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

This commit is contained in:
Miriam Baglioni 2023-06-28 11:25:14 +02:00
parent 2f04c9d149 bd17c3edc8
commit 2717edafb7
18 changed files with 197 additions and 79 deletions
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3
dhp-common/src/main/scala/eu/dnetlib/dhp/application/dedup/log/DedupLogModel.scala Normal file
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@ -0,0 +1,3 @@
package eu.dnetlib.dhp.application.dedup.log
case class DedupLogModel(tag:String, configuration:String, entity:String, startTS:Long, endTS:Long, totalMs:Long ) {}

16
dhp-common/src/main/scala/eu/dnetlib/dhp/application/dedup/log/DedupLogWriter.scala Normal file
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@ -0,0 +1,16 @@
package eu.dnetlib.dhp.application.dedup.log
import org.apache.spark.sql.{SaveMode, SparkSession}
class DedupLogWriter (path:String) {
def appendLog(dedupLogModel: DedupLogModel, spark:SparkSession): Unit = {
import spark.implicits._
val df = spark.createDataset[DedupLogModel](data = List(dedupLogModel))
df.write.mode(SaveMode.Append).save(path)
}
}

2
dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala
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@ -82,7 +82,7 @@ object BioDBToOAF {
"Springer Nature"
)
val EBICollectedFrom: KeyValue = OafMapperUtils.keyValue(
"10|opendoar____::83e60e09c222f206c725385f53d7e567c",
"10|opendoar____::3e60e09c222f206c725385f53d7e567c",
"EMBL-EBIs Protein Data Bank in Europe (PDBe)"
)
val pubmedCollectedFrom: KeyValue =

20
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateSimRels.java
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@ -4,7 +4,10 @@ package eu.dnetlib.dhp.oa.dedup;
import java.io.IOException;
import java.util.Optional;
import eu.dnetlib.dhp.application.dedup.log.DedupLogModel;
import eu.dnetlib.dhp.application.dedup.log.DedupLogWriter;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaPairRDD;
import org.apache.spark.api.java.JavaSparkContext;
@ -20,8 +23,6 @@ import org.xml.sax.SAXException;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.dedup.model.Block;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.DataInfo;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
@ -73,9 +74,16 @@ public class SparkCreateSimRels extends AbstractSparkAction {
log.info("actionSetId: '{}'", actionSetId);
log.info("workingPath: '{}'", workingPath);
final String dfLogPath = parser.get("dataframeLog");
final String runTag = Optional.ofNullable(parser.get("runTAG")).orElse("UNKNOWN");
// for each dedup configuration
for (DedupConfig dedupConf : getConfigurations(isLookUpService, actionSetId)) {
final long start = System.currentTimeMillis();
final String entity = dedupConf.getWf().getEntityType();
final String subEntity = dedupConf.getWf().getSubEntityValue();
log.info("Creating simrels for: '{}'", subEntity);
@ -85,6 +93,7 @@ public class SparkCreateSimRels extends AbstractSparkAction {
JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaPairRDD<String, MapDocument> mapDocuments = sc
.textFile(DedupUtility.createEntityPath(graphBasePath, subEntity))
.repartition(numPartitions)
@ -109,6 +118,13 @@ public class SparkCreateSimRels extends AbstractSparkAction {
Encoders.bean(Relation.class));
saveParquet(simRels, outputPath, SaveMode.Overwrite);
final long end = System.currentTimeMillis();
if (StringUtils.isNotBlank(dfLogPath)) {
final DedupLogModel model = new DedupLogModel(runTag, dedupConf.toString(),entity, start, end, end-start);
new DedupLogWriter(dfLogPath).appendLog(model, spark);
}
}
}

12
dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json
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@ -28,5 +28,17 @@
"paramLongName": "numPartitions",
"paramDescription": "number of partitions for the similarity relations intermediate phases",
"paramRequired": false
},
{
"paramName": "dl",
"paramLongName": "dataframeLog",
"paramDescription": "the path of the dataframe Log",
"paramRequired": false
},
{
"paramName": "rt",
"paramLongName": "runTAG",
"paramDescription": "the label of the current running",
"paramRequired": false
}
]

