D-Net
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dnet-hadoop
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Merge branch 'master' of https://code-repo.d4science.org/D-Net/dnet-hadoop into orcid-no-doi

This commit is contained in:
Enrico Ottonello 2020-12-07 11:02:59 +01:00
parent b1b589ada1 620e585b63
commit fa1855a4b8
22 changed files with 527 additions and 159 deletions
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2
dhp-schemas/pom.xml
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@ -6,7 +6,7 @@
<groupId>eu.dnetlib.dhp</groupId> <groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp</artifactId> <artifactId>dhp</artifactId>
<version>1.2.4-SNAPSHOT</version> <version>1.2.4-SNAPSHOT</version>
<relativePath>../</relativePath> <relativePath>../pom.xml</relativePath>
</parent> </parent>
<artifactId>dhp-schemas</artifactId> <artifactId>dhp-schemas</artifactId>

24
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/orcid/OrcidDOI.java Normal file
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@ -0,0 +1,24 @@
package eu.dnetlib.dhp.schema.orcid;
import java.util.List;
public class OrcidDOI {
private String doi;
private List<AuthorData> authors;
public String getDoi() {
return doi;
}
public void setDoi(String doi) {
this.doi = doi;
}
public List<AuthorData> getAuthors() {
return authors;
}
public void setAuthors(List<AuthorData> authors) {
this.authors = authors;
}
}

6
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala
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@ -200,7 +200,7 @@ case object Crossref2Oaf {
a.setSurname(family) a.setSurname(family)
a.setFullname(s"$given $family") a.setFullname(s"$given $family")
if (StringUtils.isNotBlank(orcid)) if (StringUtils.isNotBlank(orcid))
a.setPid(List(createSP(orcid, ORCID, PID_TYPES)).asJava) a.setPid(List(createSP(orcid, ORCID, PID_TYPES, generateDataInfo())).asJava)
a a
} }
@ -248,7 +248,7 @@ case object Crossref2Oaf {
def snsfRule(award:String): String = { def snsfRule(award:String): String = {
var tmp1 = StringUtils.substringAfter(award,"_") val tmp1 = StringUtils.substringAfter(award,"_")
val tmp2 = StringUtils.substringBefore(tmp1,"/") val tmp2 = StringUtils.substringBefore(tmp1,"/")
logger.debug(s"From $award to $tmp2") logger.debug(s"From $award to $tmp2")
tmp2 tmp2
@ -294,7 +294,7 @@ case object Crossref2Oaf {
} }
def getProjectId (nsPrefix:String, targetId:String):String = { def getProjectId (nsPrefix:String, targetId:String):String = {
"40|$nsPrefix::$targetId" s"40|$nsPrefix::$targetId"
} }

38
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/CrossrefDataset.scala
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@ -2,6 +2,7 @@ package eu.dnetlib.doiboost.crossref
import eu.dnetlib.dhp.application.ArgumentApplicationParser import eu.dnetlib.dhp.application.ArgumentApplicationParser
import org.apache.commons.io.IOUtils import org.apache.commons.io.IOUtils
import org.apache.hadoop.io.{IntWritable, Text}
import org.apache.spark.SparkConf import org.apache.spark.SparkConf
import org.apache.spark.sql.expressions.Aggregator import org.apache.spark.sql.expressions.Aggregator
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession} import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
@ -12,21 +13,23 @@ import org.slf4j.{Logger, LoggerFactory}
object CrossrefDataset { object CrossrefDataset {
val logger: Logger = LoggerFactory.getLogger(SparkMapDumpIntoOAF.getClass)
def extractTimestamp(input:String): Long = {
def to_item(input:String):CrossrefDT = {
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json: json4s.JValue = parse(input) lazy val json: json4s.JValue = parse(input)
val ts:Long = (json \ "indexed" \ "timestamp").extract[Long]
(json\"indexed"\"timestamp").extractOrElse[Long](0) val doi:String = (json \ "DOI").extract[String]
CrossrefDT(doi, input, ts)
} }
def main(args: Array[String]): Unit = { def main(args: Array[String]): Unit = {
val logger: Logger = LoggerFactory.getLogger(SparkMapDumpIntoOAF.getClass)
val conf: SparkConf = new SparkConf() val conf: SparkConf = new SparkConf()
val parser = new ArgumentApplicationParser(IOUtils.toString(CrossrefDataset.getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/crossref_to_dataset_params.json"))) val parser = new ArgumentApplicationParser(IOUtils.toString(CrossrefDataset.getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/crossref_to_dataset_params.json")))
parser.parseArgument(args) parser.parseArgument(args)
@ -49,9 +52,8 @@ object CrossrefDataset {
if (a == null) if (a == null)
return b return b
val tb = extractTimestamp(b.json)
val ta = extractTimestamp(a.json) if(a.timestamp >b.timestamp) {
if(ta >tb) {
return a return a
} }
b b
@ -63,9 +65,7 @@ object CrossrefDataset {
if (a == null) if (a == null)
return b return b
val tb = extractTimestamp(b.json) if(a.timestamp >b.timestamp) {
val ta = extractTimestamp(a.json)
if(ta >tb) {
return a return a
} }
b b
@ -78,15 +78,21 @@ object CrossrefDataset {
override def finish(reduction: CrossrefDT): CrossrefDT = reduction override def finish(reduction: CrossrefDT): CrossrefDT = reduction
} }
val sourcePath:String = parser.get("sourcePath") val workingPath:String = parser.get("workingPath")
val targetPath:String = parser.get("targetPath")
val ds:Dataset[CrossrefDT] = spark.read.load(sourcePath).as[CrossrefDT]
ds.groupByKey(_.doi) val main_ds:Dataset[CrossrefDT] = spark.read.load(s"$workingPath/crossref_ds").as[CrossrefDT]
val update =
spark.createDataset(spark.sparkContext.sequenceFile(s"$workingPath/index_update", classOf[IntWritable], classOf[Text])
.map(i =>CrossrefImporter.decompressBlob(i._2.toString))
.map(i =>to_item(i)))
main_ds.union(update).groupByKey(_.doi)
.agg(crossrefAggregator.toColumn) .agg(crossrefAggregator.toColumn)
.map(s=>s._2) .map(s=>s._2)
.write.mode(SaveMode.Overwrite).save(targetPath) .write.mode(SaveMode.Overwrite).save(s"$workingPath/crossref_ds_updated")
} }

