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dnet-hadoop
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Merge branch 'master' of code-repo.d4science.org:D-Net/dnet-hadoop

This commit is contained in:
Michele Artini 2020-05-05 17:12:22 +02:00
parent ccc609f909 0825321d0b
commit 8f30a09d84
22 changed files with 1673 additions and 415 deletions
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3
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java
View File

@ -7,6 +7,9 @@ import java.util.Objects;
public abstract class Oaf implements Serializable {
/**
* The list of datasource id/name pairs providing this relationship.
*/
protected List<KeyValue> collectedfrom;
private DataInfo dataInfo;

22
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java
View File

@ -7,16 +7,38 @@ import java.util.*;
import java.util.stream.Collectors;
import java.util.stream.Stream;
/**
* Relation models any edge between two nodes in the OpenAIRE graph. It has a source id and a target id pointing to
* graph node identifiers and it is further characterised by the semantic of the link through the fields relType,
* subRelType and relClass. Provenance information is modeled according to the dataInfo element and collectedFrom, while
* individual relationship types can provide extra information via the properties field.
*/
public class Relation extends Oaf {
/**
* Main relationship classifier, values include 'resultResult', 'resultProject', 'resultOrganization', etc.
*/
private String relType;
/**
* Further classifies a relationship, values include 'affiliation', 'similarity', 'supplement', etc.
*/
private String subRelType;
/**
* Indicates the direction of the relationship, values include 'isSupplementTo', 'isSupplementedBy', 'merges,
* 'isMergedIn'.
*/
private String relClass;
/**
* The source entity id.
*/
private String source;
/**
* The target entity id.
*/
private String target;
public String getRelType() {

146
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/GenerateNativeStoreSparkJob.java
View File

@ -1,17 +1,21 @@
package eu.dnetlib.dhp.collection;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.ByteArrayInputStream;
import java.nio.charset.StandardCharsets;
import java.util.HashMap;
import java.util.Map;
import java.util.Objects;
import java.util.Optional;
import org.apache.commons.cli.*;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.hadoop.io.IntWritable;
import org.apache.hadoop.io.Text;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaPairRDD;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
@ -23,6 +27,8 @@ import org.apache.spark.util.LongAccumulator;
import org.dom4j.Document;
import org.dom4j.Node;
import org.dom4j.io.SAXReader;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
@ -35,6 +41,8 @@ import eu.dnetlib.message.MessageType;
public class GenerateNativeStoreSparkJob {
private static final Logger log = LoggerFactory.getLogger(GenerateNativeStoreSparkJob.class);
public static MetadataRecord parseRecord(
final String input,
final String xpath,
@ -78,84 +86,90 @@ public class GenerateNativeStoreSparkJob {
final Provenance provenance = jsonMapper.readValue(parser.get("provenance"), Provenance.class);
final long dateOfCollection = new Long(parser.get("dateOfCollection"));
final SparkSession spark = SparkSession
.builder()
.appName("GenerateNativeStoreSparkJob")
.master(parser.get("master"))
.getOrCreate();
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final Map<String, String> ongoingMap = new HashMap<>();
final Map<String, String> reportMap = new HashMap<>();
final boolean test = parser.get("isTest") == null ? false : Boolean.valueOf(parser.get("isTest"));
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
final JavaPairRDD<IntWritable, Text> inputRDD = sc
.sequenceFile(parser.get("input"), IntWritable.class, Text.class);
final JavaPairRDD<IntWritable, Text> inputRDD = sc
.sequenceFile(parser.get("input"), IntWritable.class, Text.class);
final LongAccumulator totalItems = sc.sc().longAccumulator("TotalItems");
final LongAccumulator totalItems = sc.sc().longAccumulator("TotalItems");
final LongAccumulator invalidRecords = sc.sc().longAccumulator("InvalidRecords");
final LongAccumulator invalidRecords = sc.sc().longAccumulator("InvalidRecords");
final MessageManager manager = new MessageManager(
parser.get("rabbitHost"),
parser.get("rabbitUser"),
parser.get("rabbitPassword"),
false,
false,
null);
final MessageManager manager = new MessageManager(
parser.get("rabbitHost"),
parser.get("rabbitUser"),
parser.get("rabbitPassword"),
false,
false,
null);
final JavaRDD<MetadataRecord> mappeRDD = inputRDD
.map(
item -> parseRecord(
item._2().toString(),
parser.get("xpath"),
parser.get("encoding"),
provenance,
dateOfCollection,
totalItems,
invalidRecords))
.filter(Objects::nonNull)
.distinct();
final JavaRDD<MetadataRecord> mappeRDD = inputRDD
.map(
item -> parseRecord(
item._2().toString(),
parser.get("xpath"),
parser.get("encoding"),
provenance,
dateOfCollection,
totalItems,
invalidRecords))
.filter(Objects::nonNull)
.distinct();
ongoingMap.put("ongoing", "0");
if (!test) {
manager
.sendMessage(
new Message(
parser.get("workflowId"), "DataFrameCreation", MessageType.ONGOING, ongoingMap),
parser.get("rabbitOngoingQueue"),
true,
false);
}
ongoingMap.put("ongoing", "0");
if (!test) {
manager
.sendMessage(
new Message(
parser.get("workflowId"), "DataFrameCreation", MessageType.ONGOING, ongoingMap),
parser.get("rabbitOngoingQueue"),
true,
false);
}
final Encoder<MetadataRecord> encoder = Encoders.bean(MetadataRecord.class);
final Dataset<MetadataRecord> mdstore = spark.createDataset(mappeRDD.rdd(), encoder);
final LongAccumulator mdStoreRecords = sc.sc().longAccumulator("MDStoreRecords");
mdStoreRecords.add(mdstore.count());
ongoingMap.put("ongoing", "" + totalItems.value());
if (!test) {
manager
.sendMessage(
new Message(
parser.get("workflowId"), "DataFrameCreation", MessageType.ONGOING, ongoingMap),
parser.get("rabbitOngoingQueue"),
true,
false);
}
mdstore.write().format("parquet").save(parser.get("output"));
reportMap.put("inputItem", "" + totalItems.value());
reportMap.put("invalidRecords", "" + invalidRecords.value());
reportMap.put("mdStoreSize", "" + mdStoreRecords.value());
if (!test) {
manager
.sendMessage(
new Message(parser.get("workflowId"), "Collection", MessageType.REPORT, reportMap),
parser.get("rabbitReportQueue"),
true,
false);
manager.close();
}
});
final Encoder<MetadataRecord> encoder = Encoders.bean(MetadataRecord.class);
final Dataset<MetadataRecord> mdstore = spark.createDataset(mappeRDD.rdd(), encoder);
final LongAccumulator mdStoreRecords = sc.sc().longAccumulator("MDStoreRecords");
mdStoreRecords.add(mdstore.count());
ongoingMap.put("ongoing", "" + totalItems.value());
if (!test) {
manager
.sendMessage(
new Message(
parser.get("workflowId"), "DataFrameCreation", MessageType.ONGOING, ongoingMap),
parser.get("rabbitOngoingQueue"),
true,
false);
}
mdstore.write().format("parquet").save(parser.get("output"));
reportMap.put("inputItem", "" + totalItems.value());
reportMap.put("invalidRecords", "" + invalidRecords.value());
reportMap.put("mdStoreSize", "" + mdStoreRecords.value());
if (!test) {
manager
.sendMessage(
new Message(parser.get("workflowId"), "Collection", MessageType.REPORT, reportMap),
parser.get("rabbitReportQueue"),
true,
false);
manager.close();
}
}
}

97
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/TransformSparkJobNode.java
View File