13
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/entitytoorganizationfromsemrel/input_propagation_parameter.json
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@ -52,10 +52,11 @@
"paramLongName": "iterations",
"paramDescription": "the number of iterations to be computed",
"paramRequired": false
},{
"paramName": "pop",
"paramLongName": "projectOrganizationPath",
"paramDescription": "the number of iterations to be computed",
"paramRequired": true
}
},
{
"paramName": "pop",
"paramLongName": "projectOrganizationPath",
"paramDescription": "the number of iterations to be computed",
"paramRequired": true
}
]

1
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/entitytoorganizationfromsemrel/oozie_app/workflow.xml
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@ -181,6 +181,7 @@
<arg>--leavesPath</arg><arg>${workingDir}/preparedInfo/leavesPath</arg>
<arg>--childParentPath</arg><arg>${workingDir}/preparedInfo/childParentPath</arg>
<arg>--resultOrgPath</arg><arg>${workingDir}/preparedInfo/resultOrgPath</arg>
<arg>--projectOrganizationPath</arg><arg>${workingDir}/preparedInfo/projectOrganizationPath</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--workingDir</arg><arg>${workingDir}/working</arg>
<arg>--iterations</arg><arg>${iterations}</arg>

2
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryOpenOrgsForProvision.sql
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@ -18,7 +18,7 @@ SELECT
ARRAY(SELECT DISTINCT pid FROM unnest(array_cat(
array_agg(DISTINCT i.otherid || '###' || i.type || '@@@dnet:pid_types'),
array_agg(DISTINCT idup.otherid || '###' || idup.type || '@@@dnet:pid_types')
)) as t(pid) where pid IS NOT NULL),
)) as t(pid) where pid IS NOT NULL) AS pid,
(array_remove(array_cat(ARRAY[o.ec_legalbody], array_agg(od.ec_legalbody)), NULL))[1] AS eclegalbody,
(array_remove(array_cat(ARRAY[o.ec_legalperson], array_agg(od.ec_legalperson)), NULL))[1] AS eclegalperson,
(array_remove(array_cat(ARRAY[o.ec_nonprofit], array_agg(od.ec_nonprofit)), NULL))[1] AS ecnonprofit,

6
dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/updateProductionViews.sh
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@ -10,7 +10,7 @@ export SOURCE=$1
export PRODUCTION=$2
echo "Updating ${PRODUCTION} database"
impala-shell -q "create database if not exists ${PRODUCTION}"
impala-shell -d ${PRODUCTION} -q "show tables" --delimited | sed "s/^/drop view if exists ${PRODUCTION}./" | sed "s/$/;/" | impala-shell -c -f -
impala-shell -d ${SOURCE} -q "show tables" --delimited | sed "s/\(.*\)/create view ${PRODUCTION}.\1 as select * from ${SOURCE}.\1;/" | impala-shell -c -f -
impala-shell -i impala-cluster-dn1.openaire.eu -q "create database if not exists ${PRODUCTION}"
impala-shell -i impala-cluster-dn1.openaire.eu -d ${PRODUCTION} -q "show tables" --delimited | sed "s/^/drop view if exists ${PRODUCTION}./" | sed "s/$/;/" | impala-shell -c -f -
impala-shell -i impala-cluster-dn1.openaire.eu -d ${SOURCE} -q "show tables" --delimited | sed "s/\(.*\)/create view ${PRODUCTION}.\1 as select * from ${SOURCE}.\1;/" | impala-shell -c -f -
echo "Production db ready!"