70
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/SparkMapDumpIntoOAF.scala
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@ -34,85 +34,21 @@ object SparkMapDumpIntoOAF {
implicit val mapEncoderRelatons: Encoder[Relation] = Encoders.kryo[Relation] implicit val mapEncoderRelatons: Encoder[Relation] = Encoders.kryo[Relation]
implicit val mapEncoderDatasets: Encoder[oaf.Dataset] = Encoders.kryo[OafDataset] implicit val mapEncoderDatasets: Encoder[oaf.Dataset] = Encoders.kryo[OafDataset]
val sc = spark.sparkContext
val targetPath = parser.get("targetPath") val targetPath = parser.get("targetPath")
import spark.implicits._ import spark.implicits._
spark.read.load(parser.get("sourcePath")).as[CrossrefDT] spark.read.load(parser.get("sourcePath")).as[CrossrefDT]
.flatMap(k => Crossref2Oaf.convert(k.json)) .flatMap(k => Crossref2Oaf.convert(k.json))
.filter(o => o != null) .filter(o => o != null)
.write.mode(SaveMode.Overwrite).save(s"$targetPath/mixObject") .write.mode(SaveMode.Overwrite).save(s"$targetPath/mixObject")
val ds:Dataset[Oaf] = spark.read.load(s"$targetPath/mixObject").as[Oaf] val ds:Dataset[Oaf] = spark.read.load(s"$targetPath/mixObject").as[Oaf]
ds.filter(o => o.isInstanceOf[Publication]).map(o => o.asInstanceOf[Publication]).write.save(s"$targetPath/publication") ds.filter(o => o.isInstanceOf[Publication]).map(o => o.asInstanceOf[Publication]).write.mode(SaveMode.Overwrite).save(s"$targetPath/crossrefPublication")
ds.filter(o => o.isInstanceOf[Relation]).map(o => o.asInstanceOf[Relation]).write.save(s"$targetPath/relation") ds.filter(o => o.isInstanceOf[Relation]).map(o => o.asInstanceOf[Relation]).write.mode(SaveMode.Overwrite).save(s"$targetPath/crossrefRelation")
ds.filter(o => o.isInstanceOf[OafDataset]).map(o => o.asInstanceOf[OafDataset]).write.save(s"$targetPath/dataset") ds.filter(o => o.isInstanceOf[OafDataset]).map(o => o.asInstanceOf[OafDataset]).write.mode(SaveMode.Overwrite).save(s"$targetPath/crossrefDataset")
//
//
//
// sc.sequenceFile(parser.get("sourcePath"), classOf[IntWritable], classOf[Text])
// .map(k => k._2.toString).map(CrossrefImporter.decompressBlob)
// .flatMap(k => Crossref2Oaf.convert(k)).saveAsObjectFile(s"${targetPath}/mixObject")
//
// val inputRDD = sc.objectFile[Oaf](s"${targetPath}/mixObject").filter(p=> p!= null)
//
// val distinctPubs:RDD[Publication] = inputRDD.filter(k => k != null && k.isInstanceOf[Publication])
// .map(k => k.asInstanceOf[Publication]).map { p: Publication => Tuple2(p.getId, p) }.reduceByKey { case (p1: Publication, p2: Publication) =>
// var r = if (p1 == null) p2 else p1
// if (p1 != null && p2 != null) {
// if (p1.getLastupdatetimestamp != null && p2.getLastupdatetimestamp != null) {
// if (p1.getLastupdatetimestamp < p2.getLastupdatetimestamp)
// r = p2
// else
// r = p1
// } else {
// r = if (p1.getLastupdatetimestamp == null) p2 else p1
// }
// }
// r
// }.map(_._2)
//
// val pubs:Dataset[Publication] = spark.createDataset(distinctPubs)
// pubs.write.mode(SaveMode.Overwrite).save(s"${targetPath}/publication")
//
//
// val distincDatasets:RDD[OafDataset] = inputRDD.filter(k => k != null && k.isInstanceOf[OafDataset])
// .map(k => k.asInstanceOf[OafDataset]).map(p => Tuple2(p.getId, p)).reduceByKey { case (p1: OafDataset, p2: OafDataset) =>
// var r = if (p1 == null) p2 else p1
// if (p1 != null && p2 != null) {
// if (p1.getLastupdatetimestamp != null && p2.getLastupdatetimestamp != null) {
// if (p1.getLastupdatetimestamp < p2.getLastupdatetimestamp)
// r = p2
// else
// r = p1
// } else {
// r = if (p1.getLastupdatetimestamp == null) p2 else p1
// }
// }
// r
// }.map(_._2)
//
// spark.createDataset(distincDatasets).write.mode(SaveMode.Overwrite).save(s"${targetPath}/dataset")
//
//
//
// val distinctRels =inputRDD.filter(k => k != null && k.isInstanceOf[Relation])
// .map(k => k.asInstanceOf[Relation]).map(r=> (s"${r.getSource}::${r.getTarget}",r))
// .reduceByKey { case (p1: Relation, p2: Relation) =>
// if (p1 == null) p2 else p1
// }.map(_._2)
//
// val rels: Dataset[Relation] = spark.createDataset(distinctRels)
//
// rels.write.mode(SaveMode.Overwrite).save(s"${targetPath}/relations")
} }

