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- New Monitor DB workflow 

- New Organization added
This commit is contained in:
dimitrispie 2023-01-12 11:18:03 +02:00
parent becb242c17
commit 686580a220
6 changed files with 107 additions and 258 deletions
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21
dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/monitor-post.sh
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@ -1,21 +0,0 @@
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 TARGET=$2
export SHADOW=$3
impala-shell -q "invalidate metadata;"
impala-shell -d ${TARGET} -q "show tables" --delimited | sed "s/\(.*\)/compute stats ${TARGET}.\1;/" | impala-shell -f -
echo "Impala shell finished"
echo "Updating shadow monitor database"
impala-shell -q "create database if not exists ${SHADOW}"
impala-shell -d ${SHADOW} -q "show tables" --delimited | sed "s/^/drop view if exists ${SHADOW}./" | sed "s/$/;/" | impala-shell -f -
impala-shell -d ${TARGET} -q "show tables" --delimited | sed "s/\(.*\)/create view ${SHADOW}.\1 as select * from ${TARGET}.\1;/" | impala-shell -f -
echo "Shadow db ready!"

16
dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/monitor.sh
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@ -8,17 +8,11 @@ fi
export SOURCE=$1 export SOURCE=$1
export TARGET=$2 export TARGET=$2
export SHADOW=$3 export SCRIPT_PATH=$3
export SCRIPT_PATH=$4
export HIVE_OPTS="-hiveconf mapred.job.queue.name=analytics -hiveconf hive.spark.client.connect.timeout=120000ms -hiveconf hive.spark.client.server.connect.timeout=300000ms -hiveconf spark.executor.memory=19166291558 -hiveconf spark.yarn.executor.memoryOverhead=3225 -hiveconf spark.driver.memory=11596411699 -hiveconf spark.yarn.driver.memoryOverhead=1228" echo "Getting file from " $3
export HADOOP_USER_NAME="oozie" hdfs dfs -copyToLocal $3
echo "Getting file from " $SCRIPT_PATH
hdfs dfs -copyToLocal $SCRIPT_PATH
echo "Creating monitor database" echo "Creating monitor database"
#cat step20-createMonitorDB.sql | sed s/SOURCE/$1/g | sed s/TARGET/$2/g1 > foo cat createMonitorDB.sql | sed s/SOURCE/$1/g | sed s/TARGET/$2/g1 | impala-shell -f -
cat createMonitorDB.sql | sed "s/TARGET/${TARGET}/g" | sed "s/SOURCE/${SOURCE}/g" > foo echo "Impala shell finished"
hive $HIVE_OPTS -f foo
echo "Hive shell finished"

293
dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/scripts/createMonitorDB.sql
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@ -1,241 +1,148 @@
drop database if exists TARGET cascade; DROP TABLE IF EXISTS TARGET.result_new;
create database if not exists TARGET;
create view if not exists TARGET.category as select * from SOURCE.category; create table TARGET.result_new stored as parquet as
create view if not exists TARGET.concept as select * from SOURCE.concept;
create view if not exists TARGET.context as select * from SOURCE.context;
create view if not exists TARGET.country as select * from SOURCE.country;
create view if not exists TARGET.countrygdp as select * from SOURCE.countrygdp;
create view if not exists TARGET.creation_date as select * from SOURCE.creation_date;
create view if not exists TARGET.funder as select * from SOURCE.funder;
create view if not exists TARGET.fundref as select * from SOURCE.fundref;
create view if not exists TARGET.rndexpenditure as select * from SOURCE.rndexpediture;
create view if not exists TARGET.rndgdpexpenditure as select * from SOURCE.rndgdpexpenditure;
create view if not exists TARGET.doctoratestudents as select * from SOURCE.doctoratestudents;
create view if not exists TARGET.totalresearchers as select * from SOURCE.totalresearchers;
create view if not exists TARGET.totalresearchersft as select * from SOURCE.totalresearchersft;
create view if not exists TARGET.hrrst as select * from SOURCE.hrrst;
create table TARGET.result stored as parquet as
select distinct * from ( select distinct * from (
select * from SOURCE.result r where exists (select 1 from SOURCE.result_projects rp join SOURCE.project p on rp.project=p.id where rp.id=r.id) select * from SOURCE.result r where exists (select 1 from SOURCE.result_projects rp join SOURCE.project p on rp.project=p.id where rp.id=r.id)
union all union all
select * from SOURCE.result r where exists (select 1 from SOURCE.result_concepts rc where rc.id=r.id) select * from SOURCE.result r where exists (select 1 from SOURCE.result_concepts rc where rc.id=r.id)
union all union all
select * from SOURCE.result r where exists (select 1 from SOURCE.result_organization ro where ro.id=r.id and ro.organization in ( select * from SOURCE.result r where exists (select 1 from SOURCE.result_organization ro where ro.id=r.id and ro.organization in (
'openorgs____::b84450f9864182c67b8611b5593f4250', --"Athena Research and Innovation Center In Information Communication & Knowledge Technologies', --ARC" -- 'openorgs____::b8b8ca674452579f3f593d9f5e557483', -- University College Cork
'openorgs____::d41cf6bd4ab1b1362a44397e0b95c975', --National Research Council 'openorgs____::38d7097854736583dde879d12dacafca' -- Brown University
'openorgs____::d2a09b9d5eabb10c95f9470e172d05d2', --??? Not exists ??