38
dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/updateProductionViewsMonitor.sh Normal file
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@ -0,0 +1,38 @@
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
export SOURCE=$1
export PRODUCTION=$2
echo "Updating ${PRODUCTION}'_funded' database"
impala-shell -i impala-cluster-dn1.openaire.eu -q "create database if not exists ${PRODUCTION}'_funded'"
impala-shell -i impala-cluster-dn1.openaire.eu -d ${PRODUCTION}'_funded' -q "show tables" --delimited | sed "s/^/drop view if exists ${PRODUCTION}'_funded'./" | sed "s/$/;/" | impala-shell -c -f -
impala-shell -i impala-cluster-dn1.openaire.eu -d ${SOURCE}'_funded' -q "show tables" --delimited | sed "s/\(.*\)/create view ${PRODUCTION}'_funded'.\1 as select * from ${SOURCE}'_funded'.\1;/" | impala-shell -c -f -
echo "Production funded db ready!"
echo "Updating ${PRODUCTION}'_institutions' database"
impala-shell -i impala-cluster-dn1.openaire.eu -q "create database if not exists ${PRODUCTION}'_institutions'"
impala-shell -i impala-cluster-dn1.openaire.eu -d ${PRODUCTION}'_institutions' -q "show tables" --delimited | sed "s/^/drop view if exists ${PRODUCTION}'_institutions'./" | sed "s/$/;/" | impala-shell -c -f -
impala-shell -i impala-cluster-dn1.openaire.eu -d ${SOURCE}'_institutions' -q "show tables" --delimited | sed "s/\(.*\)/create view ${PRODUCTION}'_institutions'.\1 as select * from ${SOURCE}'_institutions'.\1;/" | impala-shell -c -f -
echo "Production insitutions db ready!"
echo "Updating ${PRODUCTION}'_ris_tail' database"
impala-shell -i impala-cluster-dn1.openaire.eu -q "create database if not exists ${PRODUCTION}'_ris_tail'"
impala-shell -i impala-cluster-dn1.openaire.eu -d ${PRODUCTION}'_ris_tail' -q "show tables" --delimited | sed "s/^/drop view if exists ${PRODUCTION}'_ris_tail'./" | sed "s/$/;/" | impala-shell -c -f -
impala-shell -i impala-cluster-dn1.openaire.eu -d ${SOURCE}'_RIs_tail' -q "show tables" --delimited | sed "s/\(.*\)/create view ${PRODUCTION}'_ris_tail'.\1 as select * from ${SOURCE}'_ris_tail'.\1;/" | impala-shell -c -f -
echo "Production RIS tail db ready!"
contexts="knowmad::other dh-ch::other enermaps::other gotriple::other neanias-atmospheric::other rural-digital-europe::other covid-19::other aurora::other neanias-space::other north-america-studies::other north-american-studies::other eutopia::other"
for i in ${contexts}
do
tmp=`echo "$i" | sed 's/'-'/'_'/g' | sed 's/'::'/'_'/g'`
impala-shell -i impala-cluster-dn1.openaire.eu -q "create database if not exists ${PRODUCTION}'_'${tmp}"
impala-shell -i impala-cluster-dn1.openaire.eu -d ${PRODUCTION}'_'${tmp} -q "show tables" --delimited | sed "s/^/drop view if exists ${PRODUCTION}'_'${tmp}./" | sed "s/$/;/" | impala-shell -c -f -
impala-shell -i impala-cluster-dn1.openaire.eu -d ${SOURCE}'_'${tmp} -q "show tables" --delimited | sed "s/\(.*\)/create view ${PRODUCTION}'_'${tmp}.\1 as select * from ${SOURCE}'_'${tmp}.\1;/" | impala-shell -c -f -
echo "Production ${tmp} db ready!"
done

4
dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml
View File

@ -80,10 +80,10 @@
<shell xmlns="uri:oozie:shell-action:0.1">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<exec>updateProductionViews.sh</exec>
<exec>updateProductionViewsMonitor.sh</exec>
<argument>${monitor_db_name}</argument>
<argument>${monitor_db_production_name}</argument>
<file>updateProductionViews.sh</file>
<file>updateProductionViewsMonitor.sh</file>
</shell>
<ok to="updateObservatoryViews"/>
<error to="Kill"/>

18
dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/copyDataToImpalaCluster.sh
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@ -7,7 +7,7 @@ then
fi
#export HADOOP_USER_NAME="dimitris.pierrakos"
export HADOOP_USER_NAME=$5
export HADOOP_USER_NAME=$6
export PROD_USAGE_STATS_DB="openaire_prod_usage_stats"
function copydb() {
db=$1
@ -21,8 +21,22 @@ function copydb() {
# change ownership to impala
hdfs dfs -conf /etc/impala_cluster/hdfs-site.xml -chmod -R 777 /tmp/$FILE/${db}.db
# create the databases
# drop tables from db
for i in `impala-shell --user $HADOOP_USER_NAME -i impala-cluster-dn1.openaire.eu -d ${db} --delimited -q "show tables"`;
do
`impala-shell -i impala-cluster-dn1.openaire.eu -d -d ${db} -q "drop table $i;"`;
done
# drop views from db
for i in `impala-shell --user $HADOOP_USER_NAME -i impala-cluster-dn1.openaire.eu -d ${db} --delimited -q "show tables"`;
do
`impala-shell -i impala-cluster-dn1.openaire.eu -d -d ${db} -q "drop view $i;"`;
done
# delete the database
impala-shell --user $HADOOP_USER_NAME -i impala-cluster-dn1.openaire.eu -q "drop database if exists ${db} cascade";
# create the databases
impala-shell --user $HADOOP_USER_NAME -i impala-cluster-dn1.openaire.eu -q "create database ${db}";
impala-shell --user $HADOOP_USER_NAME -q "INVALIDATE METADATA"