106
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/crossref/oozie_app/workflow.xml
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@ -16,88 +16,86 @@
<name>sparkExecutorCores</name> <name>sparkExecutorCores</name>
<description>number of cores used by single executor</description> <description>number of cores used by single executor</description>
</property> </property>
<!-- <property>--> <property>
<!-- <name>timestamp</name>--> <name>timestamp</name>
<!-- <description>Timestamp for incremental Harvesting</description>--> <description>Timestamp for incremental Harvesting</description>
<!-- </property>--> </property>
</parameters> </parameters>
<start to="ExtractCrossrefToOAF"/> <start to="ImportCrossRef"/>
<kill name="Kill"> <kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message> <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill> </kill>
<!-- <action name="ResetWorkingPath">--> <action name="ImportCrossRef">
<!-- <fs>--> <java>
<!-- <delete path='${workingPath}/input/crossref/index_dump'/>--> <job-tracker>${jobTracker}</job-tracker>
<!--&lt;!&ndash; <mkdir path='${workingPath}/input/crossref'/>&ndash;&gt;--> <name-node>${nameNode}</name-node>
<!-- </fs>--> <main-class>eu.dnetlib.doiboost.crossref.CrossrefImporter</main-class>
<!-- <ok to="ImportCrossRef"/>--> <arg>-t</arg><arg>${workingPath}/input/crossref/index_update</arg>
<!-- <error to="Kill"/>--> <arg>-n</arg><arg>${nameNode}</arg>
<!-- </action>--> <arg>-ts</arg><arg>${timestamp}</arg>
</java>
<ok to="GenerateDataset"/>
<error to="Kill"/>
</action>
<action name="GenerateDataset">
<!-- <action name="ImportCrossRef">-->
<!-- <java>-->
<!-- <job-tracker>${jobTracker}</job-tracker>-->
<!-- <name-node>${nameNode}</name-node>-->
<!-- <main-class>eu.dnetlib.doiboost.crossref.CrossrefImporter</main-class>-->
<!-- <arg>-t</arg><arg>${workingPath}/input/crossref/index_dump_1</arg>-->
<!-- <arg>-n</arg><arg>${nameNode}</arg>-->
<!-- <arg>-ts</arg><arg>${timestamp}</arg>-->
<!-- </java>-->
<!-- <ok to="End"/>-->
<!-- <error to="Kill"/>-->
<!-- </action>-->
<action name="ExtractCrossrefToOAF">
<spark xmlns="uri:oozie:spark-action:0.2"> <spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master> <master>yarn-cluster</master>
<mode>cluster</mode> <mode>cluster</mode>
<name>ExtractCrossrefToOAF</name> <name>ExtractCrossrefToOAF</name>
<class>eu.dnetlib.doiboost.crossref.CrossrefDataset</class>
<jar>dhp-doiboost-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.sql.shuffle.partitions=3840
${sparkExtraOPT}
</spark-opts>
<arg>--workingPath</arg><arg>/data/doiboost/input/crossref</arg>
<arg>--master</arg><arg>yarn-cluster</arg>
</spark>
<ok to="RenameDataset"/>
<error to="Kill"/>
</action>
<action name="RenameDataset">
<fs>
<delete path='${workingPath}/input/crossref/crossref_ds'/>
<move source="${workingPath}/input/crossref/crossref_ds_updated"
target="${workingPath}/input/crossref/crossref_ds"/>
</fs>
<ok to="ConvertCrossrefToOAF"/>
<error to="Kill"/>
</action>
<action name="ConvertCrossrefToOAF">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>ConvertCrossrefToOAF</name>
<class>eu.dnetlib.doiboost.crossref.SparkMapDumpIntoOAF</class> <class>eu.dnetlib.doiboost.crossref.SparkMapDumpIntoOAF</class>
<jar>dhp-doiboost-${projectVersion}.jar</jar> <jar>dhp-doiboost-${projectVersion}.jar</jar>
<spark-opts> <spark-opts>
--executor-memory=${sparkExecutorMemory} --executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores} --executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory} --driver-memory=${sparkDriverMemory}
--conf spark.sql.shuffle.partitions=3840
${sparkExtraOPT} ${sparkExtraOPT}
</spark-opts> </spark-opts>
<arg>--sourcePath</arg><arg>${workingPath}/input/crossref/crossref_ds</arg> <arg>--sourcePath</arg><arg>${workingPath}/input/crossref/crossref_ds</arg>
<arg>--targetPath</arg><arg>${workingPath}/input/crossref</arg> <arg>--targetPath</arg><arg>${workingPath}/process/</arg>
<arg>--master</arg><arg>yarn-cluster</arg> <arg>--master</arg><arg>yarn-cluster</arg>
</spark> </spark>
<ok to="End"/> <ok to="End"/>
<error to="Kill"/> <error to="Kill"/>
</action> </action>
<!-- <action name="GenerateDataset">-->
<!-- <spark xmlns="uri:oozie:spark-action:0.2">-->
<!-- <master>yarn-cluster</master>-->
<!-- <mode>cluster</mode>-->
<!-- <name>ExtractCrossrefToOAF</name>-->
<!-- <class>eu.dnetlib.doiboost.crossref.CrossrefDataset</class>-->
<!-- <jar>dhp-doiboost-${projectVersion}.jar</jar>-->
<!-- <spark-opts>-->
<!-- &#45;&#45;executor-memory=${sparkExecutorMemory}-->
<!-- &#45;&#45;executor-cores=${sparkExecutorCores}-->
<!-- &#45;&#45;driver-memory=${sparkDriverMemory}-->
<!-- ${sparkExtraOPT}-->
<!-- </spark-opts>-->
<!-- <arg>&#45;&#45;sourcePath</arg><arg>/data/doiboost/crossref/cr_dataset</arg>-->
<!-- <arg>&#45;&#45;targetPath</arg><arg>/data/doiboost/crossref/crossrefDataset</arg>-->
<!-- <arg>&#45;&#45;master</arg><arg>yarn-cluster</arg>-->
<!-- </spark>-->
<!-- <ok to="End"/>-->
<!-- <error to="Kill"/>-->
<!-- </action>-->
<end name="End"/> <end name="End"/>
</workflow-app> </workflow-app>

3
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/crossref_to_dataset_params.json
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@ -1,6 +1,5 @@
[ [
{"paramName":"s", "paramLongName":"sourcePath", "paramDescription": "the path of the sequencial file to read", "paramRequired": true}, {"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the working dir path", "paramRequired": true},
{"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the working dir path", "paramRequired": true},
{"paramName":"m", "paramLongName":"master", "paramDescription": "the master name", "paramRequired": true} {"paramName":"m", "paramLongName":"master", "paramDescription": "the master name", "paramRequired": true}
] ]