'openorgs____::d169c7407dd417152596908d48c11460', --Masaryk University
'openorgs____::1ec924b1759bb16d0a02f2dad8689b21', --University of Belgrade
'openorgs____::0ae431b820e4c33db8967fbb2b919150', --University of Helsinki
'openorgs____::759d59f05d77188faee99b7493b46805', --University of Minho
'openorgs____::cad284878801b9465fa51a95b1d779db', --Universidad Politécnica de Madrid
'openorgs____::eadc8da90a546e98c03f896661a2e4d4', --University of Göttingen
'openorgs____::c0286313e36479eff8676dba9b724b40', --National and Kapodistrian University of Athens
-- 'openorgs____::c80a8243a5e5c620d7931c88d93bf17a', --Université Paris Diderot
'openorgs____::c08634f0a6b0081c3dc6e6c93a4314f3', --Bielefeld University
'openorgs____::6fc85e4a8f7ecaf4b0c738d010e967ea', --University of Southern Denmark
'openorgs____::3d6122f87f9a97a99d8f6e3d73313720', --Humboldt-Universität zu Berlin
'openorgs____::16720ada63d0fa8ca41601feae7d1aa5', --TU Darmstadt
'openorgs____::ccc0a066b56d2cfaf90c2ae369df16f5', --KU Leuven
'openorgs____::4c6f119632adf789746f0a057ed73e90', --University of the Western Cape
'openorgs____::ec3665affa01aeafa28b7852c4176dbd', --Rudjer Boskovic Institute
'openorgs____::5f31346d444a7f06a28c880fb170b0f6', --Ghent University
'openorgs____::2dbe47117fd5409f9c61620813456632', --University of Luxembourg
'openorgs____::6445d7758d3a40c4d997953b6632a368', --National Institute of Informatics (NII)
'openorgs____::b77c01aa15de3675da34277d48de2ec1', -- Valencia Catholic University Saint Vincent Martyr
'openorgs____::7fe2f66cdc43983c6b24816bfe9cf6a0', -- Unviersity of Warsaw
'openorgs____::15e7921fc50d9aa1229a82a84429419e', -- University Of Thessaly
'openorgs____::11f7919dadc8f8a7251af54bba60c956', -- Technical University of Crete
'openorgs____::84f0c5f5dbb6daf42748485924efde4b', -- University of Piraeus
'openorgs____::4ac562f0376fce3539504567649cb373', -- University of Patras
'openorgs____::3e8d1f8c3f6cd7f418b09f1f58b4873b', -- Aristotle University of Thessaloniki
'openorgs____::3fcef6e1c469c10f2a84b281372c9814', -- World Bank
'openorgs____::1698a2eb1885ef8adb5a4a969e745ad3', -- École des Ponts ParisTech
'openorgs____::e15adb13c4dadd49de4d35c39b5da93a', -- Nanyang Technological University
'openorgs____::4b34103bde246228fcd837f5f1bf4212', -- Autonomous University of Barcelona
'openorgs____::72ec75fcfc4e0df1a76dc4c49007fceb', -- McMaster University
'openorgs____::51c7fc556e46381734a25a6fbc3fd398', -- University of Modena and Reggio Emilia
'openorgs____::235d7f9ad18ecd7e6dc62ea4990cb9db', -- Bilkent University
'openorgs____::31f2fa9e05b49d4cf40a19c3fed8eb06', -- Saints Cyril and Methodius University of Skopje
'openorgs____::db7686f30f22cbe73a4fde872ce812a6', -- University of Milan
'openorgs____::b8b8ca674452579f3f593d9f5e557483' -- University College Cork
) )) foo; ) )) foo;
ANALYZE TABLE TARGET.result COMPUTE STATISTICS; COMPUTE STATS TARGET.result_new;
create table TARGET.result_citations stored as parquet as select * from SOURCE.result_citations orig where exists (select 1 from TARGET.result r where r.id=orig.id); INSERT INTO TARGET.result select * from TARGET.result_new;
ANALYZE TABLE TARGET.result_citations COMPUTE STATISTICS;
create table TARGET.result_references_oc stored as parquet as select * from SOURCE.result_references_oc orig where exists (select 1 from TARGET.result r where r.id=orig.id); INSERT INTO TARGET.result_citations select * from TARGET.result_citations orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
ANALYZE TABLE TARGET.result_references_oc COMPUTE STATISTICS; COMPUTE STATS TARGET.result_citations;
create table TARGET.result_citations_oc stored as parquet as select * from SOURCE.result_citations_oc orig where exists (select 1 from TARGET.result r where r.id=orig.id); INSERT INTO TARGET.result_references_oc select * from TARGET.result_references_oc orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
ANALYZE TABLE TARGET.result_citations_oc COMPUTE STATISTICS; COMPUTE STATS TARGET.result_references_oc;
