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clean_cont
| Author | SHA1 | Date |
|---|---|---|
 Claudio Atzori
|
2f0d3dffe3 | |
 Miriam Baglioni
|
ca373979eb |
|
|
@ -0,0 +1,123 @@
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package eu.dnetlib.dhp.oa.graph.clean;
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/**
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* @author miriam.baglioni
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* @Date 28/06/22
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*/
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import java.io.Serializable;
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import java.util.Optional;
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import java.util.stream.Collectors;
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import org.apache.commons.io.IOUtils;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.sql.Dataset;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.SaveMode;
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import org.apache.spark.sql.SparkSession;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.oaf.Result;
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public class CleanContextSparkJob implements Serializable {
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private static final Logger log = LoggerFactory.getLogger(CleanContextSparkJob.class);
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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public static void main(String[] args) throws Exception {
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String jsonConfiguration = IOUtils
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.toString(
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CleanContextSparkJob.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/graph/input_clean_context_parameters.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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parser.parseArgument(args);
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Boolean isSparkSessionManaged = Optional
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.ofNullable(parser.get("isSparkSessionManaged"))
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.map(Boolean::valueOf)
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.orElse(Boolean.TRUE);
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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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String inputPath = parser.get("inputPath");
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log.info("inputPath: {}", inputPath);
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String workingPath = parser.get("workingPath");
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log.info("workingPath: {}", workingPath);
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String contextId = parser.get("contextId");
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log.info("contextId: {}", contextId);
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String verifyParam = parser.get("verifyParam");
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log.info("verifyParam: {}", verifyParam);
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String graphTableClassName = parser.get("graphTableClassName");
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log.info("graphTableClassName: {}", graphTableClassName);
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Class<? extends Result> entityClazz = (Class<? extends Result>) Class.forName(graphTableClassName);
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SparkConf conf = new SparkConf();
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runWithSparkSession(
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conf,
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isSparkSessionManaged,
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spark -> {
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cleanContext(spark, contextId, verifyParam, inputPath, entityClazz, workingPath);
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});
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}
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private static <T extends Result> void cleanContext(SparkSession spark, String contextId, String verifyParam,
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String inputPath, Class<T> entityClazz, String workingPath) {
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Dataset<T> res = spark
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.read()
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.textFile(inputPath)
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.map(
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(MapFunction<String, T>) value -> OBJECT_MAPPER.readValue(value, entityClazz),
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Encoders.bean(entityClazz));
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res.map((MapFunction<T, T>) r -> {
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if (!r
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.getTitle()
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.stream()
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.filter(
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t -> t
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.getQualifier()
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.getClassid()
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.equalsIgnoreCase(ModelConstants.MAIN_TITLE_QUALIFIER.getClassid()))
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.anyMatch(t -> t.getValue().toLowerCase().startsWith(verifyParam.toLowerCase()))) {
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return r;
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}
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r
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.setContext(
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r
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.getContext()
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.stream()
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.filter(
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c -> !c.getId().split("::")[0]
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.equalsIgnoreCase(contextId))
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.collect(Collectors.toList()));
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return r;
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}, Encoders.bean(entityClazz))
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.json(workingPath);
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spark
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.read()
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.textFile(workingPath)
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.map(
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(MapFunction<String, T>) value -> OBJECT_MAPPER.readValue(value, entityClazz),
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Encoders.bean(entityClazz))
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.json(inputPath);
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}
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}
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|
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@ -13,6 +13,23 @@
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<name>isLookupUrl</name>
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<description>the address of the lookUp service</description>
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</property>
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<property>
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<name>shouldCleanContext</name>
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<description>true if the context have to be cleaned</description>
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</property>
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<property>
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<name>contextId</name>
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<value>sobigdata</value>
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<description>It is the context id that should be removed from the result if the condition is matched.