@ -1,13 +1,17 @@
package eu.dnetlib.dhp.transformation;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.ByteArrayInputStream;
import java.util.HashMap;
import java.util.Map;
import java.util.Objects;
import java.util.Optional;
import org.apache.commons.cli.*;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoder;
import org.apache.spark.sql.Encoders;
@ -17,8 +21,11 @@ import org.dom4j.Document;
import org.dom4j.DocumentException;
import org.dom4j.Node;
import org.dom4j.io.SAXReader;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.collection.GenerateNativeStoreSparkJob;
import eu.dnetlib.dhp.model.mdstore.MetadataRecord;
import eu.dnetlib.dhp.transformation.vocabulary.Vocabulary;
import eu.dnetlib.dhp.transformation.vocabulary.VocabularyHelper;
@ -29,6 +36,8 @@ import eu.dnetlib.message.MessageType;
public class TransformSparkJobNode {
private static final Logger log = LoggerFactory.getLogger(TransformSparkJobNode.class);
public static void main(String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
@ -40,12 +49,18 @@ public class TransformSparkJobNode {
parser.parseArgument(args);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String inputPath = parser.get("input");
final String outputPath = parser.get("output");
final String workflowId = parser.get("workflowId");
final String trasformationRule = extractXSLTFromTR(
Objects.requireNonNull(DHPUtils.decompressString(parser.get("transformationRule"))));
final String master = parser.get("master");
final String rabbitUser = parser.get("rabbitUser");
final String rabbitPassword = parser.get("rabbitPassword");
final String rabbitHost = parser.get("rabbitHost");
@ -53,46 +68,48 @@ public class TransformSparkJobNode {
final long dateOfCollection = new Long(parser.get("dateOfCollection"));
final boolean test = parser.get("isTest") == null ? false : Boolean.valueOf(parser.get("isTest"));
final SparkSession spark = SparkSession
.builder()
.appName("TransformStoreSparkJob")
.master(master)
.getOrCreate();
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
final Encoder<MetadataRecord> encoder = Encoders.bean(MetadataRecord.class);
final Dataset<MetadataRecord> mdstoreInput = spark.read().format("parquet").load(inputPath).as(encoder);
final LongAccumulator totalItems = spark.sparkContext().longAccumulator("TotalItems");
final LongAccumulator errorItems = spark.sparkContext().longAccumulator("errorItems");
final LongAccumulator transformedItems = spark.sparkContext().longAccumulator("transformedItems");
final Map<String, Vocabulary> vocabularies = new HashMap<>();
vocabularies.put("dnet:languages", VocabularyHelper.getVocabularyFromAPI("dnet:languages"));
final TransformFunction transformFunction = new TransformFunction(
totalItems,
errorItems,
transformedItems,
trasformationRule,
dateOfCollection,
vocabularies);
mdstoreInput.map(transformFunction, encoder).write().format("parquet").save(outputPath);
if (rabbitHost != null) {
System.out.println("SEND FINAL REPORT");
final Map<String, String> reportMap = new HashMap<>();
reportMap.put("inputItem", "" + totalItems.value());
reportMap.put("invalidRecords", "" + errorItems.value());
reportMap.put("mdStoreSize", "" + transformedItems.value());
System.out.println(new Message(workflowId, "Transform", MessageType.REPORT, reportMap));
if (!test) {
final MessageManager manager = new MessageManager(rabbitHost, rabbitUser, rabbitPassword, false,
false,
null);
manager
.sendMessage(
new Message(workflowId, "Transform", MessageType.REPORT, reportMap),
rabbitReportQueue,
true,
false);
manager.close();
}
}
});
final Encoder<MetadataRecord> encoder = Encoders.bean(MetadataRecord.class);
final Dataset<MetadataRecord> mdstoreInput = spark.read().format("parquet").load(inputPath).as(encoder);
final LongAccumulator totalItems = spark.sparkContext().longAccumulator("TotalItems");
final LongAccumulator errorItems = spark.sparkContext().longAccumulator("errorItems");
final LongAccumulator transformedItems = spark.sparkContext().longAccumulator("transformedItems");
final Map<String, Vocabulary> vocabularies = new HashMap<>();
vocabularies.put("dnet:languages", VocabularyHelper.getVocabularyFromAPI("dnet:languages"));
final TransformFunction transformFunction = new TransformFunction(
totalItems,
errorItems,
transformedItems,
trasformationRule,
dateOfCollection,
vocabularies);
mdstoreInput.map(transformFunction, encoder).write().format("parquet").save(outputPath);
if (rabbitHost != null) {
System.out.println("SEND FINAL REPORT");
final Map<String, String> reportMap = new HashMap<>();
reportMap.put("inputItem", "" + totalItems.value());
reportMap.put("invalidRecords", "" + errorItems.value());
reportMap.put("mdStoreSize", "" + transformedItems.value());
System.out.println(new Message(workflowId, "Transform", MessageType.REPORT, reportMap));
if (!test) {
final MessageManager manager = new MessageManager(rabbitHost, rabbitUser, rabbitPassword, false, false,
null);
manager
.sendMessage(
new Message(workflowId, "Transform", MessageType.REPORT, reportMap),
rabbitReportQueue,
true,
false);
manager.close();
}
}
}
private static String extractXSLTFromTR(final String tr) throws DocumentException {

98
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/collection_input_parameters.json
View File

@ -1,16 +1,86 @@
[
{"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true},
{"paramName":"e", "paramLongName":"encoding", "paramDescription": "the encoding of the input record should be JSON or XML", "paramRequired": true},
{"paramName":"d", "paramLongName":"dateOfCollection", "paramDescription": "the date when the record has been stored", "paramRequired": true},
{"paramName":"p", "paramLongName":"provenance", "paramDescription": "the infos about the provenance of the collected records", "paramRequired": true},
{"paramName":"x", "paramLongName":"xpath", "paramDescription": "the xpath to identify the record ifentifier", "paramRequired": true},
{"paramName":"i", "paramLongName":"input", "paramDescription": "the path of the sequencial file to read", "paramRequired": true},
{"paramName":"o", "paramLongName":"output", "paramDescription": "the path of the result DataFrame on HDFS", "paramRequired": true},
{"paramName":"ru", "paramLongName":"rabbitUser", "paramDescription": "the user to connect with RabbitMq for messaging", "paramRequired": true},
{"paramName":"rp", "paramLongName":"rabbitPassword", "paramDescription": "the password to connect with RabbitMq for messaging", "paramRequired": true},
{"paramName":"rh", "paramLongName":"rabbitHost", "paramDescription": "the host of the RabbitMq server", "paramRequired": true},
{"paramName":"ro", "paramLongName":"rabbitOngoingQueue", "paramDescription": "the name of the ongoing queue", "paramRequired": true},
{"paramName":"rr", "paramLongName":"rabbitReportQueue", "paramDescription": "the name of the report queue", "paramRequired": true},
{"paramName":"w", "paramLongName":"workflowId", "paramDescription": "the identifier of the dnet Workflow", "paramRequired": true},
{"paramName":"t", "paramLongName":"isTest", "paramDescription": "the name of the report queue", "paramRequired": false}
{
"paramName": "issm",
"paramLongName": "isSparkSessionManaged",
"paramDescription": "when true will stop SparkSession after job execution",
"paramRequired": false
},
{
"paramName": "e",
"paramLongName": "encoding",
"paramDescription": "the encoding of the input record should be JSON or XML",
"paramRequired": true
},
{
"paramName": "d",
"paramLongName": "dateOfCollection",
"paramDescription": "the date when the record has been stored",
"paramRequired": true
},
{
"paramName": "p",
"paramLongName": "provenance",
"paramDescription": "the infos about the provenance of the collected records",
"paramRequired": true
},
{
"paramName": "x",
"paramLongName": "xpath",
"paramDescription": "the xpath to identify the record identifier",
"paramRequired": true
},
{
"paramName": "i",
"paramLongName": "input",
"paramDescription": "the path of the sequencial file to read",
"paramRequired": true
},
{
"paramName": "o",
"paramLongName": "output",
"paramDescription": "the path of the result DataFrame on HDFS",
"paramRequired": true
},
{
"paramName": "ru",
"paramLongName": "rabbitUser",
"paramDescription": "the user to connect with RabbitMq for messaging",
"paramRequired": true
},
{
"paramName": "rp",
"paramLongName": "rabbitPassword",
"paramDescription": "the password to connect with RabbitMq for messaging",
"paramRequired": true
},
{
"paramName": "rh",
"paramLongName": "rabbitHost",
"paramDescription": "the host of the RabbitMq server",
"paramRequired": true
},
{
"paramName": "ro",
"paramLongName": "rabbitOngoingQueue",
"paramDescription": "the name of the ongoing queue",
"paramRequired": true
},
{
"paramName": "rr",
"paramLongName": "rabbitReportQueue",
"paramDescription": "the name of the report queue",
"paramRequired": true
},
{
"paramName": "w",
"paramLongName": "workflowId",
"paramDescription": "the identifier of the dnet Workflow",
"paramRequired": true
},
{
"paramName": "t",
"paramLongName": "isTest",
"paramDescription": "the name of the report queue",
"paramRequired": false
}
]

86
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/transformation/transformation_input_parameters.json
View File

@ -1,16 +1,74 @@
[
{"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true},
{"paramName":"d", "paramLongName":"dateOfCollection", "paramDescription": "the date when the record has been stored", "paramRequired": true},
{"paramName":"i", "paramLongName":"input", "paramDescription": "the path of the sequencial file to read", "paramRequired": true},
{"paramName":"o", "paramLongName":"output", "paramDescription": "the path of the result DataFrame on HDFS", "paramRequired": true},
{"paramName":"w", "paramLongName":"workflowId", "paramDescription": "the identifier of the dnet Workflow", "paramRequired": true},
{"paramName":"tr", "paramLongName":"transformationRule","paramDescription": "the transformation Rule to apply to the input MDStore", "paramRequired": true},
{"paramName":"ru", "paramLongName":"rabbitUser", "paramDescription": "the user to connect with RabbitMq for messaging", "paramRequired": true},
{"paramName":"rp", "paramLongName":"rabbitPassword", "paramDescription": "the password to connect with RabbitMq for messaging", "paramRequired": true},
{"paramName":"rh", "paramLongName":"rabbitHost", "paramDescription": "the host of the RabbitMq server", "paramRequired": true},
{"paramName":"ro", "paramLongName":"rabbitOngoingQueue", "paramDescription": "the name of the ongoing queue", "paramRequired": true},
{"paramName":"rr", "paramLongName":"rabbitReportQueue", "paramDescription": "the name of the report queue", "paramRequired": true},
{"paramName":"t", "paramLongName":"isTest", "paramDescription": "the name of the report queue", "paramRequired": false}
{
"paramName": "issm",
"paramLongName": "isSparkSessionManaged",
"paramDescription": "when true will stop SparkSession after job execution",
"paramRequired": false
},
{
"paramName": "d",
"paramLongName": "dateOfCollection",
"paramDescription": "the date when the record has been stored",
"paramRequired": true
},
{
"paramName": "i",
"paramLongName": "input",
"paramDescription": "the path of the sequencial file to read",
"paramRequired": true
},
{
"paramName": "o",
"paramLongName": "output",
"paramDescription": "the path of the result DataFrame on HDFS",
"paramRequired": true
},
{
"paramName": "w",
"paramLongName": "workflowId",
"paramDescription": "the identifier of the dnet Workflow",
"paramRequired": true
},
{
"paramName": "tr",
"paramLongName": "transformationRule",
"paramDescription": "the transformation Rule to apply to the input MDStore",
"paramRequired": true
},
{
"paramName": "ru",
"paramLongName": "rabbitUser",
"paramDescription": "the user to connect with RabbitMq for messaging",
"paramRequired": true
},
{
"paramName": "rp",
"paramLongName": "rabbitPassword",
"paramDescription": "the password to connect with RabbitMq for messaging",
"paramRequired": true
},
{
"paramName": "rh",
"paramLongName": "rabbitHost",
"paramDescription": "the host of the RabbitMq server",
"paramRequired": true
},
{
"paramName": "ro",
"paramLongName": "rabbitOngoingQueue",
"paramDescription": "the name of the ongoing queue",
"paramRequired": true
},
{
"paramName": "rr",
"paramLongName": "rabbitReportQueue",
"paramDescription": "the name of the report queue",
"paramRequired": true
},
{
"paramName": "t",
"paramLongName": "isTest",
"paramDescription": "the name of the report queue",
"paramRequired": false
}
]