6
dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/finalizeImpalaCluster.sh
View File

@ -10,6 +10,12 @@ function createShadowDB() {
SOURCE=$1
SHADOW=$2
# drop views from db
for i in `impala-shell -i impala-cluster-dn1.openaire.eu -d ${SHADOW} --delimited -q "show tables"`;
do
`impala-shell -i impala-cluster-dn1.openaire.eu -d -d ${SHADOW} -q "drop view $i;"`;
done
impala-shell -i impala-cluster-dn1.openaire.eu -q "drop database ${SHADOW} CASCADE";
impala-shell -i impala-cluster-dn1.openaire.eu -q "create database if not exists ${SHADOW}";
# impala-shell -i impala-cluster-dn1.openaire.eu -d ${SHADOW} -q "show tables" | sed "s/^/drop view if exists ${SHADOW}./" | sed "s/$/;/" | impala-shell -i impala-cluster-dn1.openaire.eu -f -

2
dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql
View File

@ -49,5 +49,5 @@ FROM (
WHERE d.datainfo.deletedbyinference=false and d.datainfo.invisible = FALSE) d on o.datasource = d.id;
CREATE TABLE IF NOT EXISTS ${stats_db_name}.result_accessroute STORED AS PARQUET as
select distinct substr(id,4),id, accessroute from ${openaire_db_name}.result
select distinct substr(id,4) as id, accessroute from ${openaire_db_name}.result
lateral view explode (instance.accessright.openaccessroute) openaccessroute as accessroute;

8
dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15.sql
View File

@ -34,3 +34,11 @@ union all
select * from ${stats_db_name}.software_refereed
union all
select * from ${stats_db_name}.otherresearchproduct_refereed;
create table if not exists ${stats_db_name}.indi_impact_measures STORED AS PARQUET as
select substr(id, 4) as id, measures_ids.id impactmetric, cast(measures_ids.unit.value[0] as double) score,
cast(measures_ids.unit.value[0] as decimal(6,3)) score_dec, measures_ids.unit.value[1] class
from ${openaire_db_name}.result lateral view explode(measures) measures as measures_ids
where measures_ids.id!='views' and measures_ids.id!='downloads';
ANALYZE TABLE indi_impact_measures COMPUTE STATISTICS;