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Now it is just sobigdata. In a futere implementation I plan to have the contextId as value in a json
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where to specify also the constraints that should be verified to remove the context from the result</description>
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</property>
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<property>
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<name>verifyParam</name>
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<value>gcube </value>
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<description>It is the constrint to be verified. This time is hardcoded as gcube and it is searched for in
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the title. If title starts with gcube than the context sobigdata will be removed by the result if present</description>
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</property>
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<property>
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<name>sparkDriverMemory</name>
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@ -275,7 +292,131 @@
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<error to="Kill"/>
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</action>
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<join name="wait_clean" to="End"/>
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<join name="wait_clean" to="clean_context"/>
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<decision name="clean_context">
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<switch>
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<case to="fork_clean_context">${wf:conf('shouldCleanContext') eq true}</case>
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<default to="End"/>
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</switch>
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</decision>
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<fork name="fork_clean_context">
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<path start="clean_publication_context"/>
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<path start="clean_dataset_context"/>
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<path start="clean_otherresearchproduct_context"/>
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<path start="clean_software_context"/>
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</fork>
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<action name="clean_publication_context">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Clean publications context</name>
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<class>eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob</class>
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<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-cores=${sparkExecutorCores}
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--executor-memory=${sparkExecutorMemory}
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--driver-memory=${sparkDriverMemory}
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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--conf spark.sql.shuffle.partitions=7680
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</spark-opts>
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<arg>--inputPath</arg><arg>${graphOutputPath}/publication</arg>
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<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
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<arg>--workingPath</arg><arg>${workingDir}/working/publication</arg>
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<arg>--contextId</arg><arg>${contextId}</arg>
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<arg>--verifyParam</arg><arg>${verifyParam}</arg>
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</spark>
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<ok to="wait_clean_context"/>
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<error to="Kill"/>
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</action>
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<action name="clean_dataset_context">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Clean datasets Context</name>
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<class>eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob</class>
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<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-cores=${sparkExecutorCores}
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--executor-memory=${sparkExecutorMemory}
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--driver-memory=${sparkDriverMemory}
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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--conf spark.sql.shuffle.partitions=7680
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</spark-opts>
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<arg>--inputPath</arg><arg>${graphOutputPath}/dataset</arg>
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<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
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<arg>--workingPath</arg><arg>${workingDir}/working/dataset</arg>
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<arg>--contextId</arg><arg>${contextId}</arg>
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<arg>--verifyParam</arg><arg>${verifyParam}</arg>
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</spark>
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<ok to="wait_clean_context"/>
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<error to="Kill"/>
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</action>
