTerms.contains(q.getClassid()))); // TODO add more assertions to verity the cleaned values System.out.println(MAPPER.writeValueAsString(p_out)); } + private Stream getAuthorPidTypes(Publication pub) { + return pub + .getAuthor() + .stream() + .map(a -> a.getPid()) + .flatMap(p -> p.stream()) + .map(s -> s.getQualifier()); + } + private List vocs() throws IOException { return IOUtils .readLines(CleaningRuleTest.class.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/terms.txt")); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json index c45544b40..435b001b7 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json @@ -6,6 +6,28 @@ "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" + } ], "rank": 1, "surname": "Brien" @@ -16,6 +38,28 @@ "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" + } ], "rank": 2, "surname": "Ade" @@ -207,7 +251,7 @@ { "accessright": { "classid": "CLOSED", - "classname": "Closed Access", + "classname": "CLOSED", "schemeid": "dnet:access_modes", "schemename": "dnet:access_modes" }, diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java index d950a816d..cb45f3f32 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java @@ -1165,10 +1165,10 @@ public class XmlRecordFactory implements Serializable { .asXmlElement( "distributionlocation", instance.getDistributionlocation())); } - if (instance.getRefereed() != null && isNotBlank(instance.getRefereed().getValue())) { + if (instance.getRefereed() != null && !instance.getRefereed().isBlank()) { fields .add( - XmlSerializationUtils.asXmlElement("refereed", instance.getRefereed().getValue())); + XmlSerializationUtils.mapQualifier("refereed", instance.getRefereed())); } if (instance.getProcessingchargeamount() != null && isNotBlank(instance.getProcessingchargeamount().getValue())) { From f1bce643910514f956fff7180a04631e7adf21e5 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Wed, 10 Jun 2020 21:36:31 +0200 Subject: [PATCH 4/8] WIP: graph cleaner implementation --- .../oa/graph/clean/NormalizeEmptyFields.java | 88 +++++++++++++++++++ 1 file changed, 88 insertions(+) create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/NormalizeEmptyFields.java diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/NormalizeEmptyFields.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/NormalizeEmptyFields.java new file mode 100644 index 000000000..77537801f --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/NormalizeEmptyFields.java @@ -0,0 +1,88 @@ + +package eu.dnetlib.dhp.oa.graph.clean; + +import eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils; +import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup; +import eu.dnetlib.dhp.schema.oaf.Oaf; +import eu.dnetlib.dhp.schema.oaf.Qualifier; +import org.apache.commons.lang3.StringUtils; +import org.apache.spark.api.java.function.MapFunction; + +import java.lang.reflect.Field; +import java.util.Arrays; +import java.util.LinkedList; +import java.util.List; +import java.util.Objects; + +public class NormalizeEmptyFields implements MapFunction { + + private VocabularyGroup vocabularies; + + public NormalizeEmptyFields(VocabularyGroup vocabularies) { + this.vocabularies = vocabularies; + } + + @Override + public T call(T value) throws Exception { + + doNormalize(value); + + return value; + } + + private void doNormalize(Object o) { + if (Objects.isNull(o)) { + return; + } + + if (o instanceof Iterable) { + for (Object oi : (Iterable) o) { + doNormalize(oi); + } + } else { + + Class clazz = o.getClass(); + + if (clazz.isPrimitive() + || o instanceof Integer + || o instanceof Double + || o instanceof Float + || o instanceof Long + || o instanceof Boolean + || o instanceof String) { + return; + } else { + try { + for (Field field : getAllFields(new LinkedList<>(), clazz)) { + field.setAccessible(true); + Object value = field.get(o); + if (value instanceof Qualifier && Objects.isNull(value)) { + field.set(o, OafMapperUtils.unknown("", "")); + } else if (value instanceof Field && Objects.isNull(value)) { + + } else { + doNormalize(value); + } + } + } catch (IllegalAccessException | IllegalArgumentException e) { + throw new RuntimeException(e); + } + } + } + } + + private static List getAllFields(List fields, Class clazz) { + fields.addAll(Arrays.asList(clazz.getDeclaredFields())); + + final Class superclass = clazz.getSuperclass(); + if (Objects.nonNull(superclass) && superclass.getPackage().equals(Oaf.class.getPackage())) { + getAllFields(fields, superclass); + } + + return fields; + } + + public VocabularyGroup getVocabularies() { + return vocabularies; + } +} From d1d92c4d8c07caa363d9c8e6e3176a0ac0cd9ed4 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Thu, 11 Jun 2020 10:12:00 +0200 Subject: [PATCH 5/8] fixed integration of claims in the graph --- .../main/java/eu/dnetlib/dhp/oa/graph/clean/OafNavigator.java | 4 ++++ .../dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java | 2 ++ 2 files changed, 6 insertions(+) create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/OafNavigator.java diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/OafNavigator.