9
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java
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@ -190,15 +190,6 @@ public class CleaningFunctions {
} }
} }
final Set<String> collectedFrom = Optional
.ofNullable(r.getCollectedfrom())
.map(
c -> c
.stream()
.map(KeyValue::getKey)
.collect(Collectors.toCollection(HashSet::new)))
.orElse(new HashSet<>());
for (Author a : r.getAuthor()) { for (Author a : r.getAuthor()) {
if (Objects.isNull(a.getPid())) { if (Objects.isNull(a.getPid())) {
a.setPid(Lists.newArrayList()); a.setPid(Lists.newArrayList());

32
dhp-workflows/dhp-stats-promote/pom.xml Normal file
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@ -0,0 +1,32 @@
<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<parent>
<artifactId>dhp-workflows</artifactId>
<groupId>eu.dnetlib.dhp</groupId>
<version>1.2.4-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>
<artifactId>dhp-stats-promote</artifactId>
<dependencies>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-core_2.11</artifactId>
</dependency>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-sql_2.11</artifactId>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>pl.project13.maven</groupId>
<artifactId>git-commit-id-plugin</artifactId>
<version>2.1.11</version>
<configuration>
<failOnNoGitDirectory>false</failOnNoGitDirectory>
</configuration>
</plugin>
</plugins>
</build>
</project>

34
dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/config-default.xml Normal file
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@ -0,0 +1,34 @@
<configuration>
<property>
<name>jobTracker</name>
<value>${jobTracker}</value>
</property>
<property>
<name>nameNode</name>
<value>${nameNode}</value>
</property>
<property>
<name>oozie.use.system.libpath</name>
<value>true</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>spark2</value>
</property>
<property>
<name>hive_metastore_uris</name>
<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
</property>
<property>
<name>hive_jdbc_url</name>
<value>jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000</value>
</property>
<property>
<name>oozie.wf.workflow.notification.url</name>
<value>{serviceUrl}/v1/oozieNotification/jobUpdate?jobId=$jobId%26status=$status</value>
</property>
<property>
<name>stats_tool_api_url</name>
<value>${stats_tool_api_url}</value>
</property>
</configuration>

18
dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/impala-shell.sh Normal file
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@ -0,0 +1,18 @@
export PYTHON_EGG_CACHE=/home/$(whoami)/.python-eggs
export link_folder=/tmp/impala-shell-python-egg-cache-$(whoami)
if ! [ -L $link_folder ]
then
rm -Rf "$link_folder"
ln -sfn ${PYTHON_EGG_CACHE}${link_folder} ${link_folder}
fi
echo "Getting file from " $3
hdfs dfs -copyToLocal $3
echo "Running impala shell make the new database visible"
impala-shell -q "INVALIDATE METADATA;"
echo "Running impala shell to compute new table stats"
impala-shell -d $1 -f $2
echo "Impala shell finished"
rm $2

4
dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/promoteCache.sh Normal file
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@ -0,0 +1,4 @@
#!/usr/bin/env bash
curl --request GET $1/cache/promoteCache

8
dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/computeProductionStats.sql Normal file
View File

@ -0,0 +1,8 @@
------------------------------------------------------
------------------------------------------------------
-- Impala table statistics - Needed to make the tables
-- visible for impala
------------------------------------------------------
------------------------------------------------------
INVALIDATE METADATA ${stats_db_name};