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<action name="clean_otherresearchproduct_context">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Clean otherresearchproducts context</name>
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<class>eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob</class>
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<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-cores=${sparkExecutorCores}
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--executor-memory=${sparkExecutorMemory}
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--driver-memory=${sparkDriverMemory}
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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--conf spark.sql.shuffle.partitions=7680
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</spark-opts>
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<arg>--inputPath</arg><arg>${graphOutputPath}/otherresearchproduct</arg>
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<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
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<arg>--workingPath</arg><arg>${workingDir}/working/otherresearchproduct</arg>
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<arg>--contextId</arg><arg>${contextId}</arg>
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<arg>--verifyParam</arg><arg>${verifyParam}</arg>
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</spark>
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<ok to="wait_clean_context"/>
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<error to="Kill"/>
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</action>
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<action name="clean_software_context">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Clean softwares context</name>
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<class>eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob</class>
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<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-cores=${sparkExecutorCores}
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--executor-memory=${sparkExecutorMemory}
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--driver-memory=${sparkDriverMemory}
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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--conf spark.sql.shuffle.partitions=7680
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</spark-opts>
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<arg>--inputPath</arg><arg>${graphOutputPath}/software</arg>
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<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
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<arg>--workingPath</arg><arg>${workingDir}/working/software</arg>
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<arg>--contextId</arg><arg>${contextId}</arg>
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<arg>--verifyParam</arg><arg>${verifyParam}</arg>
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</spark>
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<ok to="wait_clean_context"/>
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<error to="Kill"/>
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</action>
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|
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<join name="wait_clean_context" to="End"/>
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<end name="End"/>
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</workflow-app>
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|
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@ -0,0 +1,37 @@
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[
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{
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"paramName": "issm",
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"paramLongName": "isSparkSessionManaged",
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"paramDescription": "when true will stop SparkSession after job execution",
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"paramRequired": false
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},
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{
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"paramName": "in",
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"paramLongName": "inputPath",
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"paramDescription": "the path to the graph data dump to read",
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"paramRequired": true
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},
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{
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"paramName": "wp",
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"paramLongName": "workingPath",
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"paramDescription": "the path to store the output graph",
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"paramRequired": true
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},
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{
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"paramName": "ci",
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"paramLongName": "contextId",
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"paramDescription": "the id of the context to be removed",
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"paramRequired": true
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},
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{
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"paramName": "class",
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"paramLongName": "graphTableClassName",