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/OafNavigator.java new file mode 100644 index 000000000..c329a3111 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/OafNavigator.java @@ -0,0 +1,4 @@ +package eu.dnetlib.dhp.oa.graph.clean; + +public class OafNavigator { +} 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 f52587d73..3568dc52a 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 @@ -141,8 +141,10 @@ public class GenerateEntitiesApplication { switch (type.toLowerCase()) { case "oaf-store-cleaned": + case "oaf-store-claim": return new OafToOafMapper(vocs, false).processMdRecord(s); case "odf-store-cleaned": + case "odf-store-claim": return new OdfToOafMapper(vocs, false).processMdRecord(s); case "oaf-store-intersection": return new OafToOafMapper(vocs, true).processMdRecord(s); From ba8a024af930df4dbdf75ceb2ef113dd71fcfa74 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 12 Jun 2020 10:45:11 +0200 Subject: [PATCH 6/8] avoid NPEs merging titles --- .../eu/dnetlib/dhp/schema/oaf/Result.java | 13 ++- .../oa/graph/clean/NormalizeEmptyFields.java | 88 ------------------- 2 files changed, 5 insertions(+), 96 deletions(-) delete mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/NormalizeEmptyFields.java diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java index 09e77a244..c9d0ac7c7 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java @@ -254,28 +254,25 @@ public class Result extends OafEntity implements Serializable { final StructuredProperty p = baseMainTitle; title = title.stream().filter(t -> t != p).collect(Collectors.toList()); } -// -// -// title.remove(baseMainTitle); } StructuredProperty newMainTitle = null; if (r.getTitle() != null) { newMainTitle = getMainTitle(r.getTitle()); - if (newMainTitle != null) { + if (newMainTitle != null && title != null) { final StructuredProperty p = newMainTitle; title = title.stream().filter(t -> t != p).collect(Collectors.toList()); } - - // r.getTitle().remove(newMainTitle); } - if (newMainTitle != null && compareTrust(this, r) < 0) + if (newMainTitle != null && compareTrust(this, r) < 0) { baseMainTitle = newMainTitle; + } title = mergeLists(title, r.getTitle()); - if (title != null && baseMainTitle != null) + if (title != null && baseMainTitle != null) { title.add(baseMainTitle); + } relevantdate = mergeLists(relevantdate, r.getRelevantdate()); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/NormalizeEmptyFields.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/NormalizeEmptyFields.java deleted file mode 100644 index 77537801f..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/NormalizeEmptyFields.java +++ /dev/null @@ -1,88 +0,0 @@ - -package eu.dnetlib.dhp.oa.graph.clean; - -import eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils; -import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup; -import eu.dnetlib.dhp.schema.oaf.Oaf; -import eu.dnetlib.dhp.schema.oaf.Qualifier; -import org.apache.commons.lang3.StringUtils; -import org.apache.spark.api.java.function.MapFunction; - -import java.lang.reflect.Field; -import java.util.Arrays; -import java.util.LinkedList; -import java.util.List; -import java.util.Objects; - -public class NormalizeEmptyFields implements MapFunction { - - private VocabularyGroup vocabularies; - - public NormalizeEmptyFields(VocabularyGroup vocabularies) { - this.vocabularies = vocabularies; - } - - @Override - public T call(T value) throws Exception { - - doNormalize(value); - - return value; - } - - private void doNormalize(Object o) { - if (Objects.isNull(o)) { - return; - } - - if (o instanceof Iterable) { - for (Object oi : (Iterable) o) { - doNormalize(oi); - } - } else { - - Class clazz = o.getClass(); - - if (clazz.isPrimitive() - || o instanceof Integer - || o instanceof Double - || o instanceof Float - || o instanceof Long - || o instanceof Boolean - || o instanceof String) { - return; - } else { - try { - for (Field field : getAllFields(new LinkedList<>(), clazz)) { - field.setAccessible(true); - Object value = field.get(o); - if (value instanceof Qualifier && Objects.isNull(value)) { - field.set(o, OafMapperUtils.unknown("", "")); - } else if (value instanceof Field && Objects.isNull(value)) { - - } else { - doNormalize(value); - } - } - } catch (IllegalAccessException | IllegalArgumentException e) { - throw new