86
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/CollectionJobTest.java
View File

@ -9,65 +9,60 @@ import java.nio.file.Path;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOUtils;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.apache.spark.SparkConf;
import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.*;
import org.junit.jupiter.api.io.TempDir;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.model.mdstore.MetadataRecord;
import eu.dnetlib.dhp.model.mdstore.Provenance;
import eu.dnetlib.dhp.schema.common.ModelSupport;
public class CollectionJobTest {
private Path testDir;
private static SparkSession spark;
@BeforeEach
public void setup() throws IOException {
testDir = Files.createTempDirectory("dhp-collection");
@BeforeAll
public static void beforeAll() {
SparkConf conf = new SparkConf();
conf.setAppName(CollectionJobTest.class.getSimpleName());
conf.setMaster("local");
spark = SparkSession.builder().config(conf).getOrCreate();
}
@AfterEach
public void teadDown() throws IOException {
FileUtils.deleteDirectory(testDir.toFile());
@AfterAll
public static void afterAll() {
spark.stop();
}
@Test
public void tesCollection() throws Exception {
public void tesCollection(@TempDir Path testDir) throws Exception {
final Provenance provenance = new Provenance("pippo", "puppa", "ns_prefix");
Assertions.assertNotNull(new ObjectMapper().writeValueAsString(provenance));
GenerateNativeStoreSparkJob
.main(
new String[] {
"-mt",
"local",
"-w",
"wid",
"-e",
"XML",
"-d",
"" + System.currentTimeMillis(),
"-p",
new ObjectMapper().writeValueAsString(provenance),
"-x",
"./*[local-name()='record']/*[local-name()='header']/*[local-name()='identifier']",
"-i",
this.getClass().getResource("/eu/dnetlib/dhp/collection/native.seq").toString(),
"-o",
testDir.toString() + "/store",
"-t",
"true",
"-ru",
"",
"-rp",
"",
"-rh",
"",
"-ro",
"",
"-rr",
""
"issm", "true",
"-w", "wid",
"-e", "XML",
"-d", "" + System.currentTimeMillis(),
"-p", new ObjectMapper().writeValueAsString(provenance),
"-x", "./*[local-name()='record']/*[local-name()='header']/*[local-name()='identifier']",
"-i", this.getClass().getResource("/eu/dnetlib/dhp/collection/native.seq").toString(),
"-o", testDir.toString() + "/store",
"-t", "true",
"-ru", "",
"-rp", "",
"-rh", "",
"-ro", "",
"-rr", ""
});
System.out.println(new ObjectMapper().writeValueAsString(provenance));
// TODO introduce useful assertions
}
@Test
@ -85,9 +80,8 @@ public class CollectionJobTest {
null,
null);
assert record != null;
System.out.println(record.getId());
System.out.println(record.getOriginalId());
assertNotNull(record.getId());
assertNotNull(record.getOriginalId());
}
@Test
@ -112,10 +106,12 @@ public class CollectionJobTest {
System.currentTimeMillis(),
null,
null);
assert record != null;
record.setBody("ciao");
assert record1 != null;
record1.setBody("mondo");
assertNotNull(record);
assertNotNull(record1);
assertEquals(record, record1);
}
}

58
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java
View File

@ -12,10 +12,14 @@ import java.util.Map;
import javax.xml.transform.stream.StreamSource;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.sql.SparkSession;
import org.apache.spark.util.LongAccumulator;
import org.dom4j.Document;
import org.dom4j.Node;
import org.dom4j.io.SAXReader;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.DisplayName;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
@ -23,6 +27,7 @@ import org.junit.jupiter.api.io.TempDir;
import org.mockito.Mock;
import org.mockito.junit.jupiter.MockitoExtension;
import eu.dnetlib.dhp.collection.CollectionJobTest;
import eu.dnetlib.dhp.model.mdstore.MetadataRecord;
import eu.dnetlib.dhp.transformation.functions.Cleaner;
import eu.dnetlib.dhp.transformation.vocabulary.Vocabulary;
@ -33,6 +38,21 @@ import net.sf.saxon.s9api.*;
@ExtendWith(MockitoExtension.class)
public class TransformationJobTest {
private static SparkSession spark;
@BeforeAll
public static void beforeAll() {
SparkConf conf = new SparkConf();
conf.setAppName(CollectionJobTest.class.getSimpleName());
conf.setMaster("local");
spark = SparkSession.builder().config(conf).getOrCreate();
}
@AfterAll
public static void afterAll() {
spark.stop();
}
@Mock
private LongAccumulator accumulator;
@ -78,31 +98,21 @@ public class TransformationJobTest {
TransformSparkJobNode
.main(
new String[] {
"-mt",
"local",
"-i",
mdstore_input,
"-o",
mdstore_output,
"-d",
"1",
"-w",
"1",
"-tr",
xslt,
"-t",
"true",
"-ru",
"",
"-rp",
"",
"-rh",
"",
"-ro",
"",
"-rr",
""
"-issm", "true",
"-i", mdstore_input,
"-o", mdstore_output,
"-d", "1",
"-w", "1",
"-tr", xslt,
"-t", "true",
"-ru", "",
"-rp", "",
"-rh", "",
"-ro", "",
"-rr", ""
});
// TODO introduce useful assertions
}
@Test

2
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java
View File

@ -94,7 +94,7 @@ public class SparkPropagateRelation extends AbstractSparkAction {
FieldType.TARGET,
getDeletedFn());
save(newRels.union(updated), outputRelationPath, SaveMode.Overwrite);
save(newRels.union(updated).union(mergeRels), outputRelationPath, SaveMode.Overwrite);
}
private static Dataset<Relation> processDataset(

2
dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java
View File

@ -420,7 +420,7 @@ public class SparkDedupTest implements Serializable {
long relations = jsc.textFile(testDedupGraphBasePath + "/relation").count();
assertEquals(826, relations);
assertEquals(5022, relations);
// check deletedbyinference
final Dataset<Relation> mergeRels = spark