24
dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15_5.sql
View File

@ -1,21 +1,21 @@
-------------------------------------------
--- Extra tables, mostly used by indicators
create table ${stats_db_name}.result_projectcount STORED AS PARQUET as
create table if not exists ${stats_db_name}.result_projectcount STORED AS PARQUET as
select r.id, count(distinct p.id) as count
from ${stats_db_name}.result r
left outer join ${stats_db_name}.result_projects rp on rp.id=r.id
left outer join ${stats_db_name}.project p on p.id=rp.project
group by r.id;
create table ${stats_db_name}.result_fundercount STORED AS PARQUET as
create table if not exists ${stats_db_name}.result_fundercount STORED AS PARQUET as
select r.id, count(distinct p.funder) as count
from ${stats_db_name}.result r
left outer join ${stats_db_name}.result_projects rp on rp.id=r.id
left outer join ${stats_db_name}.project p on p.id=rp.project
group by r.id;
create table ${stats_db_name}.project_resultcount STORED AS PARQUET as
create table if not exists ${stats_db_name}.project_resultcount STORED AS PARQUET as
with rcount as (
select p.id as pid, count(distinct r.id) as `count`, r.type as type
from ${stats_db_name}.project p
@ -29,14 +29,14 @@ select rcount.pid, sum(case when rcount.type='publication' then rcount.count els
from rcount
group by rcount.pid;
create view ${stats_db_name}.rndexpenditure as select * from stats_ext.rndexpediture;
create view ${stats_db_name}.rndgdpexpenditure as select * from stats_ext.rndgdpexpenditure;
create view ${stats_db_name}.doctoratestudents as select * from stats_ext.doctoratestudents;
create view ${stats_db_name}.totalresearchers as select * from stats_ext.totalresearchers;
create view ${stats_db_name}.totalresearchersft as select * from stats_ext.totalresearchersft;
create view ${stats_db_name}.hrrst as select * from stats_ext.hrrst;
create or replace view ${stats_db_name}.rndexpenditure as select * from stats_ext.rndexpediture;
create or replace view ${stats_db_name}.rndgdpexpenditure as select * from stats_ext.rndgdpexpenditure;
create or replace view ${stats_db_name}.doctoratestudents as select * from stats_ext.doctoratestudents;
create or replace view ${stats_db_name}.totalresearchers as select * from stats_ext.totalresearchers;
create or replace view ${stats_db_name}.totalresearchersft as select * from stats_ext.totalresearchersft;
create or replace view ${stats_db_name}.hrrst as select * from stats_ext.hrrst;
create table ${stats_db_name}.result_instance stored as parquet as
create table if not exists ${stats_db_name}.result_instance stored as parquet as
select distinct r.*
from (
select substr(r.id, 4) as id, inst.accessright.classname as accessright, inst.accessright.openaccessroute as accessright_uw, substr(inst.collectedfrom.key, 4) as collectedfrom,
@ -44,7 +44,7 @@ from (
from ${openaire_db_name}.result r lateral view explode(r.instance) instances as inst lateral view explode(inst.pid) pids as p) r
join ${stats_db_name}.result res on res.id=r.id;
create table ${stats_db_name}.result_apc STORED AS PARQUET as
create table if not exists ${stats_db_name}.result_apc STORED AS PARQUET as
select r.id, r.amount, r.currency
from (
select substr(r.id, 4) as id, cast(inst.processingchargeamount.value as float) as amount, inst.processingchargecurrency.value as currency
@ -52,4 +52,4 @@ from (
join ${stats_db_name}.result res on res.id=r.id
where r.amount is not null;
create view ${stats_db_name}.issn_gold_oa_dataset as select * from ${external_stats_db_name}.issn_gold_oa_dataset;
create or replace view ${stats_db_name}.issn_gold_oa_dataset as select * from ${external_stats_db_name}.issn_gold_oa_dataset;