RuntimeException(e); - } - } - } - } - - private static List getAllFields(List fields, Class clazz) { - fields.addAll(Arrays.asList(clazz.getDeclaredFields())); - - final Class superclass = clazz.getSuperclass(); - if (Objects.nonNull(superclass) && superclass.getPackage().equals(Oaf.class.getPackage())) { - getAllFields(fields, superclass); - } - - return fields; - } - - public VocabularyGroup getVocabularies() { - return vocabularies; - } -} From 97b1c4057c12d9624aadef55bbd13678ad9ba379 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 12 Jun 2020 10:45:18 +0200 Subject: [PATCH 7/8] WIP: graph cleaner implementation --- .../dhp/oa/graph/clean/CleaningRule.java | 90 +++++------ .../dhp/oa/graph/clean/OafNavigator.java | 147 ++++++++++++++++++ .../oa/graph/raw/common/VocabularyGroup.java | 5 +- .../dhp/oa/graph/clean/CleaningRuleTest.java | 7 + .../eu/dnetlib/dhp/oa/graph/clean/result.json | 22 +++ 5 files changed, 217 insertions(+), 54 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRule.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRule.java index 51b930962..88fc61298 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRule.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRule.java @@ -1,86 +1,70 @@ package eu.dnetlib.dhp.oa.graph.clean; -import java.lang.reflect.Field; -import java.util.Arrays; -import java.util.LinkedList; -import java.util.List; -import java.util.Objects; - +import com.google.common.collect.Maps; +import eu.dnetlib.dhp.schema.oaf.Field; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import org.apache.commons.lang3.StringUtils; import org.apache.spark.api.java.function.MapFunction; import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup; import eu.dnetlib.dhp.schema.oaf.Oaf; import eu.dnetlib.dhp.schema.oaf.Qualifier; +import java.util.Map; +import java.util.Objects; +import java.util.function.Function; + public class CleaningRule implements MapFunction { private VocabularyGroup vocabularies; + private Map> mapping = Maps.newHashMap(); + + public CleaningRule(VocabularyGroup vocabularies) { this.vocabularies = vocabularies; + + mapping.put(Qualifier.class, o -> patchQualifier(o)); + mapping.put(StructuredProperty.class, o -> patchSp(o)); + mapping.put(Field.class, o -> patchStringField(o)); } @Override public T call(T value) throws Exception { - doClean(value); + OafNavigator.apply(value, mapping); return value; } - private void doClean(Object o) { - if (Objects.isNull(o)) { - return; - } - - if (o instanceof Iterable) { - for (Object oi : (Iterable) o) { - doClean(oi); - } - } else { - - Class clazz = o.getClass(); - - if (clazz.isPrimitive() - || o instanceof Integer - || o instanceof Double - || o instanceof Float - || o instanceof Long - || o instanceof Boolean - || o instanceof String) { - return; - } else { - try { - for (Field field : getAllFields(new LinkedList<>(), clazz)) { - field.setAccessible(true); - Object value = field.get(o); - if (value instanceof Qualifier) { - Qualifier q = (Qualifier) value; - if (vocabularies.vocabularyExists(q.getSchemeid())) { - field.set(o, vocabularies.lookup(q.getSchemeid(), q.getClassid())); - } - - } else { - doClean(value); - } - } - } catch (IllegalAccessException | IllegalArgumentException e) { - throw new RuntimeException(e); - } - } + private Object patchQualifier(Object o) { + Qualifier q = (Qualifier) o; + if (vocabularies.vocabularyExists(q.getSchemeid())) { + return vocabularies.lookup(q.getSchemeid(), q.getClassid()); } + return o; } - private static List getAllFields(List fields, Class clazz) { - fields.addAll(Arrays.asList(clazz.getDeclaredFields())); + private Object patchSp(Object o) { + StructuredProperty sp = (StructuredProperty) o; + if (StringUtils.isBlank(sp.getValue())) { + return null; + } + return o; + } - final Class superclass = clazz.getSuperclass(); - if (Objects.nonNull(superclass) && superclass.getPackage().equals(Oaf.class.getPackage())) { - getAllFields(fields, superclass); + private Object patchStringField(Object o) { + Field f = (Field) o; + try { + if (StringUtils.isBlank((String) f.getValue())) { + return null; + } + } catch (ClassCastException e) { + // ignored on purpose } - return fields; + return o; } public VocabularyGroup getVocabularies() { diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/OafNavigator.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/OafNavigator.java index c329a3111..40facc110 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/OafNavigator.