70
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml
View File

@ -115,11 +115,11 @@
<delete path="${contentPath}/db_claims"/>
</prepare>
<main-class>eu.dnetlib.dhp.oa.graph.raw.MigrateDbEntitiesApplication</main-class>
<arg>-p</arg><arg>${contentPath}/db_claims</arg>
<arg>-pgurl</arg><arg>${postgresURL}</arg>
<arg>-pguser</arg><arg>${postgresUser}</arg>
<arg>-pgpasswd</arg><arg>${postgresPassword}</arg>
<arg>-a</arg><arg>claims</arg>
<arg>--hdfsPath</arg><arg>${contentPath}/db_claims</arg>
<arg>--postgresUrl</arg><arg>${postgresURL}</arg>
<arg>--postgresUser</arg><arg>${postgresUser}</arg>
<arg>--postgresPassword</arg><arg>${postgresPassword}</arg>
<arg>--action</arg><arg>claims</arg>
</java>
<ok to="ImportODF_claims"/>
<error to="Kill"/>
@ -165,10 +165,10 @@
<delete path="${contentPath}/db_records"/>
</prepare>
<main-class>eu.dnetlib.dhp.oa.graph.raw.MigrateDbEntitiesApplication</main-class>
<arg>-p</arg><arg>${contentPath}/db_records</arg>
<arg>-pgurl</arg><arg>${postgresURL}</arg>
<arg>-pguser</arg><arg>${postgresUser}</arg>
<arg>-pgpasswd</arg><arg>${postgresPassword}</arg>
<arg>--hdfsPath</arg><arg>${contentPath}/db_records</arg>
<arg>--postgresUrl</arg><arg>${postgresURL}</arg>
<arg>--postgresUser</arg><arg>${postgresUser}</arg>
<arg>--postgresPassword</arg><arg>${postgresPassword}</arg>
</java>
<ok to="ImportODF"/>
<error to="Kill"/>
@ -180,12 +180,12 @@
<delete path="${contentPath}/odf_records"/>
</prepare>
<main-class>eu.dnetlib.dhp.oa.graph.raw.MigrateMongoMdstoresApplication</main-class>
<arg>-p</arg><arg>${contentPath}/odf_records</arg>
<arg>-mongourl</arg><arg>${mongoURL}</arg>
<arg>-mongodb</arg><arg>${mongoDb}</arg>
<arg>-f</arg><arg>ODF</arg>
<arg>-l</arg><arg>store</arg>
<arg>-i</arg><arg>cleaned</arg>
<arg>--hdfsPath</arg><arg>${contentPath}/odf_records</arg>
<arg>--mongoBaseUrl</arg><arg>${mongoURL}</arg>
<arg>--mongoDb</arg><arg>${mongoDb}</arg>
<arg>--mdFormat</arg><arg>ODF</arg>
<arg>--mdLayout</arg><arg>store</arg>
<arg>--mdInterpretation</arg><arg>cleaned</arg>
</java>
<ok to="ImportOAF"/>
<error to="Kill"/>
@ -197,12 +197,12 @@
<delete path="${contentPath}/oaf_records"/>
</prepare>
<main-class>eu.dnetlib.dhp.oa.graph.raw.MigrateMongoMdstoresApplication</main-class>
<arg>-p</arg><arg>${contentPath}/oaf_records</arg>
<arg>-mongourl</arg><arg>${mongoURL}</arg>
<arg>-mongodb</arg><arg>${mongoDb}</arg>
<arg>-f</arg><arg>OAF</arg>
<arg>-l</arg><arg>store</arg>
<arg>-i</arg><arg>cleaned</arg>
<arg>--hdfsPath</arg><arg>${contentPath}/oaf_records</arg>
<arg>--mongoBaseUrl</arg><arg>${mongoURL}</arg>
<arg>--mongoDb</arg><arg>${mongoDb}</arg>
<arg>--mdFormat</arg><arg>OAF</arg>
<arg>--mdLayout</arg><arg>store</arg>
<arg>--mdInterpretation</arg><arg>cleaned</arg>
</java>
<ok to="wait_import"/>
<error to="Kill"/>
@ -231,11 +231,11 @@
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>-s</arg><arg>${contentPath}/db_claims,${contentPath}/oaf_claims,${contentPath}/odf_claims</arg>
<arg>-t</arg><arg>${workingDir}/entities_claim</arg>
<arg>-pgurl</arg><arg>${postgresURL}</arg>
<arg>-pguser</arg><arg>${postgresUser}</arg>
<arg>-pgpasswd</arg><arg>${postgresPassword}</arg>
<arg>--sourcePaths</arg><arg>${contentPath}/db_claims,${contentPath}/oaf_claims,${contentPath}/odf_claims</arg>
<arg>--targetPath</arg><arg>${workingDir}/entities_claim</arg>
<arg>--postgresUrl</arg><arg>${postgresURL}</arg>
<arg>--postgresUser</arg><arg>${postgresUser}</arg>
<arg>--postgresPassword</arg><arg>${postgresPassword}</arg>
</spark>
<ok to="GenerateGraph_claims"/>
<error to="Kill"/>
@ -257,8 +257,8 @@
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>-s</arg><arg>${workingDir}/entities_claim</arg>
<arg>-g</arg><arg>${workingDir}/graph_claims</arg>
<arg>--sourcePath</arg><arg>${workingDir}/entities_claim</arg>
<arg>--graphRawPath</arg><arg>${workingDir}/graph_claims</arg>
</spark>
<ok to="wait_graphs"/>
<error to="Kill"/>
@ -280,11 +280,11 @@
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>-s</arg><arg>${contentPath}/db_records,${contentPath}/oaf_records,${contentPath}/odf_records</arg>
<arg>-t</arg><arg>${workingDir}/entities</arg>
<arg>-pgurl</arg><arg>${postgresURL}</arg>
<arg>-pguser</arg><arg>${postgresUser}</arg>
<arg>-pgpasswd</arg><arg>${postgresPassword}</arg>
<arg>--sourcePaths</arg><arg>${contentPath}/db_records,${contentPath}/oaf_records,${contentPath}/odf_records</arg>
<arg>--targetPath</arg><arg>${workingDir}/entities</arg>
<arg>--postgresUrl</arg><arg>${postgresURL}</arg>
<arg>--postgresUser</arg><arg>${postgresUser}</arg>
<arg>--postgresPassword</arg><arg>${postgresPassword}</arg>
</spark>
<ok to="GenerateGraph"/>
<error to="Kill"/>
@ -307,8 +307,8 @@
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=7680
</spark-opts>
<arg>-s</arg><arg>${workingDir}/entities</arg>
<arg>-g</arg><arg>${workingDir}/graph_raw</arg>
<arg>--sourcePath</arg><arg>${workingDir}/entities</arg>
<arg>--graphRawPath</arg><arg>${workingDir}/graph_raw</arg>
</spark>
<ok to="wait_graphs"/>
<error to="Kill"/>

85
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_db/oozie_app/workflow.xml
View File

@ -1,8 +1,8 @@
<workflow-app name="import db entities (step 1)" xmlns="uri:oozie:workflow:0.5">
<workflow-app name="import DB entities" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>migrationPathStep1</name>
<description>the base path to store hdfs file</description>
<name>contentPath</name>
<description>path location to store (or reuse) content from the aggregator</description>
</property>
<property>
<name>postgresURL</name>
@ -16,6 +16,7 @@
<name>postgresPassword</name>
<description>the password postgres</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
@ -28,31 +29,81 @@
<name>sparkExecutorCores</name>
<description>number of cores used by single executor</description>
</property>
<property>
<name>oozieActionShareLibForSpark2</name>
<description>oozie action sharelib for spark 2.*</description>
</property>
<property>
<name>spark2ExtraListeners</name>
<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
<description>spark 2.* extra listeners classname</description>
</property>
<property>
<name>spark2SqlQueryExecutionListeners</name>
<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
<description>spark 2.* sql query execution listeners classname</description>
</property>
<property>
<name>spark2YarnHistoryServerAddress</name>
<description>spark 2.* yarn history server address</description>
</property>
<property>
<name>spark2EventLogDir</name>
<description>spark 2.* event log dir location</description>
</property>
</parameters>
<start to="ResetWorkingPath"/>
<global>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<configuration>
<property>
<name>mapreduce.job.queuename</name>
<value>${queueName}</value>
</property>
<property>
<name>oozie.launcher.mapred.job.queue.name</name>
<value>${oozieLauncherQueueName}</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>${oozieActionShareLibForSpark2}</value>
</property>
</configuration>
</global>
<start to="ImportDB"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="ResetWorkingPath">
<fs>
<delete path='${migrationPathStep1}/db_records'/>
</fs>
<ok to="ImportDB"/>
<action name="ImportDB">
<java>
<prepare>
<delete path="${contentPath}/db_records"/>
</prepare>
<main-class>eu.dnetlib.dhp.oa.graph.raw.MigrateDbEntitiesApplication</main-class>
<arg>--hdfsPath</arg><arg>${contentPath}/db_records</arg>
<arg>--postgresUrl</arg><arg>${postgresURL}</arg>
<arg>--postgresUser</arg><arg>${postgresUser}</arg>
<arg>--postgresPassword</arg><arg>${postgresPassword}</arg>
</java>
<ok to="ImportDB_claims"/>
<error to="Kill"/>
</action>
<action name="ImportDB">
<action name="ImportDB_claims">
<java>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.dhp.migration.step1.MigrateDbEntitiesApplication</main-class>
<arg>-p</arg><arg>${migrationPathStep1}/db_records</arg>
<arg>-pgurl</arg><arg>${postgresURL}</arg>
<arg>-pguser</arg><arg>${postgresUser}</arg>
<arg>-pgpasswd</arg><arg>${postgresPassword}</arg>
<prepare>
<delete path="${contentPath}/db_claims"/>
</prepare>
<main-class>eu.dnetlib.dhp.oa.graph.raw.MigrateDbEntitiesApplication</main-class>
<arg>--hdfsPath</arg><arg>${contentPath}/db_claims</arg>
<arg>--postgresUrl</arg><arg>${postgresURL}</arg>
<arg>--postgresUser</arg><arg>${postgresUser}</arg>
<arg>--postgresPassword</arg><arg>${postgresPassword}</arg>
<arg>--action</arg><arg>claims</arg>
</java>
<ok to="End"/>
<error to="Kill"/>

4
dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJob.java
View File

@ -113,7 +113,7 @@ public class XmlIndexingJob {
});
}
private static String toIndexRecord(Transformer tr, final String record) {
protected static String toIndexRecord(Transformer tr, final String record) {
final StreamResult res = new StreamResult(new StringWriter());
try {
tr.transform(new StreamSource(new StringReader(record)), res);
@ -135,7 +135,7 @@ public class XmlIndexingJob {
* @throws IOException could happen
* @throws TransformerException could happen
*/
private static String getLayoutTransformer(String format, String fields, String xslt)
protected static String getLayoutTransformer(String format, String fields, String xslt)
throws TransformerException {
final Transformer layoutTransformer = SaxonTransformerFactory.newInstance(xslt);