93
dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql
View File

@ -342,40 +342,6 @@ FROM publication_datasources pd
ANALYZE TABLE indi_pub_hybrid_oa_with_cc COMPUTE STATISTICS;
create table if not exists indi_pub_bronze_oa stored as parquet as
WITH hybrid_oa AS (
SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_print as issn
FROM STATS_EXT.plan_s_jn
WHERE issn_print != ""
UNION ALL
SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_online as issn
FROM STATS_EXT.plan_s_jn
WHERE issn_online != "" and (journal_is_in_doaj = FALSE OR journal_is_oa = FALSE)),
issn AS (
SELECT *
FROM (
SELECT id, issn_printed as issn
FROM datasource
WHERE issn_printed IS NOT NULL
UNION ALL
SELECT id,issn_online as issn
FROM datasource
WHERE issn_online IS NOT NULL ) as issn
WHERE LENGTH(issn) > 7)
SELECT DISTINCT pd.id, coalesce(is_bronze_oa, 0) as is_hybrid_oa
FROM publication_datasources pd
LEFT OUTER JOIN (
SELECT pd.id, 1 as is_bronze_oa from publication_datasources pd
JOIN datasource d on d.id=pd.datasource
JOIN issn on issn.id=pd.datasource
JOIN hybrid_oa ON issn.issn = hybrid_oa.issn
JOIN indi_result_has_cc_licence cc on pd.id=cc.id
JOIN indi_pub_gold_oa ga on pd.id=ga.id
JOIN indi_pub_hybrid_oa_with_cc hy on hy.id=pd.id
where cc.has_cc_license=0 and ga.is_gold=0 and hy.is_hybrid_oa=0) tmp on pd.id=tmp.id;
ANALYZE TABLE indi_pub_bronze_oa COMPUTE STATISTICS;
create table if not exists indi_pub_hybrid stored as parquet as
WITH gold_oa AS ( SELECT
issn_l,
@ -775,26 +741,61 @@ from result p
ANALYZE TABLE indi_result_with_pid COMPUTE STATISTICS;
create table if not exists indi_impact_measures as
select distinct substr(id, 4), measures_ids.id impactmetric, measures_ids.unit.value[0] score,
cast(measures_ids.unit.value[0] as decimal(6,3)) score_dec, measures_ids.unit.value[1] class
from result lateral view explode(measures) measures as measures_ids
where measures_ids.id!='views' and measures_ids.id!='downloads';
ANALYZE TABLE indi_impact_measures COMPUTE STATISTICS;
CREATE TEMPORARY TABLE pub_fos_totals as
select rf.id, count(distinct lvl3) totals from result_fos rf
group by rf.id;
create table if not exists indi_pub_interdisciplinarity as
select distinct p.id, coalesce(indi_pub_is_interdisciplinary, 0)
as indi_pub_is_interdisciplinary
select distinct p.id as id, coalesce(is_interdisciplinary, 0)
as is_interdisciplinary
from pub_fos_totals p
left outer join (
select pub_fos_totals.id, 1 as indi_pub_is_interdisciplinary from pub_fos_totals
where totals>10) tmp on p.id=tmp.id;
select pub_fos_totals.id, 1 as is_interdisciplinary from pub_fos_totals
where totals>1) tmp on p.id=tmp.id;
drop table pub_fos_totals purge;
ANALYZE TABLE indi_pub_interdisciplinarity COMPUTE STATISTICS;
create table if not exists indi_pub_bronze_oa stored as parquet as
select distinct p.id, coalesce(is_bronze_oa,0) as is_bronze_oa
from publication p
left outer join
(select p.id, 1 as is_bronze_oa from publication p
join indi_result_has_cc_licence cc on cc.id=p.id
join indi_pub_gold_oa ga on ga.id=p.id
where cc.has_cc_license=0 and ga.is_gold=0) tmp on tmp.id=p.id;
-- create table if not exists indi_pub_bronze_oa stored as parquet as
-- WITH hybrid_oa AS (
-- SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_print as issn
-- FROM STATS_EXT.plan_s_jn
-- WHERE issn_print != ""
-- UNION ALL
-- SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_online as issn
-- FROM STATS_EXT.plan_s_jn
-- WHERE issn_online != "" and (journal_is_in_doaj = FALSE OR journal_is_oa = FALSE)),
-- issn AS (
-- SELECT *
-- FROM (
-- SELECT id, issn_printed as issn
-- FROM datasource
-- WHERE issn_printed IS NOT NULL
-- UNION ALL
-- SELECT id,issn_online as issn
-- FROM datasource
-- WHERE issn_online IS NOT NULL ) as issn
-- WHERE LENGTH(issn) > 7)
--SELECT DISTINCT pd.id, coalesce(is_bronze_oa, 0) as is_bronze_oa
--FROM publication_datasources pd
-- LEFT OUTER JOIN (
-- SELECT pd.id, 1 as is_bronze_oa from publication_datasources pd
-- JOIN datasource d on d.id=pd.datasource
-- JOIN issn on issn.id=pd.datasource
-- JOIN hybrid_oa ON issn.issn = hybrid_oa.issn
-- JOIN indi_result_has_cc_licence cc on pd.id=cc.id
-- JOIN indi_pub_gold_oa ga on pd.id=ga.id
-- JOIN indi_pub_hybrid_oa_with_cc hy on hy.id=pd.id
-- where cc.has_cc_license=0 and ga.is_gold=0 and hy.is_hybrid_oa=0) tmp on pd.id=tmp.id;
ANALYZE TABLE indi_pub_bronze_oa COMPUTE STATISTICS;

4
dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_institutions.sql
View File

@ -50,7 +50,9 @@ create table TARGET.result stored as parquet as
'openorgs____::846cb428d3f52a445f7275561a7beb5d', -- University of Manitoba
'openorgs____::eb391317ed0dc684aa81ac16265de041', -- Universitat Rovira i Virgili
'openorgs____::66aa9fc2fceb271423dfabcc38752dc0', -- Lund University
'openorgs____::3cff625a4370d51e08624cc586138b2f' -- IMT Atlantique
'openorgs____::3cff625a4370d51e08624cc586138b2f', -- IMT Atlantique
'openorgs____::c0b262bd6eab819e4c994914f9c010e2', -- National Institute of Geophysics and Volcanology
'openorgs____::1624ff7c01bb641b91f4518539a0c28a' -- Vrije Universiteit Amsterdam
))) foo;
ANALYZE TABLE TARGET.result COMPUTE STATISTICS;