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/OafNavigator.java @@ -1,4 +1,151 @@ + package eu.dnetlib.dhp.oa.graph.clean; +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.ObjectMapper; +import com.google.common.collect.Lists; +import eu.dnetlib.dhp.schema.oaf.Oaf; +import scala.Tuple2; + +import java.beans.BeanInfo; +import java.beans.IntrospectionException; +import java.beans.Introspector; +import java.beans.PropertyDescriptor; +import java.lang.reflect.Field; +import java.lang.reflect.InvocationTargetException; +import java.util.*; +import java.util.function.Function; + public class OafNavigator { + + public static E apply(E oaf, Map> mapping) { + reflect(oaf, mapping); + return oaf; + } + + public static void reflect(Object o, Map> mapping) { + visit(o, mapping); + } + + public static void visit(final Object thingy, Map> mapping) { + + try { + final Class clazz = thingy.getClass(); + + if (!isPrimitive(thingy) && clazz.getPackage().equals(Oaf.class.getPackage())) { + + final BeanInfo beanInfo = Introspector.getBeanInfo(clazz); + + for (final PropertyDescriptor descriptor : beanInfo.getPropertyDescriptors()) { + try { + final Object value = descriptor.getReadMethod().invoke(thingy); + + if (value != null && !isPrimitive(value)) { + + System.out.println("VISITING " + descriptor.getName() + " " + descriptor.getPropertyType()); + + if (Iterable.class.isAssignableFrom(descriptor.getPropertyType())) { + for(Object vi : (Iterable) value) { + + visit(vi, mapping); + } + } else { + + if (mapping.keySet().contains(value.getClass())) { + final Object newValue = mapping.get(value.getClass()).apply(value); + System.out.println("PATCHING " + descriptor.getName()+ " " + descriptor.getPropertyType()); + System.out.println("OLD VALUE " + getObjectMapper().writeValueAsString(value)); + System.out.println("NEW VALUE " + getObjectMapper().writeValueAsString(newValue)); + descriptor.getWriteMethod().invoke(newValue); + } + + visit(value, mapping); + } + } + + } catch (final IllegalArgumentException e) { + // handle this please + } catch (final IllegalAccessException e) { + // and this also + } catch (final InvocationTargetException e) { + // and this, too + } catch (JsonProcessingException e) { + e.printStackTrace(); + } + } + } + } catch (final IntrospectionException e) { + // do something sensible here + } + } + + private static ObjectMapper getObjectMapper() { + final ObjectMapper mapper = new ObjectMapper(); + return mapper; + } + + private static void navigate(Object o, Map> mapping) { + if (Objects.isNull(o) || isPrimitive(o)) { + return; + } else { + try { + for (Field field : getAllFields(o.getClass())) { + System.out.println(field.getName()); + field.setAccessible(true); + Object value = field.get(o); + + if (Objects.nonNull(value)) { + final Class fieldType = field.getType(); + if ((fieldType.isArray() && !fieldType.getComponentType().isPrimitive())) { + Object[] fs = (Object[]) value; + for (Object fi : fs) { + navigate(fi, mapping); + } + } if (Iterable.class.isAssignableFrom(fieldType)) { + Iterable fs = (Iterable) value; + for (Object fi : fs) { + navigate(fi, mapping); + } + } else { + if (mapping.keySet().contains(value.getClass())) { + System.out.println("PATCHING " + field.getName()); + field.set(o, mapping.get(value.getClass()).apply(value)); + } + } + } + } + + } catch (IllegalAccessException | IllegalArgumentException e) { + throw new RuntimeException(e); + } + } + } + + private static boolean isPrimitive(Object o) { + return o.getClass().isPrimitive() + || o instanceof Class + || o instanceof Integer + || o instanceof Double + || o instanceof Float + || o instanceof Long + || o instanceof Boolean + || o instanceof String + || o instanceof Byte; + } + + private static List getAllFields(Class clazz) { + return getAllFields(new LinkedList<>(), clazz); + } + + private static List getAllFields(List fields, Class clazz) { + fields.addAll(Arrays.asList(clazz.getDeclaredFields())); + + final Class superclass = clazz.getSuperclass(); + if (Objects.nonNull(superclass) && superclass.getPackage().equals(Oaf.class.getPackage())) { + getAllFields(fields, superclass); + } + + return fields; + } + } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/VocabularyGroup.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/VocabularyGroup.java index ec95ade00..447228bf9 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/VocabularyGroup.