207
dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/updateProductionViews.sql Normal file
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@ -0,0 +1,207 @@
------------------------------------------------------
------------------------------------------------------
-- Shadow schema table exchange
------------------------------------------------------
------------------------------------------------------
-- Dropping old views
DROP VIEW IF EXISTS ${stats_db_production_name}.category;
DROP VIEW IF EXISTS ${stats_db_production_name}.concept;
DROP VIEW IF EXISTS ${stats_db_production_name}.context;
DROP VIEW IF EXISTS ${stats_db_production_name}.country;
DROP VIEW IF EXISTS ${stats_db_production_name}.countrygdp;
DROP VIEW IF EXISTS ${stats_db_production_name}.creation_date;
DROP VIEW IF EXISTS ${stats_db_production_name}.dataset;
DROP VIEW IF EXISTS ${stats_db_production_name}.dataset_citations;
DROP VIEW IF EXISTS ${stats_db_production_name}.dataset_classifications;
DROP VIEW IF EXISTS ${stats_db_production_name}.dataset_concepts;
DROP VIEW IF EXISTS ${stats_db_production_name}.dataset_datasources;
DROP VIEW IF EXISTS ${stats_db_production_name}.dataset_languages;
DROP VIEW IF EXISTS ${stats_db_production_name}.dataset_licenses;
DROP VIEW IF EXISTS ${stats_db_production_name}.dataset_oids;
DROP VIEW IF EXISTS ${stats_db_production_name}.dataset_pids;
DROP VIEW IF EXISTS ${stats_db_production_name}.dataset_refereed;
DROP VIEW IF EXISTS ${stats_db_production_name}.dataset_sources;
DROP VIEW IF EXISTS ${stats_db_production_name}.dataset_topics;
DROP VIEW IF EXISTS ${stats_db_production_name}.datasource;
DROP VIEW IF EXISTS ${stats_db_production_name}.datasource_languages;
DROP VIEW IF EXISTS ${stats_db_production_name}.datasource_oids;
DROP VIEW IF EXISTS ${stats_db_production_name}.datasource_organizations;
DROP VIEW IF EXISTS ${stats_db_production_name}.datasource_results;
DROP VIEW IF EXISTS ${stats_db_production_name}.datasource_sources;
DROP VIEW IF EXISTS ${stats_db_production_name}.funder;
DROP VIEW IF EXISTS ${stats_db_production_name}.fundref;
DROP VIEW IF EXISTS ${stats_db_production_name}.numbers_country;
DROP VIEW IF EXISTS ${stats_db_production_name}.organization;
DROP VIEW IF EXISTS ${stats_db_production_name}.organization_datasources;
DROP VIEW IF EXISTS ${stats_db_production_name}.organization_pids;
DROP VIEW IF EXISTS ${stats_db_production_name}.organization_projects;
DROP VIEW IF EXISTS ${stats_db_production_name}.organization_sources;
DROP VIEW IF EXISTS ${stats_db_production_name}.otherresearchproduct;
DROP VIEW IF EXISTS ${stats_db_production_name}.otherresearchproduct_citations;
DROP VIEW IF EXISTS ${stats_db_production_name}.otherresearchproduct_classifications;
DROP VIEW IF EXISTS ${stats_db_production_name}.otherresearchproduct_concepts;
DROP VIEW IF EXISTS ${stats_db_production_name}.otherresearchproduct_datasources;
DROP VIEW IF EXISTS ${stats_db_production_name}.otherresearchproduct_languages;
DROP VIEW IF EXISTS ${stats_db_production_name}.otherresearchproduct_licenses;
DROP VIEW IF EXISTS ${stats_db_production_name}.otherresearchproduct_oids;
DROP VIEW IF EXISTS ${stats_db_production_name}.otherresearchproduct_pids;
DROP VIEW IF EXISTS ${stats_db_production_name}.otherresearchproduct_refereed;
DROP VIEW IF EXISTS ${stats_db_production_name}.otherresearchproduct_sources;
DROP VIEW IF EXISTS ${stats_db_production_name}.otherresearchproduct_topics;
DROP VIEW IF EXISTS ${stats_db_production_name}.project;
DROP VIEW IF EXISTS ${stats_db_production_name}.project_oids;
DROP VIEW IF EXISTS ${stats_db_production_name}.project_organizations;
DROP VIEW IF EXISTS ${stats_db_production_name}.project_results;
DROP VIEW IF EXISTS ${stats_db_production_name}.project_resultcount;
DROP VIEW IF EXISTS ${stats_db_production_name}.project_results_publication;
DROP VIEW IF EXISTS ${stats_db_production_name}.publication;
DROP VIEW IF EXISTS ${stats_db_production_name}.publication_citations;
DROP VIEW IF EXISTS ${stats_db_production_name}.publication_classifications;
DROP VIEW IF EXISTS ${stats_db_production_name}.publication_concepts;
DROP VIEW IF EXISTS ${stats_db_production_name}.publication_datasources;
DROP VIEW IF EXISTS ${stats_db_production_name}.publication_languages;
DROP VIEW IF EXISTS ${stats_db_production_name}.publication_licenses;
DROP VIEW IF EXISTS ${stats_db_production_name}.publication_oids;
DROP VIEW IF EXISTS ${stats_db_production_name}.publication_pids;
DROP VIEW IF EXISTS ${stats_db_production_name}.publication_refereed;
DROP VIEW IF EXISTS ${stats_db_production_name}.publication_sources;
DROP VIEW IF EXISTS ${stats_db_production_name}.publication_topics;
DROP VIEW IF EXISTS ${stats_db_production_name}.result;
DROP VIEW IF EXISTS ${stats_db_production_name}.result_affiliated_country;
DROP VIEW IF EXISTS ${stats_db_production_name}.result_citations;
DROP VIEW IF EXISTS ${stats_db_production_name}.result_classifications;
DROP VIEW IF EXISTS ${stats_db_production_name}.result_concepts;
DROP VIEW IF EXISTS ${stats_db_production_name}.result_datasources;
DROP VIEW IF EXISTS ${stats_db_production_name}.result_deposited_country;
DROP VIEW IF EXISTS ${stats_db_production_name}.result_fundercount;
DROP VIEW IF EXISTS ${stats_db_production_name}.result_gold;
DROP VIEW IF EXISTS ${stats_db_production_name}.result_greenoa;
DROP VIEW IF EXISTS ${stats_db_production_name}.result_languages;
DROP VIEW IF EXISTS ${stats_db_production_name}.result_licenses;
DROP VIEW IF EXISTS ${stats_db_production_name}.result_oids;
DROP VIEW IF EXISTS ${stats_db_production_name}.result_organization;
DROP VIEW IF EXISTS ${stats_db_production_name}.result_peerreviewed;
DROP VIEW IF EXISTS ${stats_db_production_name}.result_pids;
DROP VIEW IF EXISTS ${stats_db_production_name}.result_projectcount;
DROP VIEW IF EXISTS ${stats_db_production_name}.result_projects;
DROP VIEW IF EXISTS ${stats_db_production_name}.result_refereed;
DROP VIEW IF EXISTS ${stats_db_production_name}.result_sources;
DROP VIEW IF EXISTS ${stats_db_production_name}.result_topics;
DROP VIEW IF EXISTS ${stats_db_production_name}.rndexpediture;
DROP VIEW IF EXISTS ${stats_db_production_name}.roarmap;
DROP VIEW IF EXISTS ${stats_db_production_name}.software;
DROP VIEW IF EXISTS ${stats_db_production_name}.software_citations;
DROP VIEW IF EXISTS ${stats_db_production_name}.software_classifications;
DROP VIEW IF EXISTS ${stats_db_production_name}.software_concepts;
DROP VIEW IF EXISTS ${stats_db_production_name}.software_datasources;
DROP VIEW IF EXISTS ${stats_db_production_name}.software_languages;
DROP VIEW IF EXISTS ${stats_db_production_name}.software_licenses;
DROP VIEW IF EXISTS ${stats_db_production_name}.software_oids;
DROP VIEW IF EXISTS ${stats_db_production_name}.software_pids;
DROP VIEW IF EXISTS ${stats_db_production_name}.software_refereed;
DROP VIEW IF EXISTS ${stats_db_production_name}.software_sources;
DROP VIEW IF EXISTS ${stats_db_production_name}.software_topics;
-- Creating the shadow database, in case it doesn't exist
CREATE database IF NOT EXISTS ${stats_db_production_name};
-- Creating new views
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.category AS SELECT * FROM ${stats_db_name}.category;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.concept AS SELECT * FROM ${stats_db_name}.concept;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.context AS SELECT * FROM ${stats_db_name}.context;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.country AS SELECT * FROM ${stats_db_name}.country;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.countrygdp AS SELECT * FROM ${stats_db_name}.countrygdp;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.creation_date AS SELECT * FROM ${stats_db_name}.creation_date;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.dataset AS SELECT * FROM ${stats_db_name}.dataset;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.dataset_citations AS SELECT * FROM ${stats_db_name}.dataset_citations;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.dataset_classifications AS SELECT * FROM ${stats_db_name}.dataset_classifications;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.dataset_concepts AS SELECT * FROM ${stats_db_name}.dataset_concepts;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.dataset_datasources AS SELECT * FROM ${stats_db_name}.dataset_datasources;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.dataset_languages AS SELECT * FROM ${stats_db_name}.dataset_languages;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.dataset_licenses AS SELECT * FROM ${stats_db_name}.dataset_licenses;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.dataset_oids AS SELECT * FROM ${stats_db_name}.dataset_oids;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.dataset_pids AS SELECT * FROM ${stats_db_name}.dataset_pids;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.dataset_refereed AS SELECT * FROM ${stats_db_name}.dataset_refereed;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.dataset_sources AS SELECT * FROM ${stats_db_name}.dataset_sources;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.dataset_topics AS SELECT * FROM ${stats_db_name}.dataset_topics;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.datasource AS SELECT * FROM ${stats_db_name}.datasource;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.datasource_languages AS SELECT * FROM ${stats_db_name}.datasource_languages;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.datasource_oids AS SELECT * FROM ${stats_db_name}.datasource_oids;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.datasource_organizations AS SELECT * FROM ${stats_db_name}.datasource_organizations;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.datasource_results AS SELECT * FROM ${stats_db_name}.datasource_results;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.datasource_sources AS SELECT * FROM ${stats_db_name}.datasource_sources;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.funder AS SELECT * FROM ${stats_db_name}.funder;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.fundref AS SELECT * FROM ${stats_db_name}.fundref;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.numbers_country AS SELECT * FROM ${stats_db_name}.numbers_country;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.organization AS SELECT * FROM ${stats_db_name}.organization;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.organization_datasources AS SELECT * FROM ${stats_db_name}.organization_datasources;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.organization_pids AS SELECT * FROM ${stats_db_name}.organization_pids;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.organization_projects AS SELECT * FROM ${stats_db_name}.organization_projects;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.organization_sources AS SELECT * FROM ${stats_db_name}.organization_sources;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.otherresearchproduct AS SELECT * FROM ${stats_db_name}.otherresearchproduct;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.otherresearchproduct_citations AS SELECT * FROM ${stats_db_name}.otherresearchproduct_citations;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.otherresearchproduct_classifications AS SELECT * FROM ${stats_db_name}.otherresearchproduct_classifications;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.otherresearchproduct_concepts AS SELECT * FROM ${stats_db_name}.otherresearchproduct_concepts;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.otherresearchproduct_datasources AS SELECT * FROM ${stats_db_name}.otherresearchproduct_datasources;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.otherresearchproduct_languages AS SELECT * FROM ${stats_db_name}.otherresearchproduct_languages;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.otherresearchproduct_licenses AS SELECT * FROM ${stats_db_name}.otherresearchproduct_licenses;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.otherresearchproduct_oids AS SELECT * FROM ${stats_db_name}.otherresearchproduct_oids;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.otherresearchproduct_pids AS SELECT * FROM ${stats_db_name}.otherresearchproduct_pids;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.otherresearchproduct_refereed AS SELECT * FROM ${stats_db_name}.otherresearchproduct_refereed;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.otherresearchproduct_sources AS SELECT * FROM ${stats_db_name}.otherresearchproduct_sources;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.otherresearchproduct_topics AS SELECT * FROM ${stats_db_name}.otherresearchproduct_topics;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.project AS SELECT * FROM ${stats_db_name}.project;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.project_oids AS SELECT * FROM ${stats_db_name}.project_oids;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.project_organizations AS SELECT * FROM ${stats_db_name}.project_organizations;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.project_results AS SELECT * FROM ${stats_db_name}.project_results;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.project_resultcount AS SELECT * FROM ${stats_db_name}.project_resultcount;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.project_results_publication AS SELECT * FROM ${stats_db_name}.project_results_publication;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.publication AS SELECT * FROM ${stats_db_name}.publication;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.publication_citations AS SELECT * FROM ${stats_db_name}.publication_citations;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.publication_classifications AS SELECT * FROM ${stats_db_name}.publication_classifications;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.publication_concepts AS SELECT * FROM ${stats_db_name}.publication_concepts;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.publication_datasources AS SELECT * FROM ${stats_db_name}.publication_datasources;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.publication_languages AS SELECT * FROM ${stats_db_name}.publication_languages;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.publication_licenses AS SELECT * FROM ${stats_db_name}.publication_licenses;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.publication_oids AS SELECT * FROM ${stats_db_name}.publication_oids;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.publication_pids AS SELECT * FROM ${stats_db_name}.publication_pids;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.publication_refereed AS SELECT * FROM ${stats_db_name}.publication_refereed;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.publication_sources AS SELECT * FROM ${stats_db_name}.publication_sources;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.publication_topics AS SELECT * FROM ${stats_db_name}.publication_topics;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result AS SELECT * FROM ${stats_db_name}.result;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_affiliated_country AS SELECT * FROM ${stats_db_name}.result_affiliated_country;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_citations AS SELECT * FROM ${stats_db_name}.result_citations;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_classifications AS SELECT * FROM ${stats_db_name}.result_classifications;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_concepts AS SELECT * FROM ${stats_db_name}.result_concepts;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_datasources AS SELECT * FROM ${stats_db_name}.result_datasources;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_deposited_country AS SELECT * FROM ${stats_db_name}.result_deposited_country;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_fundercount AS SELECT * FROM ${stats_db_name}.result_fundercount;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_gold AS SELECT * FROM ${stats_db_name}.result_gold;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_greenoa AS SELECT * FROM ${stats_db_name}.result_greenoa;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_languages AS SELECT * FROM ${stats_db_name}.result_languages;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_licenses AS SELECT * FROM ${stats_db_name}.result_licenses;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_oids AS SELECT * FROM ${stats_db_name}.result_oids;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_organization AS SELECT * FROM ${stats_db_name}.result_organization;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_peerreviewed AS SELECT * FROM ${stats_db_name}.result_peerreviewed;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_pids AS SELECT * FROM ${stats_db_name}.result_pids;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_projectcount AS SELECT * FROM ${stats_db_name}.result_projectcount;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_projects AS SELECT * FROM ${stats_db_name}.result_projects;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_refereed AS SELECT * FROM ${stats_db_name}.result_refereed;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_sources AS SELECT * FROM ${stats_db_name}.result_sources;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.result_topics AS SELECT * FROM ${stats_db_name}.result_topics;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.rndexpediture AS SELECT * FROM ${stats_db_name}.rndexpediture;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.roarmap AS SELECT * FROM ${stats_db_name}.roarmap;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.software AS SELECT * FROM ${stats_db_name}.software;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.software_citations AS SELECT * FROM ${stats_db_name}.software_citations;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.software_classifications AS SELECT * FROM ${stats_db_name}.software_classifications;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.software_concepts AS SELECT * FROM ${stats_db_name}.software_concepts;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.software_datasources AS SELECT * FROM ${stats_db_name}.software_datasources;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.software_languages AS SELECT * FROM ${stats_db_name}.software_languages;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.software_licenses AS SELECT * FROM ${stats_db_name}.software_licenses;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.software_oids AS SELECT * FROM ${stats_db_name}.software_oids;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.software_pids AS SELECT * FROM ${stats_db_name}.software_pids;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.software_refereed AS SELECT * FROM ${stats_db_name}.software_refereed;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.software_sources AS SELECT * FROM ${stats_db_name}.software_sources;
CREATE VIEW IF NOT EXISTS ${stats_db_production_name}.software_topics AS SELECT * FROM ${stats_db_name}.software_topics;