create table TARGET.result_classifications stored as parquet as select * from SOURCE.result_classifications orig where exists (select 1 from TARGET.result r where r.id=orig.id); INSERT INTO TARGET.result_citations_oc select * from TARGET.result_citations_oc orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
ANALYZE TABLE TARGET.result_classifications COMPUTE STATISTICS; COMPUTE STATS TARGET.result_citations_oc;
create table TARGET.result_apc stored as parquet as select * from SOURCE.result_apc orig where exists (select 1 from TARGET.result r where r.id=orig.id); INSERT INTO TARGET.result_classifications select * from TARGET.result_classifications orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
ANALYZE TABLE TARGET.result_apc COMPUTE STATISTICS; COMPUTE STATS TARGET.result_classifications;
create table TARGET.result_concepts stored as parquet as select * from SOURCE.result_concepts orig where exists (select 1 from TARGET.result r where r.id=orig.id); INSERT INTO TARGET.result_apc select * from TARGET.result_apc orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
ANALYZE TABLE TARGET.result_concepts COMPUTE STATISTICS; COMPUTE STATS TARGET.result_apc;
create table TARGET.result_datasources stored as parquet as select * from SOURCE.result_datasources orig where exists (select 1 from TARGET.result r where r.id=orig.id); INSERT INTO TARGET.result_concepts select * from TARGET.result_concepts orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
ANALYZE TABLE TARGET.result_datasources COMPUTE STATISTICS; COMPUTE STATS TARGET.result_concepts;
create table TARGET.result_fundercount stored as parquet as select * from SOURCE.result_fundercount orig where exists (select 1 from TARGET.result r where r.id=orig.id); INSERT INTO TARGET.result_datasources select * from TARGET.result_datasources orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
ANALYZE TABLE TARGET.result_fundercount COMPUTE STATISTICS; COMPUTE STATS TARGET.result_datasources;
create table TARGET.result_gold stored as parquet as select * from SOURCE.result_gold orig where exists (select 1 from TARGET.result r where r.id=orig.id); INSERT INTO TARGET.result_fundercount select * from TARGET.result_fundercount orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
ANALYZE TABLE TARGET.result_gold COMPUTE STATISTICS; COMPUTE STATS TARGET.result_fundercount;
create table TARGET.result_greenoa stored as parquet as select * from SOURCE.result_greenoa orig where exists (select 1 from TARGET.result r where r.id=orig.id); INSERT INTO TARGET.result_gold select * from TARGET.result_gold orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
ANALYZE TABLE TARGET.result_greenoa COMPUTE STATISTICS; COMPUTE STATS TARGET.result_gold;
create table TARGET.result_languages stored as parquet as select * from SOURCE.result_languages orig where exists (select 1 from TARGET.result r where r.id=orig.id); INSERT INTO TARGET.result_greenoa select * from TARGET.result_greenoa orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
ANALYZE TABLE TARGET.result_languages COMPUTE STATISTICS; COMPUTE STATS TARGET.result_greenoa;
create table TARGET.result_licenses stored as parquet as select * from SOURCE.result_licenses orig where exists (select 1 from TARGET.result r where r.id=orig.id); INSERT INTO TARGET.result_languages select * from TARGET.result_languages orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
ANALYZE TABLE TARGET.result_licenses COMPUTE STATISTICS; COMPUTE STATS TARGET.result_languages;
create table TARGET.licenses_normalized STORED AS PARQUET as select * from SOURCE.licenses_normalized; INSERT INTO TARGET.result_licenses select * from TARGET.result_licenses orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
ANALYZE TABLE TARGET.licenses_normalized COMPUTE STATISTICS; COMPUTE STATS TARGET.result_licenses;