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/VocabularyGroup.java @@ -105,7 +105,10 @@ public class VocabularyGroup implements Serializable { } public Qualifier getTermAsQualifier(final String vocId, final String id) { - return vocs.get(vocId.toLowerCase()).getTermAsQualifier(id); + if (vocabularyExists(vocId)) { + return vocs.get(vocId.toLowerCase()).getTermAsQualifier(id); + } + return OafMapperUtils.qualifier(id, id, "", ""); } public Qualifier getSynonymAsQualifier(final String vocId, final String syn) { diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRuleTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRuleTest.java index 019285cc3..dcc98b200 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRuleTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRuleTest.java @@ -7,6 +7,7 @@ import static org.mockito.Mockito.lenient; import java.io.IOException; import java.util.HashSet; import java.util.List; +import java.util.Objects; import java.util.Set; import java.util.stream.Collectors; import java.util.stream.Stream; @@ -15,6 +16,7 @@ import org.apache.commons.io.IOUtils; import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.Test; import org.junit.jupiter.api.extension.ExtendWith; +import org.junit.platform.commons.util.StringUtils; import org.mockito.Mock; import org.mockito.junit.jupiter.MockitoExtension; @@ -82,6 +84,11 @@ public class CleaningRuleTest { // TODO add more assertions to verity the cleaned values System.out.println(MAPPER.writeValueAsString(p_out)); + assertTrue( + p_out + .getPid() + .stream() + .allMatch(sp -> StringUtils.isNotBlank(sp.getValue()))); } private Stream getAuthorPidTypes(Publication pub) { diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json index 435b001b7..89ebe5af5 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json @@ -380,6 +380,28 @@ "schemename": "dnet:pid_types" }, "value": "10.1007/s109090161569x" + }, + { + "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": "doi", + "classname": "doi", + "schemeid": "dnet:pid_types", + "schemename": "dnet:pid_types" + }, + "value": "" } ], "relevantdate": [ From cdb1956fe9cade7202c69733a264a2fb55b7f297 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 12 Jun 2020 11:36:59 +0200 Subject: [PATCH 8/8] WIP: graph cleaner implementation --- .../dhp/oa/graph/clean/OafNavigator2.java | 94 +++++++++++++++++++ 1 file changed, 94 insertions(+) create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/OafNavigator2.java diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/OafNavigator2.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/OafNavigator2.java new file mode 100644 index 000000000..74f064e47 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/OafNavigator2.java @@ -0,0 +1,94 @@ + +package eu.dnetlib.dhp.oa.graph.clean; + +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.schema.oaf.Oaf; + +import java.lang.reflect.Field; +import java.util.*; +import java.util.function.Function; + +public class OafNavigator2 { + + public static E apply(E oaf, Map> mapping) { + navigate(oaf, mapping); + return oaf; + } + + private static void navigate(Object o, Map> mapping) { + if (Objects.isNull(o) || isPrimitive(o)) { + return; + } else { + try { + for (Field field : getAllFields(o.getClass())) { + System.out.println("VISITING " + field.getName() + " in " + o.getClass()); + field.setAccessible(true); + Object value = field.get(o); + + if (Objects.nonNull(value)) { + final Class fieldType = field.getType(); + if ((fieldType.isArray() && !fieldType.getComponentType().isPrimitive())) { + Object[] fs = (Object[]) value; + for (Object fi : fs) { + navigate(fi, mapping); + } + } if (Iterable.class.isAssignableFrom(fieldType)) { + Iterable fs = (Iterable) value; + for (Object fi : fs) { + navigate(fi, mapping); + } + } else { + final Function cleaningFn = mapping.get(value.getClass()); + if (Objects.nonNull(cleaningFn)) { + final Object newValue = cleaningFn.apply(value); + if (!Objects.equals(value, newValue)) { + System.out.println("PATCHING " + field.getName()+ " " + value.getClass()); + System.out.println("OLD VALUE " + getObjectMapper().writeValueAsString(value)); + System.out.println("NEW VALUE " + getObjectMapper().writeValueAsString(newValue)); + field.set(o, newValue); + } + } + } + } + } + + } catch (IllegalAccessException | IllegalArgumentException | JsonProcessingException e) { + throw new RuntimeException(e); + } + } + } + + private static ObjectMapper getObjectMapper() { + final ObjectMapper mapper = new ObjectMapper(); + return mapper; + } + + private static boolean isPrimitive(Object o) { + return o.getClass().isPrimitive() + || o instanceof Class + || o instanceof Integer + || o instanceof Double + || o instanceof Float + || o instanceof Long + || o instanceof Boolean + || o instanceof String + || o instanceof Byte; + } + + private static List getAllFields(Class clazz) { + return getAllFields(new LinkedList<>(), clazz); + } + + private static List getAllFields(List fields, Class clazz) { + fields.addAll(Arrays.asList(clazz.getDeclaredFields())); + + final Class superclass = clazz.getSuperclass(); + if (Objects.nonNull(superclass) && superclass.getPackage().equals(Oaf.class.getPackage())) { + getAllFields(fields, superclass); + } + + return fields; + } + +}