60
dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java
View File

@ -9,10 +9,7 @@ import java.io.IOException;
import java.io.Serializable;
import java.io.StringReader;
import java.io.StringWriter;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.*;
import java.util.stream.Collectors;
import javax.xml.transform.*;
@ -47,7 +44,7 @@ import eu.dnetlib.dhp.schema.oaf.Result;
public class XmlRecordFactory implements Serializable {
public static final String REL_SUBTYPE_DEDUP = "dedup";
private static final String REL_SUBTYPE_DEDUP = "dedup";
private final Map<String, LongAccumulator> accumulators;
private final Set<String> specialDatasourceTypes;
@ -100,8 +97,8 @@ public class XmlRecordFactory implements Serializable {
final List<String> relations = je
.getLinks()
.stream()
.filter(t -> !REL_SUBTYPE_DEDUP.equalsIgnoreCase(t.getRelation().getSubRelType()))
.map(link -> mapRelation(link, templateFactory, contexts))
.filter(link -> !isDuplicate(link))
.map(link -> mapRelation(contexts, templateFactory, type, link))
.collect(Collectors.toCollection(ArrayList::new));
final String mainType = ModelSupport.getMainType(type);
@ -936,7 +933,7 @@ public class XmlRecordFactory implements Serializable {
metadata.add(XmlSerializationUtils.mapQualifier("datasourcetypeui", dsType));
}
private String mapRelation(Tuple2 link, TemplateFactory templateFactory, Set<String> contexts) {
private List<String> mapFields(Tuple2 link, Set<String> contexts) {
final Relation rel = link.getRelation();
final RelatedEntity re = link.getRelatedEntity();
final String targetType = link.getRelatedEntity().getType();
@ -1040,38 +1037,47 @@ public class XmlRecordFactory implements Serializable {
default:
throw new IllegalArgumentException("invalid target type: " + targetType);
}
final DataInfo info = rel.getDataInfo();
final String scheme = ModelSupport.getScheme(re.getType(), targetType);
if (StringUtils.isBlank(scheme)) {
throw new IllegalArgumentException(
String.format("missing scheme for: <%s - %s>", re.getType(), targetType));
}
final String accumulatorName = getRelDescriptor(rel.getRelType(), rel.getSubRelType(), rel.getRelClass());
if (accumulators.containsKey(accumulatorName)) {
accumulators.get(accumulatorName).add(1);
}
return metadata;
}
private String mapRelation(Set<String> contexts, TemplateFactory templateFactory, EntityType type, Tuple2 link) {
final Relation rel = link.getRelation();
final String targetType = link.getRelatedEntity().getType();
final String scheme = ModelSupport.getScheme(type.toString(), targetType);
if (StringUtils.isBlank(scheme)) {
throw new IllegalArgumentException(
String.format("missing scheme for: <%s - %s>", type.toString(), targetType));
}
final HashSet<String> fields = Sets.newHashSet(mapFields(link, contexts));
return templateFactory
.getRel(
targetType, rel.getTarget(), Sets.newHashSet(metadata), rel.getRelClass(), scheme, info);
targetType, rel.getTarget(), fields, rel.getRelClass(), scheme, rel.getDataInfo());
}
private List<String> listChildren(
final OafEntity entity, JoinedEntity je, TemplateFactory templateFactory) {
final List<String> children = Lists.newArrayList();
EntityType entityType = EntityType.valueOf(je.getEntity().getType());
children
.addAll(
je
.getLinks()
.stream()
.filter(link -> REL_SUBTYPE_DEDUP.equalsIgnoreCase(link.getRelation().getSubRelType()))
.map(link -> mapRelation(link, templateFactory, null))
.collect(Collectors.toCollection(ArrayList::new)));
List<String> children = je
.getLinks()
.stream()
.filter(link -> isDuplicate(link))
.map(link -> {
final String targetType = link.getRelatedEntity().getType();
final String name = ModelSupport.getMainType(EntityType.valueOf(targetType));
final HashSet<String> fields = Sets.newHashSet(mapFields(link, null));
return templateFactory
.getChild(name, link.getRelatedEntity().getId(), Lists.newArrayList(fields));
})
.collect(Collectors.toCollection(ArrayList::new));
if (MainEntityType.result.toString().equals(ModelSupport.getMainType(entityType))) {
final List<Instance> instances = ((Result) entity).getInstance();
@ -1178,6 +1184,10 @@ public class XmlRecordFactory implements Serializable {
return children;
}
private boolean isDuplicate(Tuple2 link) {
return REL_SUBTYPE_DEDUP.equalsIgnoreCase(link.getRelation().getSubRelType());
}
private List<String> listExtraInfo(OafEntity entity) {
final List<ExtraInfo> extraInfo = entity.getExtraInfo();
return extraInfo != null

6
dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/template/child.st
View File

@ -1,3 +1,3 @@
<name$if(hasId)$ objidentifier="$id$"$else$$endif>>
$metadata:{ it | $it$ }$
</name>
<$name$$if(hasId)$ objidentifier="$id$"$else$$endif$>
$metadata:{$it$}$
</$name$>

42
dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/GraphJoinerTest.java
View File

@ -1,42 +0,0 @@
package eu.dnetlib.dhp.oa.provision;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import org.junit.jupiter.api.BeforeEach;
public class GraphJoinerTest {
private final ClassLoader cl = getClass().getClassLoader();
private Path workingDir;
private Path inputDir;
private Path outputDir;
@BeforeEach
public void before() throws IOException {
workingDir = Files.createTempDirectory("promote_action_set");
inputDir = workingDir.resolve("input");
outputDir = workingDir.resolve("output");
}
private static void copyFiles(Path source, Path target) throws IOException {
Files
.list(source)
.forEach(
f -> {
try {
if (Files.isDirectory(f)) {
Path subTarget = Files.createDirectories(target.resolve(f.getFileName()));
copyFiles(f, subTarget);
} else {
Files.copy(f, target.resolve(f.getFileName()));
}
} catch (IOException e) {
e.printStackTrace();
throw new RuntimeException(e);
}
});
}
}

39
dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java Normal file
View File

@ -0,0 +1,39 @@
package eu.dnetlib.dhp.oa.provision;
import java.io.IOException;
import java.io.StringReader;
import java.io.StringWriter;
import java.nio.file.Files;
import java.nio.file.Path;
import javax.xml.transform.Transformer;
import javax.xml.transform.TransformerException;
import javax.xml.transform.stream.StreamResult;
import javax.xml.transform.stream.StreamSource;
import org.apache.commons.io.IOUtils;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import eu.dnetlib.dhp.utils.saxon.SaxonTransformerFactory;
public class IndexRecordTransformerTest {
@Test
public void testTrasformRecord() throws IOException, TransformerException {
String fields = IOUtils.toString(getClass().getResourceAsStream("fields.xml"));
String record = IOUtils.toString(getClass().getResourceAsStream("record.xml"));
String xslt = IOUtils.toString(getClass().getResourceAsStream("layoutToRecordTransformer.xsl"));
String transformer = XmlIndexingJob.getLayoutTransformer("DMF", fields, xslt);
Transformer tr = SaxonTransformerFactory.newInstance(transformer);
String a = XmlIndexingJob.toIndexRecord(tr, record);
System.out.println(a);
}
}

166
dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/fields.xml Normal file
View File