87
dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml Normal file
View File

@ -0,0 +1,87 @@
<workflow-app name="Graph Stats" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>stats_db_name</name>
<description>the target stats database name</description>
</property>
<property>
<name>stats_db_production_name</name>
<description>the name of the production schema</description>
</property>
<property>
<name>stats_tool_api_url</name>
<description>The url of the API of the stats tool. Is used to trigger the cache promote.</description>
</property>
<property>
<name>hive_metastore_uris</name>
<description>hive server metastore URIs</description>
</property>
<property>
<name>hive_jdbc_url</name>
<description>hive server jdbc url</description>
</property>
<property>
<name>hive_timeout</name>
<description>the time period, in seconds, after which Hive fails a transaction if a Hive client has not sent a hearbeat. The default value is 300 seconds.</description>
</property>
</parameters>
<global>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<configuration>
<property>
<name>hive.metastore.uris</name>
<value>${hive_metastore_uris}</value>
</property>
<property>
<name>hive.txn.timeout</name>
<value>${hive_timeout}</value>
</property>
</configuration>
</global>
<start to="updateProductionViews"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="updateProductionViews">
<hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url>
<script>scripts/updateProductionViews.sql</script>
<param>stats_db_name=${stats_db_name}</param>
<param>stats_db_production_name=${stats_db_production_name}</param>
</hive2>
<ok to="computeProductionStats"/>
<error to="Kill"/>
</action>
<action name="computeProductionStats">
<shell xmlns="uri:oozie:shell-action:0.1">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<exec>impala-shell.sh</exec>
<argument>${stats_db_production_name}</argument>
<argument>computeProductionStats.sql</argument>
<argument>${wf:appPath()}/scripts/computeProductionStats.sql</argument>
<file>impala-shell.sh</file>
</shell>
<ok to="promoteCache"/>
<error to="Kill"/>
</action>
<action name="promoteCache">
<shell xmlns="uri:oozie:shell-action:0.1">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<exec>promoteCache.sh</exec>
<argument>${stats_tool_api_url}</argument>
<file>promoteCache.sh</file>
</shell>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

4
dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/config-default.xml
View File

@ -27,4 +27,8 @@
<name>oozie.wf.workflow.notification.url</name> <name>oozie.wf.workflow.notification.url</name>
<value>{serviceUrl}/v1/oozieNotification/jobUpdate?jobId=$jobId%26status=$status</value> <value>{serviceUrl}/v1/oozieNotification/jobUpdate?jobId=$jobId%26status=$status</value>
</property> </property>
<property>
<name>stats_tool_api_url</name>
<value>${stats_tool_api_url}</value>
</property>
</configuration> </configuration>

2
dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql
View File

@ -11,7 +11,7 @@ CREATE TABLE ${stats_db_name}.project_oids AS SELECT substr(p.id, 4) AS id, oids
-- Project_organizations Table -- Project_organizations Table
DROP TABLE IF EXISTS ${stats_db_name}.project_organizations; DROP TABLE IF EXISTS ${stats_db_name}.project_organizations;
CREATE TABLE ${stats_db_name}.project_organizations AS SELECT substr(r.source, 4) AS id, substr(r.target, 4) AS organization from ${openaire_db_name}.relation r WHERE r.reltype='projectOrganization'; CREATE TABLE ${stats_db_name}.project_organizations AS SELECT substr(r.source, 4) AS id, substr(r.target, 4) AS organization from ${openaire_db_name}.relation r WHERE r.reltype='projectOrganization' and r.datainfo.deletedbyinference=false;
-- Project_results Table -- Project_results Table
DROP TABLE IF EXISTS ${stats_db_name}.project_results; DROP TABLE IF EXISTS ${stats_db_name}.project_results;