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"paramDescription": "class name moelling the graph table",
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"paramRequired": true
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},{
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"paramName": "vf",
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"paramLongName": "verifyParam",
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"paramDescription": "the parameter to be verified to remove the context",
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"paramRequired": true
|
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}
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]
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|
|
@ -0,0 +1,292 @@
|
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package eu.dnetlib.dhp.oa.graph.clean;
|
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|
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/**
|
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* @author miriam.baglioni
|
||||
* @Date 28/06/22
|
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*/
|
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|
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import java.io.IOException;
|
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import java.nio.file.Files;
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import java.nio.file.Path;
|
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import java.util.List;
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import org.apache.commons.io.FileUtils;
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import org.apache.spark.SparkConf;
|
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import org.apache.spark.api.java.JavaRDD;
|
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import org.apache.spark.api.java.JavaSparkContext;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.SparkSession;
|
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import org.junit.jupiter.api.AfterAll;
|
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import org.junit.jupiter.api.Assertions;
|
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import org.junit.jupiter.api.BeforeAll;
|
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import org.junit.jupiter.api.Test;
|
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import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
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import eu.dnetlib.dhp.oa.graph.dump.DumpJobTest;
|
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import eu.dnetlib.dhp.schema.oaf.Publication;
|
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import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
|
||||
|
||||
public class CleanContextTest {
|
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|
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
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|
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private static SparkSession spark;
|
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|
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private static Path workingDir;
|
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|
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private static final Logger log = LoggerFactory.getLogger(CleanContextTest.class);
|
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|
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@BeforeAll
|
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public static void beforeAll() throws IOException {
|
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workingDir = Files.createTempDirectory(DumpJobTest.class.getSimpleName());
|
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log.info("using work dir {}", workingDir);
|
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|
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SparkConf conf = new SparkConf();
|
||||
conf.setAppName(DumpJobTest.class.getSimpleName());
|
||||
|
||||
conf.setMaster("local[*]");
|
||||
conf.set("spark.driver.host", "localhost");
|
||||
conf.set("hive.metastore.local", "true");
|
||||
conf.set("spark.ui.enabled", "false");
|
||||
conf.set("spark.sql.warehouse.dir", workingDir.toString());
|
||||
conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
|
||||
|
||||
spark = SparkSession
|
||||
.builder()
|
||||
.appName(DumpJobTest.class.getSimpleName())
|
||||
.config(conf)
|
||||
.getOrCreate();
|
||||
}
|
||||
|
||||
@AfterAll
|
||||
public static void afterAll() throws IOException {
|
||||
FileUtils.deleteDirectory(workingDir.toFile());
|
||||
spark.stop();
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testResultClean() throws Exception {
|
||||
final String sourcePath = getClass()
|
||||
.getResource("/eu/dnetlib/dhp/oa/graph/clean/publication_clean_context.json")
|
||||
.getPath();
|
||||
final String prefix = "gcube ";
|
||||
|
||||
spark
|
||||
.read()
|
||||
.textFile(sourcePath)
|
||||
.map(
|
||||
(MapFunction<String, Publication>) r -> OBJECT_MAPPER.readValue(r, Publication.class),
|
||||
Encoders.bean(Publication.class))
|
||||
.write()
|
||||
.json(workingDir.toString() + "/publication");
|
||||
|
||||
CleanContextSparkJob.main(new String[] {
|
||||
"--isSparkSessionManaged", Boolean.FALSE.toString(),
|
||||
"--inputPath", workingDir.toString() + "/publication",
|
||||
"-graphTableClassName", Publication.class.getCanonicalName(),
|
||||
"-workingPath", workingDir.toString() + "/working",
|
||||
"-contextId", "sobigdata",
|
||||
"-verifyParam", "gCube "
|
||||
});
|
||||
|
||||
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||
JavaRDD<Publication> tmp = sc
|
||||
.textFile(workingDir.toString() + "/publication")
|
||||
.map(item -> OBJECT_MAPPER.readValue(item, Publication.class));
|
||||
|
||||
Assertions.assertEquals(7, tmp.count());