create table TARGET.result_oids stored as parquet as select * from SOURCE.result_oids orig where exists (select 1 from TARGET.result r where r.id=orig.id); INSERT INTO TARGET.result_oids select * from TARGET.result_oids orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
ANALYZE TABLE TARGET.result_oids COMPUTE STATISTICS; COMPUTE STATS TARGET.result_oids;
create table TARGET.result_organization stored as parquet as select * from SOURCE.result_organization orig where exists (select 1 from TARGET.result r where r.id=orig.id); INSERT INTO TARGET.result_organization select * from TARGET.result_organization orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
ANALYZE TABLE TARGET.result_organization COMPUTE STATISTICS; COMPUTE STATS TARGET.result_organization;
create table TARGET.result_peerreviewed stored as parquet as select * from SOURCE.result_peerreviewed orig where exists (select 1 from TARGET.result r where r.id=orig.id); INSERT INTO TARGET.result_peerreviewed select * from TARGET.result_peerreviewed orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
ANALYZE TABLE TARGET.result_peerreviewed COMPUTE STATISTICS; COMPUTE STATS TARGET.result_peerreviewed;
create table TARGET.result_pids stored as parquet as select * from SOURCE.result_pids orig where exists (select 1 from TARGET.result r where r.id=orig.id); INSERT INTO TARGET.result_pids select * from TARGET.result_pids orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
ANALYZE TABLE TARGET.result_pids COMPUTE STATISTICS; COMPUTE STATS TARGET.result_pids;
create table TARGET.result_projectcount stored as parquet as select * from SOURCE.result_projectcount orig where exists (select 1 from TARGET.result r where r.id=orig.id); INSERT INTO TARGET.result_projectcount select * from TARGET.result_projectcount orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
ANALYZE TABLE TARGET.result_projectcount COMPUTE STATISTICS; COMPUTE STATS TARGET.result_projectcount;
create table TARGET.result_projects stored as parquet as select * from SOURCE.result_projects orig where exists (select 1 from TARGET.result r where r.id=orig.id); INSERT INTO TARGET.result_projects select * from TARGET.result_projects orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
ANALYZE TABLE TARGET.result_projects COMPUTE STATISTICS; COMPUTE STATS TARGET.result_projects;
create table TARGET.result_refereed stored as parquet as select * from SOURCE.result_refereed orig where exists (select 1 from TARGET.result r where r.id=orig.id); INSERT INTO TARGET.result_refereed select * from TARGET.result_refereed orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
ANALYZE TABLE TARGET.result_refereed COMPUTE STATISTICS; COMPUTE STATS TARGET.result_refereed;
create table TARGET.result_sources stored as parquet as select * from SOURCE.result_sources orig where exists (select 1 from TARGET.result r where r.id=orig.id); INSERT INTO TARGET.result_sources select * from TARGET.result_sources orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
ANALYZE TABLE TARGET.result_sources COMPUTE STATISTICS; COMPUTE STATS TARGET.result_sources;
create table TARGET.result_topics stored as parquet as select * from SOURCE.result_topics orig where exists (select 1 from TARGET.result r where r.id=orig.id); INSERT INTO TARGET.result_topics select * from TARGET.result_topics orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
ANALYZE TABLE TARGET.result_topics COMPUTE STATISTICS; COMPUTE STATS TARGET.result_topics;
create table TARGET.result_fos stored as parquet as select * from SOURCE.result_fos orig where exists (select 1 from TARGET.result r where r.id=orig.id); INSERT INTO TARGET.result_fos select * from TARGET.result_fos orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
ANALYZE TABLE TARGET.result_fos COMPUTE STATISTICS; COMPUTE STATS TARGET.result_fos;
create view TARGET.foo1 as select * from SOURCE.result_result rr where rr.source in (select id from TARGET.result); create view TARGET.foo1 as select * from TARGET.result_result rr where rr.source in (select id from TARGET.result_new);