2
dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql
View File

@ -25,7 +25,7 @@ CREATE OR REPLACE VIEW ${stats_db_name}.result_pids AS SELECT * FROM ${stats_db_
CREATE OR REPLACE VIEW ${stats_db_name}.result_topics AS SELECT * FROM ${stats_db_name}.publication_topics UNION ALL SELECT * FROM ${stats_db_name}.software_topics UNION ALL SELECT * FROM ${stats_db_name}.dataset_topics UNION ALL SELECT * FROM ${stats_db_name}.otherresearchproduct_topics; CREATE OR REPLACE VIEW ${stats_db_name}.result_topics AS SELECT * FROM ${stats_db_name}.publication_topics UNION ALL SELECT * FROM ${stats_db_name}.software_topics UNION ALL SELECT * FROM ${stats_db_name}.dataset_topics UNION ALL SELECT * FROM ${stats_db_name}.otherresearchproduct_topics;
DROP TABLE IF EXISTS ${stats_db_name}.result_organization; DROP TABLE IF EXISTS ${stats_db_name}.result_organization;
CREATE TABLE ${stats_db_name}.result_organization AS SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS organization FROM ${openaire_db_name}.relation r WHERE r.reltype='resultOrganization'; CREATE TABLE ${stats_db_name}.result_organization AS SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS organization FROM ${openaire_db_name}.relation r WHERE r.reltype='resultOrganization' and r.datainfo.deletedbyinference=false;
DROP TABLE IF EXISTS ${stats_db_name}.result_projects; DROP TABLE IF EXISTS ${stats_db_name}.result_projects;
CREATE TABLE ${stats_db_name}.result_projects AS select pr.result AS id, pr.id AS project, datediff(p.enddate, p.startdate) AS daysfromend FROM ${stats_db_name}.result r JOIN ${stats_db_name}.project_results pr ON r.id=pr.result JOIN ${stats_db_name}.project_tmp p ON p.id=pr.id; CREATE TABLE ${stats_db_name}.result_projects AS select pr.result AS id, pr.id AS project, datediff(p.enddate, p.startdate) AS daysfromend FROM ${stats_db_name}.result r JOIN ${stats_db_name}.project_results pr ON r.id=pr.result JOIN ${stats_db_name}.project_tmp p ON p.id=pr.id;

2
dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql
View File

@ -47,7 +47,7 @@ DROP TABLE IF EXISTS ${stats_db_name}.datasource_oids;
CREATE TABLE ${stats_db_name}.datasource_oids AS SELECT substr(d.id, 4) AS id, oids.ids AS oid FROM ${openaire_db_name}.datasource d LATERAL VIEW explode(d.originalid) oids AS ids; CREATE TABLE ${stats_db_name}.datasource_oids AS SELECT substr(d.id, 4) AS id, oids.ids AS oid FROM ${openaire_db_name}.datasource d LATERAL VIEW explode(d.originalid) oids AS ids;
DROP TABLE IF EXISTS ${stats_db_name}.datasource_organizations; DROP TABLE IF EXISTS ${stats_db_name}.datasource_organizations;
CREATE TABLE ${stats_db_name}.datasource_organizations AS SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS organization FROM ${openaire_db_name}.relation r WHERE r.reltype='datasourceOrganization'; CREATE TABLE ${stats_db_name}.datasource_organizations AS SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS organization FROM ${openaire_db_name}.relation r WHERE r.reltype='datasourceOrganization' and r.datainfo.deletedbyinference=false;
-- datasource sources: -- datasource sources:
-- where the datasource info have been collected from. -- where the datasource info have been collected from.

4
dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/updateCache.sh Normal file
View File

@ -0,0 +1,4 @@
#!/usr/bin/env bash
curl --request GET $1/cache/updateCache

22
dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml
View File

@ -17,6 +17,10 @@
<name>stats_db_shadow_name</name> <name>stats_db_shadow_name</name>
<description>the name of the shadow schema</description> <description>the name of the shadow schema</description>
</property> </property>
<property>
<name>stats_tool_api_url</name>
<description>The url of the API of the stats tool. Is used to trigger the cache update.</description>
</property>
<property> <property>
<name>hive_metastore_uris</name> <name>hive_metastore_uris</name>
<description>hive server metastore URIs</description> <description>hive server metastore URIs</description>
@ -255,7 +259,7 @@
<action name="Step17"> <action name="Step17">
<hive2 xmlns="uri:oozie:hive2-action:0.1"> <hive2 xmlns="uri:oozie:hive2-action:0.1">
<jdbc-url>${hive_jdbc_url}</jdbc-url> <jdbc-url>${hive_jdbc_url}</jdbc-url>
<script>scripts/step17.sql</script> <script>scripts/updateProductionViews.sql</script>
<param>stats_db_name=${stats_db_name}</param> <param>stats_db_name=${stats_db_name}</param>
<param>stats_db_shadow_name=${stats_db_shadow_name}</param> <param>stats_db_shadow_name=${stats_db_shadow_name}</param>
</hive2> </hive2>
@ -283,10 +287,22 @@
<name-node>${nameNode}</name-node> <name-node>${nameNode}</name-node>
<exec>impala-shell.sh</exec> <exec>impala-shell.sh</exec>
<argument>${stats_db_shadow_name}</argument> <argument>${stats_db_shadow_name}</argument>
<argument>step19.sql</argument> <argument>computeProductionStats.sql</argument>
<argument>${wf:appPath()}/scripts/step19.sql</argument> <argument>${wf:appPath()}/scripts/computeProductionStats.sql</argument>
<file>impala-shell.sh</file> <file>impala-shell.sh</file>
</shell> </shell>
<ok to="Step20"/>
<error to="Kill"/>
</action>
<action name="Step20">
<shell xmlns="uri:oozie:shell-action:0.1">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<exec>updateCache.sh</exec>
<argument>${stats_tool_api_url}</argument>
<file>updateCache.sh</file>
</shell>
<ok to="End"/> <ok to="End"/>
<error to="Kill"/> <error to="Kill"/>
</action> </action>

2
dhp-workflows/pom.xml
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@ -7,7 +7,7 @@
<groupId>eu.dnetlib.dhp</groupId> <groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp</artifactId> <artifactId>dhp</artifactId>
<version>1.2.4-SNAPSHOT</version> <version>1.2.4-SNAPSHOT</version>
<relativePath>../</relativePath> <relativePath>../pom.xml</relativePath>
</parent> </parent>
<artifactId>dhp-workflows</artifactId> <artifactId>dhp-workflows</artifactId>