@ -0,0 +1,166 @@
<LAYOUT name="index">
<FIELDS>
<FIELD indexable="false" name="oafentity" result="true" stat="false" tokenizable="false" xpath="//*[local-name() = 'entity']"/>
<FIELD indexable="true" name="oaftype" result="false" stat="false" tokenizable="false" value="local-name(//*[local-name()='entity']/*[local-name() != 'extraInfo'])"/>
<FIELD indexable="true" name="objIdentifier" result="false" stat="false" tokenizable="false" xpath="//header/dri:objIdentifier"/><!-- DATASOURCE FIELDS -->
<FIELD indexable="true" name="datasourceofficialname" result="false" stat="false" xpath="//*[local-name()='entity']/*[local-name()='datasource']/officialname"/>
<FIELD indexable="true" name="datasourceenglishname" result="false" stat="false" xpath="//*[local-name()='entity']/*[local-name()='datasource']/englishname"/>
<FIELD indexable="true" name="datasourceoddescription" result="false" stat="false" xpath="//*[local-name()='entity']/*[local-name()='datasource']/oddescription"/>
<FIELD indexable="true" name="datasourceodsubjects" result="false" stat="false" tokenizable="false" xpath="//*[local-name()='entity']/*[local-name()='datasource']/odsubjects"/>
<FIELD indexable="true" name="datasourceodlanguages" result="false" stat="false" tokenizable="false" xpath="//*[local-name()='entity']/*[local-name()='datasource']/odlanguages"/>
<FIELD indexable="true" name="datasourceodcontenttypes" result="false" stat="false" tokenizable="false" xpath="//*[local-name()='entity']/*[local-name()='datasource']/odcontenttypes"/>
<FIELD indexable="true" multivalued="false" name="datasourcetypename" result="false" stat="false" tokenizable="false" xpath="//*[local-name()='entity']/*[local-name()='datasource']/datasourcetype/@classname"/>
<FIELD indexable="true" multivalued="false" name="datasourcetypeuiid" result="false" stat="false" tokenizable="false" xpath="//*[local-name()='entity']/*[local-name()='datasource']/datasourcetypeui/@classid"/>
<FIELD indexable="true" multivalued="false" name="datasourcetypeuiname" result="false" stat="false" tokenizable="false" xpath="//*[local-name()='entity']/*[local-name()='datasource']/datasourcetypeui/@classname"/>
<FIELD indexable="true" multivalued="false" name="datasourcecompatibilityid" result="false" stat="false" tokenizable="false" xpath="//*[local-name()='entity']/*[local-name()='datasource']/openairecompatibility/@classid"/>
<FIELD indexable="true" multivalued="false" name="datasourcecompatibilityname" result="false" stat="false" tokenizable="false" xpath="//*[local-name()='entity']/*[local-name()='datasource']/openairecompatibility/@classname"/>
<FIELD indexable="true" multivalued="true" name="datasourcesubject" result="false" stat="false" type="ngramtext" xpath="//*[local-name()='entity']/*[local-name()='datasource']/subjects"/>
<FIELD indexable="true" name="versioning" result="false" stat="false" tokenizable="false" xpath="//*[local-name()='entity']/*[local-name()='datasource']/versioning"/><!-- ORGANIZATION FIELDS -->
<FIELD indexable="true" name="organizationlegalshortname" result="false" stat="false" type="ngramtext" xpath="distinct-values(//*[local-name()='entity']/*[local-name()='organization']//legalshortname)"/>
<FIELD indexable="true" name="organizationlegalname" result="false" stat="false" type="ngramtext" xpath="distinct-values(//*[local-name()='entity']/*[local-name()='organization']//legalname)"/>
<FIELD indexable="true" name="organizationalternativenames" result="false" stat="false" type="ngramtext" xpath="distinct-values(//*[local-name()='entity']/*[local-name()='organization']//alternativeNames)"/>
<FIELD indexable="true" name="organizationeclegalbody" result="false" stat="false" xpath="//*[local-name()='entity']/*[local-name()='organization']/eclegalbody"/>
<FIELD indexable="true" name="organizationeclegalperson" result="false" stat="false" xpath="//*[local-name()='entity']/*[local-name()='organization']/eclegalperson"/>
<FIELD indexable="true" name="organizationecnonprofit" result="false" stat="false" xpath="//*[local-name()='entity']/*[local-name()='organization']/ecnonprofit"/>
<FIELD indexable="true" name="organizationecresearchorganization" result="false" stat="false" xpath="//*[local-name()='entity']/*[local-name()='organization']/ecresearchorganization"/>
<FIELD indexable="true" name="organizationecinternationalorganizationeurinterests" result="false" stat="false" xpath="//*[local-name()='entity']/*[local-name()='organization']/ecinternationalorganizationeurinterests"/>
<FIELD indexable="true" name="organizationecinternationalorganization" result="false" stat="false" xpath="//*[local-name()='entity']/*[local-name()='organization']/ecinternationalorganization"/>
<FIELD indexable="true" name="organizationecenterprise" result="false" stat="false" xpath="//*[local-name()='entity']/*[local-name()='organization']/ecenterprise"/>
<FIELD indexable="true" name="organizationecsmevalidated" result="false" stat="false" xpath="//*[local-name()='entity']/*[local-name()='organization']/ecsmevalidated"/>
<FIELD indexable="true" name="organizationecnutscode" result="false" stat="false" xpath="//*[local-name()='entity']/*[local-name()='organization']/ecnutscode"/>
<FIELD indexable="true" multivalued="false" name="organizationcountryname" result="false" stat="false" tokenizable="false" xpath="//*[local-name()='entity']/*[local-name()='organization']/country/@classname"/><!-- PROJECT FIELDS -->
<FIELD indexable="true" name="projectcode" result="false" stat="false" type="ngramtext" xpath="//*[local-name()='entity']/*[local-name()='project']/code"/>
<FIELD indexable="true" name="projectcode_nt" result="false" stat="false" tokenizable="false" xpath="//*[local-name()='entity']/*[local-name()='project']/code"/>
<FIELD indexable="true" name="projectacronym" result="false" stat="false" type="ngramtext" xpath="//*[local-name()='entity']/*[local-name()='project']/acronym"/>
<FIELD indexable="true" name="projecttitle" result="false" stat="false" type="ngramtext" xpath="//*[local-name()='entity']/*[local-name()='project']/title"/>
<FIELD indexable="true" multivalued="false" name="projectstartdate" result="false" stat="false" type="pdate" value="//*[local-name()='entity']/*[local-name()='project']/startdate"/>
<FIELD indexable="true" multivalued="false" name="projectstartyear" result="false" stat="false" tokenizable="false" value="dnet:extractYear(//*[local-name()='entity']/*[local-name()='project']/startdate)"/>
<FIELD indexable="true" multivalued="false" name="projectenddate" result="false" stat="false" type="pdate" value="//*[local-name()='entity']/*[local-name()='project']/enddate"/>
<FIELD indexable="true" multivalued="false" name="projectendyear" result="false" stat="false" tokenizable="false" value="dnet:extractYear(//*[local-name()='entity']/*[local-name()='project']/enddate)"/>
<FIELD indexable="true" multivalued="false" name="projectcallidentifier" result="false" stat="false" tokenizable="false" xpath="//*[local-name()='entity']/*[local-name()='project']/callidentifier"/>
<FIELD indexable="true" name="projectkeywords" result="false" stat="false" xpath="//*[local-name()='entity']/*[local-name()='project']/keywords"/>
<FIELD indexable="true" multivalued="false" name="projectduration" result="false" stat="false" tokenizable="false" xpath="//*[local-name()='entity']/*[local-name()='project']/duration"/>
<FIELD indexable="true" multivalued="false" name="projectecsc39" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']/*[local-name()='project']/ecsc39)"/>
<FIELD indexable="true" multivalued="false" name="projectoamandatepublications" result="false" stat="false" tokenizable="false" xpath="//*[local-name()='entity']/*[local-name()='project']/oamandatepublications"/>
<FIELD indexable="true" multivalued="false" name="projectecarticle29_3" result="false" stat="false" tokenizable="false" xpath="//*[local-name()='entity']/*[local-name()='project']/ecarticle29_3"/>
<FIELD indexable="true" name="projectsubject" result="false" stat="false" tokenizable="false" xpath="//*[local-name()='entity']/*[local-name()='project']/subjects"/>
<FIELD indexable="true" multivalued="false" name="projectcontracttypename" result="false" stat="false" tokenizable="false" xpath="//*[local-name()='entity']/*[local-name()='project']/contracttype/@classname"/>
<FIELD indexable="true" name="fundinglevel0_id" result="false" stat="false" tokenizable="false" xpath="//*[local-name()='entity']/*[local-name()='project']/fundingtree//funding_level_0/id"/>
<FIELD indexable="true" name="fundinglevel0_name" result="false" stat="false" tokenizable="false" xpath="//*[local-name()='entity']/*[local-name()='project']/fundingtree//funding_level_0/name"/>
<FIELD indexable="true" name="fundinglevel0_description" result="false" stat="false" xpath="//*[local-name()='entity']/*[local-name()='project']/fundingtree//funding_level_0/description"/>
<FIELD indexable="true" name="fundinglevel1_id" result="false" stat="false" tokenizable="false" xpath="//*[local-name()='entity']/*[local-name()='project']/fundingtree//funding_level_1/id"/>
<FIELD indexable="true" name="fundinglevel1_name" result="false" stat="false" tokenizable="false" xpath="//*[local-name()='entity']/*[local-name()='project']/fundingtree//funding_level_1/name"/>
<FIELD indexable="true" name="fundinglevel1_description" result="false" stat="false" xpath="//*[local-name()='entity']/*[local-name()='project']/fundingtree//funding_level_1/description"/>
<FIELD indexable="true" name="fundinglevel2_id" result="false" stat="false" tokenizable="false" xpath="//*[local-name()='entity']/*[local-name()='project']/fundingtree//funding_level_2/id"/>
<FIELD indexable="true" name="fundinglevel2_name" result="false" stat="false" tokenizable="false" xpath="//*[local-name()='entity']/*[local-name()='project']/fundingtree//funding_level_2/name"/>
<FIELD indexable="true" name="fundinglevel2_description" result="false" stat="false" xpath="//*[local-name()='entity']/*[local-name()='project']/fundingtree//funding_level_2/description"/><!-- PROJECTS' FUNDER FIELDS: indexable only with the new funding path/context handling -->
<FIELD indexable="true" name="funder" result="false" stat="false" tokenizable="false" value="concat(./id/text(), '||', ./name/text(), '||', ./shortname/text())" xpath="//*[local-name()='entity']/*[local-name()='project']/fundingtree/funder"/>
<FIELD indexable="true" name="fundershortname" result="false" stat="false" tokenizable="false" xpath="//*[local-name()='entity']/*[local-name()='project']/fundingtree/funder/shortname"/>
<FIELD indexable="true" name="funderid" result="false" stat="false" tokenizable="false" xpath="//*[local-name()='entity']/*[local-name()='project']/fundingtree/funder/id"/>
<FIELD indexable="true" name="fundername" result="false" stat="false" tokenizable="false" xpath="//*[local-name()='entity']/*[local-name()='project']/fundingtree/funder/name"/>
<FIELD indexable="true" name="funderoriginalname" result="false" stat="false" tokenizable="false" xpath="//*[local-name()='entity']/*[local-name()='project']/fundingtree/funder/originalname"/>
<FIELD indexable="true" name="funderjurisdiction" result="false" stat="false" tokenizable="false" xpath="//*[local-name()='entity']/*[local-name()='project']/fundingtree/funder/jurisdiction"/><!-- RESULT FIELDS -->
<FIELD indexable="true" name="resulttitle" result="false" stat="false" xpath="//*[local-name() = 'entity']/*[local-name() ='result']/title | //*[local-name()='entity']/*[local-name()='result']/children/result/title"/>
<FIELD indexable="true" name="resultsubject" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']/*[local-name()='result']/subject)"/>
<FIELD indexable="true" name="resultsubjectclass" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']/*[local-name()='result']/subject/@classname)"/>
<FIELD indexable="true" multivalued="false" name="resultembargoenddate" result="false" stat="false" type="pdate" value="//*[local-name()='entity']/*[local-name()='result']/embargoenddate"/>
<FIELD indexable="true" multivalued="false" name="resultembargoendyear" result="false" stat="false" tokenizable="false" value="dnet:extractYear(//*[local-name()='entity']/*[local-name()='result']/embargoenddate)"/>
<FIELD indexable="true" multivalued="false" name="resulttypeid" result="false" stat="false" tokenizable="false" xpath="//*[local-name()='entity']/*[local-name()='result']/resulttype/@classid"/>
<FIELD indexable="true" multivalued="false" name="resulttypename" result="false" stat="false" tokenizable="false" xpath="//*[local-name()='entity']/*[local-name()='result']/resulttype/@classname"/>
<FIELD indexable="true" multivalued="false" name="resultlanguagename" result="false" stat="false" tokenizable="false" xpath="//*[local-name()='entity']/*[local-name()='result']/language/@classname"/>
<FIELD indexable="true" name="resultpublisher" result="false" stat="false" xpath="//*[local-name()='entity']/*[local-name()='result']/*[local-name()='publisher']"/>
<FIELD indexable="true" name="resultdescription" result="false" stat="false" xpath="//*[local-name()='entity']/*[local-name()='result']//*[local-name()='description']"/>
<FIELD indexable="true" name="resultlicense" result="false" stat="false" tokenizable="false" xpath="//*[local-name()='entity']/*[local-name()='result']/children/instance/license"/>
<FIELD indexable="true" name="resultaccessright" result="false" stat="false" tokenizable="false" xpath="//*[local-name()='entity']/*[local-name()='result']/children/instance/accessright/@classname"/>
<FIELD indexable="true" multivalued="false" name="resultbestaccessright" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']/*[local-name()='result']/bestaccessright/@classname)"/>
<FIELD indexable="true" multivalued="false" name="resultdateofacceptance" result="false" stat="false" type="pdate" value="//*[local-name()='entity']/*[local-name()='result']/dateofacceptance"/>