|
||||
|
||||
// original result with sobigdata context and gcube as starting string in the main title for the publication
|
||||
Assertions
|
||||
.assertEquals(
|
||||
0,
|
||||
tmp
|
||||
.filter(p -> p.getId().equals("50|DansKnawCris::0224aae28af558f21768dbc6439c7a95"))
|
||||
.collect()
|
||||
.get(0)
|
||||
.getContext()
|
||||
.size());
|
||||
|
||||
// original result with sobigdata context without gcube as starting string in the main title for the publication
|
||||
Assertions
|
||||
.assertEquals(
|
||||
1,
|
||||
tmp
|
||||
.filter(p -> p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9"))
|
||||
.collect()
|
||||
.get(0)
|
||||
.getContext()
|
||||
.size());
|
||||
Assertions
|
||||
.assertEquals(
|
||||
"sobigdata::projects::2",
|
||||
tmp
|
||||
.filter(p -> p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9"))
|
||||
.collect()
|
||||
.get(0)
|
||||
.getContext()
|
||||
.get(0)
|
||||
.getId());
|
||||
|
||||
// original result with sobigdata context with gcube as starting string in the subtitle
|
||||
Assertions
|
||||
.assertEquals(
|
||||
1,
|
||||
tmp
|
||||
.filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af"))
|
||||
.collect()
|
||||
.get(0)
|
||||
.getContext()
|
||||
.size());
|
||||
Assertions
|
||||
.assertEquals(
|
||||
"sobigdata::projects::2",
|
||||
tmp
|
||||
.filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af"))
|
||||
.collect()
|
||||
.get(0)
|
||||
.getContext()
|
||||
.get(0)
|
||||
.getId());
|
||||
List<StructuredProperty> titles = tmp
|
||||
.filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af"))
|
||||
.collect()
|
||||
.get(0)
|
||||
.getTitle();
|
||||
Assertions.assertEquals(1, titles.size());
|
||||
Assertions.assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix));
|
||||
Assertions.assertEquals("subtitle", titles.get(0).getQualifier().getClassid());
|
||||
|
||||
// original result with sobigdata context with gcube not as starting string in the main title
|
||||
Assertions
|
||||
.assertEquals(
|
||||
1,
|
||||
tmp
|
||||
.filter(p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f"))
|
||||
.collect()
|
||||
.get(0)
|
||||
.getContext()
|
||||
.size());
|
||||
Assertions
|
||||
.assertEquals(
|
||||
"sobigdata::projects::1",
|
||||
tmp
|
||||
.filter(p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f"))
|
||||
.collect()
|
||||
.get(0)
|
||||
.getContext()
|
||||
.get(0)
|
||||
.getId());
|
||||
titles = tmp
|
||||
.filter(p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f"))
|
||||
.collect()
|
||||
.get(0)
|
||||
.getTitle();
|
||||
Assertions.assertEquals(1, titles.size());
|
||||
Assertions.assertFalse(titles.get(0).getValue().toLowerCase().startsWith(prefix));
|
||||
Assertions.assertTrue(titles.get(0).getValue().toLowerCase().contains(prefix.trim()));
|
||||
Assertions.assertEquals("main title", titles.get(0).getQualifier().getClassid());
|
||||
|
||||
// original result with sobigdata in context and also other contexts with gcube as starting string for the main
|
||||
// title
|
||||
Assertions
|
||||
.assertEquals(
|
||||
1,
|
||||
tmp
|
||||
.filter(p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53"))
|
||||
.collect()
|
||||
.get(0)
|
||||
.getContext()
|
||||
.size());
|
||||
Assertions
|
||||
.assertEquals(
|
||||
"dh-ch",
|
||||
tmp
|
||||
.filter(p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53"))
|
||||
.collect()
|
||||
.get(0)
|
||||
.getContext()
|
||||
.get(0)
|
||||
.getId());
|
||||
titles = tmp
|
||||
.filter(p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53"))
|
||||
.collect()
|
||||
.get(0)
|
||||
.getTitle();
|
||||
Assertions.assertEquals(1, titles.size());
|
||||
Assertions.assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix));
|
||||
Assertions.assertEquals("main title", titles.get(0).getQualifier().getClassid());
|
||||
|
||||
// original result with multiple main title one of which whith gcube as starting string and with 2 contextes
|
||||
Assertions
|
||||
.assertEquals(
|
||||
1,
|
||||
tmp
|
||||
.filter(p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff"))
|
||||
.collect()
|
||||
.get(0)
|
||||
.getContext()
|
||||
.size());
|
||||
Assertions
|
||||
.assertEquals(
|
||||
"dh-ch",
|
||||
tmp
|
||||
.filter(p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff"))
|
||||
.collect()
|
||||
.get(0)
|
||||
.getContext()
|
||||
.get(0)
|
||||
.getId());
|
||||
titles = tmp
|
||||
.filter(p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff"))
|
||||
.collect()
|
||||
.get(0)
|
||||
.getTitle();
|
||||
Assertions.assertEquals(2, titles.size());
|
||||
Assertions
|
||||
.assertTrue(
|
||||
titles
|
||||
.stream()
|
||||
.anyMatch(
|
||||
t -> t.getQualifier().getClassid().equals("main title")
|
||||
&& t.getValue().toLowerCase().startsWith(prefix)));
|
||||
|
||||
// original result without sobigdata in context with gcube as starting string for the main title
|
||||
Assertions
|
||||
.assertEquals(
|
||||
1,
|
||||
tmp
|
||||
.filter(p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8"))
|
||||
.collect()
|
||||
.get(0)
|
||||
.getContext()
|
||||
.size());
|
||||
Assertions
|
||||
.assertEquals(
|
||||
"dh-ch",
|
||||
tmp
|
||||
.filter(p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8"))
|
||||
.collect()
|
||||
.get(0)
|
||||
.getContext()
|
||||
.get(0)
|
||||
.getId());
|
||||
titles = tmp
|
||||
.filter(p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8"))
|
||||
.collect()
|
||||
.get(0)
|
||||
.getTitle();
|
||||
Assertions.assertEquals(2, titles.size());
|
||||
|
||||
Assertions
|
||||
.assertTrue(
|
||||
titles
|
||||
.stream()
|
||||
.anyMatch(
|
||||
t -> t.getQualifier().getClassid().equals("main title")
|
||||
&& t.getValue().toLowerCase().startsWith(prefix)));
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
File diff suppressed because one or more lines are too long
Loading…
Reference in New Issue