<FIELD indexable="true" multivalued="false" name="resultacceptanceyear" result="false" stat="false" tokenizable="false" value="dnet:extractYear(//*[local-name()='entity']/*[local-name()='result']/dateofacceptance)"/>
<FIELD indexable="true" multivalued="true" name="resultauthor" result="false" stat="false" xpath="//*[local-name()='entity']/*[local-name()='result']/creator"/>
<FIELD indexable="true" multivalued="true" name="resultauthor_nt" result="false" stat="false" type="string_ci" xpath="//*[local-name()='entity']/*[local-name()='result']/creator"/>
<FIELD indexable="true" multivalued="true" name="authorid" result="false" stat="false" type="string_ci" xpath="//*[local-name()='entity']/*[local-name()='result']/creator/@*[local-name() != 'rank' and local-name() != 'name' and local-name() != 'surname']"/>
<FIELD indexable="true" multivalued="true" name="authoridtype" result="false" stat="false" type="string_ci" xpath="//*[local-name()='entity']/*[local-name()='result']/creator/@*[local-name() != 'rank' and local-name() != 'name' and local-name() != 'surname']/local-name()"/>
<FIELD indexable="true" name="resulthostingdatasource" result="false" stat="false" tokenizable="false" value="distinct-values(concat(./@id, '||', ./@name))" xpath="//*[local-name()='entity']/*[local-name()='result']/children/instance/*[local-name()='hostedby']"/>
<FIELD indexable="true" name="resulthostingdatasourceid" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']/*[local-name()='result']/children/instance/*[local-name()='hostedby']/@id)"/>
<FIELD indexable="true" name="resulthostingdatasourcename" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']/*[local-name()='result']/children/instance/*[local-name()='hostedby']/@name)"/>
<FIELD indexable="true" name="instancetypename" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']/*[local-name()='result']/children/instance/*[local-name()='instancetype']/@classname)"/>
<FIELD indexable="true" name="resultdupid" result="false" stat="false" tokenizable="false" xpath="//*[local-name()='entity']/*//children/result/@objidentifier"/>
<FIELD indexable="true" name="organizationdupid" result="false" stat="false" tokenizable="false" xpath="//*[local-name()='entity']/*//children/organization/@objidentifier"/>
<FIELD indexable="true" name="externalrefsite" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']/*//children/externalreference/sitename)"/>
<FIELD indexable="true" name="externalreflabel" result="false" stat="false" tokenizable="true" xpath="distinct-values(//*[local-name()='entity']/*//children/externalreference/label)"/>
<FIELD indexable="true" name="externalrefclass" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']/*//children/externalreference/qualifier/@classid)"/>
<FIELD indexable="true" name="externalrefid" result="false" stat="false" tokenizable="false" xpath="(//*[local-name()='entity']/*//children/externalreference/refidentifier)"/>
<FIELD indexable="true" name="resultidentifier" result="false" stat="false" xpath="distinct-values(//*[local-name()='entity']/*[local-name()='result']/children/instance/webresource/*[local-name()='url'])"/>
<FIELD indexable="true" name="resultsource" result="false" stat="false" xpath="distinct-values(//*[local-name()='entity']/*[local-name()='result']/source)"/><!-- REL FIELDS -->
<FIELD indexable="true" name="reldatasourcecompatibilityid" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']/*//rel[./to/@type='datasource']/openairecompatibility/@classid)"/>
<FIELD indexable="true" name="relproject" result="false" stat="false" tokenizable="false" value="distinct-values(concat(./text(), '||', dnet:pickFirst(../acronym/text(), ../title/text())))" xpath="//*[local-name()='entity']/*//rel/to[@type='project']"/>
<FIELD indexable="true" name="relprojectid" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']/*//rel/to[@type='project'])"/>
<FIELD indexable="true" name="relprojectcode" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']/*//rel[./to/@type='project']/code)"/>
<FIELD indexable="true" name="relprojectname" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']/*//rel[./to/@type='project']/acronym)"/>
<FIELD indexable="true" name="relprojecttitle" result="false" stat="false" xpath="distinct-values(//*[local-name()='entity']/*//rel[./to/@type='project']/title)"/>
<FIELD indexable="true" name="relcontracttypeid" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']/*//rel[./to/@type='project']/contracttype/@classid)"/>
<FIELD indexable="true" name="relcontracttypename" result="false" stat="false" xpath="distinct-values(//*[local-name()='entity']/*//rel[./to/@type='project']/contracttype/@classname)"/>
<FIELD indexable="true" name="relorganizationcountryid" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']/*//rel[./to/@type='organization']/country/@classid)"/>
<FIELD indexable="true" name="relorganizationcountryname" result="false" stat="false" xpath="distinct-values(//*[local-name()='entity']/*//rel[./to/@type='organization']/country/@classname)"/>
<FIELD indexable="true" name="relorganizationid" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']/*//rel/to[@type='organization'])"/>
<FIELD indexable="true" name="relorganizationname" result="false" stat="false" xpath="distinct-values(//*[local-name()='entity']/*//rel[./to/@type='organization']/legalname)"/>
<FIELD indexable="true" name="relorganizationshortname" result="false" stat="false" xpath="distinct-values(//*[local-name()='entity']/*//rel[./to/@type='organization']/legalshortname)"/>
<FIELD indexable="true" name="relresultid" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']/*//rel/to[@type='result'])"/>
<FIELD indexable="true" name="relresulttype" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']/*//rel/resulttype/@classid)"/>
<FIELD indexable="true" name="relclass" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']/*//rel/to/@class)"/>
<FIELD indexable="true" name="relfundinglevel0_id" result="false" stat="false" tokenizable="false" xpath="//*[local-name()='entity']//rel/funding/funding_level_0"/>
<FIELD indexable="true" name="relfundinglevel0_name" result="false" stat="false" tokenizable="false" xpath="//*[local-name()='entity']//rel/funding/funding_level_0/@name/string()"/>
<FIELD indexable="true" name="relfundinglevel1_id" result="false" stat="false" tokenizable="false" xpath="//*[local-name()='entity']//rel/funding/funding_level_1"/>
<FIELD indexable="true" name="relfundinglevel1_name" result="false" stat="false" tokenizable="false" xpath="//*[local-name()='entity']//rel/funding/funding_level_1/@name/string()"/>
<FIELD indexable="true" name="relfundinglevel2_id" result="false" stat="false" tokenizable="false" xpath="//*[local-name()='entity']//rel/funding/funding_level_2"/>
<FIELD indexable="true" name="relfundinglevel2_name" result="false" stat="false" tokenizable="false" xpath="//*[local-name()='entity']//rel/funding/funding_level_2/@name/string()"/>
<FIELD indexable="true" name="relinferred" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']//rel/@inferred)"/>
<FIELD indexable="true" name="reltrust" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']//rel/@trust)"/>
<FIELD indexable="true" name="relinferenceprovenance" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']//rel/@inferenceprovenance)"/>
<FIELD indexable="true" name="relprovenanceactionclassid" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']//rel/@provenanceaction)"/><!-- PROJECTS' FUNDER FIELDS: indexable only with the new funding path/context handling -->
<FIELD indexable="true" name="relfunder" result="false" stat="false" tokenizable="false" value="distinct-values(concat(@id, '||', @name, '||', @shortname))" xpath="//*[local-name()='entity']//rel/funding/funder"/>
<FIELD indexable="true" name="relfunderid" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']//rel/funding/funder/@id)"/>
<FIELD indexable="true" name="relfundershortname" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']//rel/funding/funder/@shortname)"/>
<FIELD indexable="true" name="relfundername" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']//rel/funding/funder/@name)"/>
<FIELD indexable="true" name="relfunderjurisdiction" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']//rel/funding/funder/@jurisdiction)"/><!-- Collected from of the related entity. Available for result-result relationships -->
<FIELD indexable="true" name="relcollectedfromid" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']/*//rel/collectedfrom/@id)"/>
<FIELD indexable="true" name="relcollectedfromname" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']/*//rel/collectedfrom/@name)"/><!-- COMMON FIELDS -->
<FIELD indexable="true" multivalued="false" name="dateofcollection" result="false" stat="false" type="pdate" value="//header/*[local-name()='dateOfCollection']"/>
<FIELD indexable="true" name="collectedfrom" result="false" stat="false" tokenizable="false" value="distinct-values(concat(./@id, '||', ./@name))" xpath="//*[local-name()='entity']/*/*[local-name()='collectedfrom'] | //*[local-name()='entity']/*//*[local-name() = 'instance']/*[local-name()='collectedfrom']"/>
<FIELD indexable="true" name="collectedfromdatasourceid" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']/*/*[local-name()='collectedfrom']/@id | //*[local-name()='entity']/*//*[local-name() = 'instance']/*[local-name()='collectedfrom']/@id)"/>
<FIELD indexable="true" name="collectedfromname" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']/*/*[local-name()='collectedfrom']/@name | //*[local-name()='entity']/*//*[local-name() = 'instance']/*[local-name()='collectedfrom']/@name)"/>
<FIELD indexable="true" name="originalid" result="false" stat="false" tokenizable="false" type="string_ci" xpath="//*[local-name()='entity']/*/*[local-name()='originalId']"/>
<FIELD indexable="true" name="pid" result="false" stat="false" tokenizable="false" type="string_ci" xpath="//*[local-name()='entity']/*[local-name()='result']/pid/text()"/>
<FIELD indexable="true" name="pidclassid" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']/*[local-name()='result']/pid/@classid)"/>
<FIELD indexable="true" name="pidclassname" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']/*[local-name()='result']/pid/@classname)"/>
<FIELD indexable="true" name="inferred" result="false" stat="false" tokenizable="false" xpath="//*[local-name()='entity']//datainfo/inferred"/>
<FIELD indexable="true" name="deletedbyinference" result="false" stat="false" tokenizable="false" xpath="//*[local-name()='entity']//datainfo/deletedbyinference"/>
<FIELD indexable="true" name="trust" result="false" stat="false" tokenizable="false" xpath="//*[local-name()='entity']//datainfo/trust"/>
<FIELD indexable="true" name="inferenceprovenance" result="false" stat="false" tokenizable="false" xpath="//*[local-name()='entity']//datainfo/inferenceprovenance"/>
<FIELD indexable="true" name="provenanceactionclassid" result="false" stat="false" tokenizable="false" xpath="//*[local-name()='entity']//datainfo/provenanceaction/@classid"/>
<FIELD indexable="true" name="contextid" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']/*[local-name()='result']/context/@id)"/>
<FIELD indexable="true" name="contexttype" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']/*[local-name()='result']/context/@type)"/>
<FIELD indexable="true" name="contextname" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']/*[local-name()='result']/context/@label)"/><!-- Need special fields for community (research initiative) context in order to exclude funders from the context browse -->
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<creator rank="1">Jain, Subhash C.</creator>
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<description>Withania somnifera has been used in traditional medicine for a variety
of neural disorders. Recently, chronic neurodegenerative conditions have been
shown to benefit from treatment with this extract. To evaluate the action of
this extract on traumatically injured neurons, the efficacy of W. somnifera root
extract as a neuroprotective agent was examined in cultured model neurons
exposed to an in vitro injury system designed to mimic mild traumatic brain
injury (TBI). Neuronal health was evaluated by staining with annexin V (an
early, apoptotic feature) and monitoring released lactate dehydrogenase activity
(a terminal cell loss parameter). Potential mechanisms underlying the observed
neuroprotection were examined. Additionally, morphological changes were
monitored following injury and treatment. Although no differences were found in
the expression of the antioxidant transcription factor nuclear factor erythroid
2-like 2 (Nrf2) or other Nrf2-related downstream components, significant changes
were seen in apoptotic signaling. Treatment with the extract resulted in an
increased length of neurites projecting from the neuronal cell body after
injury. W. somnifera extract treatment also resulted in reduced cell death in
the model neuron TBI system. The cell death factor Bax was involved (its
expression was reduced 2-fold by the treatment) and injury-induced reduction in
neurite lengths and numbers was reversed by the treatment. This all indicates
that W. somnifera root extract was neuroprotective and could have therapeutic
potential to target factors involved in secondary injury and long-term sequelae
of mild TBI.</description>
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schemename="dnet:subject_classification_typologies" inferred="false">traumatic
brain injury</subject>
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<publisher>SAGE Publishing</publisher>
<source>Cell Transplantation, Vol 26 (2017)</source>
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</result>

6
dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/config-default.xml
View File

@ -15,12 +15,12 @@
<name>oozie.action.sharelib.for.spark</name>
<value>spark2</value>
</property>
<property>
<name>hive_metastore_uris</name>
<property>
<name>hiveMetastoreUris</name>
<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
</property>
<property>
<name>hive_jdbc_url</name>
<name>hiveJdbcUrl</name>
<value>jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000</value>
</property>
<property>

166
dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml
View File

@ -14,11 +14,11 @@
<description>the external stats that should be added since they are not included in the graph database</description>
</property>
<property>
<name>hive_metastore_uris</name>
<name>hiveMetastoreUris</name>
<description>hive server metastore URIs</description>
</property>
<property>
<name>hive_jdbc_url</name>
<name>hiveJdbcUrl</name>
<description>hive server jdbc url</description>
</property>
</parameters>
@ -29,7 +29,7 @@
<configuration>
<property>
<name>hive.metastore.uris</name>
<value>${hive_metastore_uris}</value>
<value>${hiveMetastoreUris}</value>
</property>
</configuration>
</global>
@ -42,7 +42,7 @@
<action name="Step1">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step1.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -53,7 +53,7 @@
<action name="Step2_1">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step2_1.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -64,7 +64,7 @@
<action name="Step2_2">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step2_2.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -75,7 +75,7 @@
<action name="Step2_3">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step2_3.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -86,7 +86,7 @@
<action name="Step2_4">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step2_4.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -97,7 +97,7 @@
<action name="Step2_5">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step2_5.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -108,7 +108,7 @@
<action name="Step2_6">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step2_6.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -119,7 +119,7 @@
<action name="Step2_7">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step2_7.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -130,7 +130,7 @@
<action name="Step2_8">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step2_8.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -141,7 +141,7 @@
<action name="Step2_9">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step2_9.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -152,7 +152,7 @@
<action name="Step3">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step3.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -163,7 +163,7 @@
<action name="Step4_1">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step4_1.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -174,7 +174,7 @@
<action name="Step4_2">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step4_2.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -185,7 +185,7 @@
<action name="Step4_3">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step4_3.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -196,7 +196,7 @@
<action name="Step4_4">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step4_4.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -207,7 +207,7 @@
<action name="Step4_5">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step4_5.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -218,7 +218,7 @@
<action name="Step4_6">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step4_6.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -229,7 +229,7 @@
<action name="Step4_7">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step4_7.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -240,7 +240,7 @@
<action name="Step4_8">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step4_8.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -251,7 +251,7 @@
<action name="Step4_9">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step4_9.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -262,7 +262,7 @@
<action name="Step4_10">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step4_10.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -273,7 +273,7 @@
<action name="Step5_1">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step5_1.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -284,7 +284,7 @@
<action name="Step5_2">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step5_2.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -295,7 +295,7 @@
<action name="Step5_3">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step5_3.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -306,7 +306,7 @@
<action name="Step5_4">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step5_4.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -317,7 +317,7 @@
<action name="Step5_5">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step5_5.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -328,7 +328,7 @@
<action name="Step5_6">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step5_6.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -339,7 +339,7 @@
<action name="Step5_7">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step5_7.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -350,7 +350,7 @@
<action name="Step5_8">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step5_8.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -361,7 +361,7 @@
<action name="Step5_9">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step5_9.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -372,7 +372,7 @@
<action name="Step5_10">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step5_10.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -383,7 +383,7 @@
<action name="Step6_1">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step6_1.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -394,7 +394,7 @@
<action name="Step6_2">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step6_2.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -405,7 +405,7 @@
<action name="Step6_3">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step6_3.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -416,7 +416,7 @@
<action name="Step6_4">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step6_4.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -427,7 +427,7 @@
<action name="Step6_5">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step6_5.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -438,7 +438,7 @@
<action name="Step6_6">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step6_6.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -449,7 +449,7 @@
<action name="Step6_7">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step6_7.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -460,7 +460,7 @@
<action name="Step6_8">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step6_8.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -471,7 +471,7 @@
<action name="Step6_9">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step6_9.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -482,7 +482,7 @@
<action name="Step6_10">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step6_10.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -493,7 +493,7 @@
<action name="Step7_1">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step7_1.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -504,7 +504,7 @@
<action name="Step7_2">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step7_2.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -515,7 +515,7 @@
<action name="Step7_3">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step7_3.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -526,7 +526,7 @@
<action name="Step7_4">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step7_4.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -537,7 +537,7 @@
<action name="Step7_5">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step7_5.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -548,7 +548,7 @@
<action name="Step8_1">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step8_1.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -559,7 +559,7 @@
<action name="Step8_2">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step8_2.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -570,7 +570,7 @@
<action name="Step8_3">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step8_3.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -581,7 +581,7 @@
<action name="Step8_4">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step8_4.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -592,7 +592,7 @@
<action name="Step8_5">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step8_5.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -603,7 +603,7 @@
<action name="Step8_6">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step8_6.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -614,7 +614,7 @@
<action name="Step8_7">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step8_7.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -625,7 +625,7 @@
<action name="Step8_8">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step8_8.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -636,7 +636,7 @@
<action name="Step8_9">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step8_9.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -647,7 +647,7 @@
<action name="Step8_10">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step8_10.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -658,7 +658,7 @@
<action name="Step8_11">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step8_11.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -669,7 +669,7 @@
<action name="Step9_1">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step9_1.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -680,7 +680,7 @@
<action name="Step9_2">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step9_2.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -691,7 +691,7 @@
<action name="Step9_3">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step9_3.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -702,7 +702,7 @@
<action name="Step9_4">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step9_4.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -713,7 +713,7 @@
<action name="Step9_5">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step9_5.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -724,7 +724,7 @@
<action name="Step9_6">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step9_6.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -735,7 +735,7 @@
<action name="Step9_7">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step9_7.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -746,7 +746,7 @@
<action name="Step9_8">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step9_8.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -757,7 +757,7 @@
<action name="Step9_9">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step9_9.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -768,7 +768,7 @@
<action name="Step10_1">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step10_1.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -779,7 +779,7 @@
<action name="Step10_2">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step10_2.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -790,7 +790,7 @@
<action name="Step10_3">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step10_3.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -801,7 +801,7 @@
<action name="Step11">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step11.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -813,7 +813,7 @@
<action name="Step12_1">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step12_1.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -824,7 +824,7 @@
<action name="Step12_2">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step12_2.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -835,7 +835,7 @@
<action name="Step12_3">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step12_3.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -846,7 +846,7 @@
<action name="Step12_4">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step12_4.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -857,7 +857,7 @@
<action name="Step12_5">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step12_5.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -868,7 +868,7 @@
<action name="Step12_6">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step12_6.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -879,7 +879,7 @@
<action name="Step12_7">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step12_7.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -890,7 +890,7 @@
<action name="Step12_8">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step12_8.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -901,7 +901,7 @@
<action name="Step13">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step13.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>
@ -912,7 +912,7 @@
<action name="Step14">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<jdbc-url>${hiveJdbcUrl}</jdbc-url>
<script>scripts/step14.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>openaire_db_name=${openaire_db_name}</param>