create view TARGET.foo2 as select * from SOURCE.result_result rr where rr.target in (select id from TARGET.result); create view TARGET.foo2 as select * from TARGET.result_result rr where rr.target in (select id from TARGET.result_new);
create table TARGET.result_result STORED AS PARQUET as select distinct * from (select * from TARGET.foo1 union all select * from TARGET.foo2) foufou; INSERT INTO TARGET.result_result select distinct * from (select * from TARGET.foo1 union all select * from TARGET.foo2) foufou;
drop view TARGET.foo1; drop view TARGET.foo1;
drop view TARGET.foo2; drop view TARGET.foo2;
ANALYZE TABLE TARGET.result_result COMPUTE STATISTICS; COMPUTE STATS TARGET.result_result;
-- datasources
create view if not exists TARGET.datasource as select * from SOURCE.datasource;
create view if not exists TARGET.datasource_oids as select * from SOURCE.datasource_oids;
create view if not exists TARGET.datasource_organizations as select * from SOURCE.datasource_organizations;
create view if not exists TARGET.datasource_sources as select * from SOURCE.datasource_sources;
create table TARGET.datasource_results stored as parquet as select id as result, datasource as id from TARGET.result_datasources;
ANALYZE TABLE TARGET.datasource_results COMPUTE STATISTICS;
-- organizations
create view if not exists TARGET.organization as select * from SOURCE.organization;
create view if not exists TARGET.organization_datasources as select * from SOURCE.organization_datasources;
create view if not exists TARGET.organization_pids as select * from SOURCE.organization_pids;
create view if not exists TARGET.organization_projects as select * from SOURCE.organization_projects;
create view if not exists TARGET.organization_sources as select * from SOURCE.organization_sources;
-- projects
create view if not exists TARGET.project as select * from SOURCE.project;
create view if not exists TARGET.project_oids as select * from SOURCE.project_oids;
create view if not exists TARGET.project_organizations as select * from SOURCE.project_organizations;
create view if not exists TARGET.project_resultcount as select * from SOURCE.project_resultcount;
create view if not exists TARGET.project_classification as select * from SOURCE.project_classification;
create table TARGET.project_results stored as parquet as select id as result, project as id from TARGET.result_projects;
ANALYZE TABLE TARGET.project_results COMPUTE STATISTICS;
-- indicators -- indicators
-- Sprint 1 ---- -- Sprint 1 ----
create table TARGET.indi_pub_green_oa stored as parquet as select * from SOURCE.indi_pub_green_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id); INSERT INTO TARGET.indi_pub_green_oa select * from TARGET.indi_pub_green_oa orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
ANALYZE TABLE TARGET.indi_pub_green_oa COMPUTE STATISTICS; COMPUTE STATS TARGET.indi_pub_green_oa;
create table TARGET.indi_pub_grey_lit stored as parquet as select * from SOURCE.indi_pub_grey_lit orig where exists (select 1 from TARGET.result r where r.id=orig.id); INSERT INTO TARGET.indi_pub_grey_lit select * from TARGET.indi_pub_grey_lit orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
ANALYZE TABLE TARGET.indi_pub_grey_lit COMPUTE STATISTICS; COMPUTE STATS TARGET.indi_pub_grey_lit;
create table TARGET.indi_pub_doi_from_crossref stored as parquet as select * from SOURCE.indi_pub_doi_from_crossref orig where exists (select 1 from TARGET.result r where r.id=orig.id); INSERT INTO TARGET.indi_pub_doi_from_crossref select * from TARGET.indi_pub_doi_from_crossref orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
ANALYZE TABLE TARGET.indi_pub_doi_from_crossref COMPUTE STATISTICS; COMPUTE STATS TARGET.indi_pub_doi_from_crossref;
-- Sprint 2 ---- -- Sprint 2 ----
create table TARGET.indi_result_has_cc_licence stored as parquet as select * from SOURCE.indi_result_has_cc_licence orig where exists (select 1 from TARGET.result r where r.id=orig.id); INSERT INTO TARGET.indi_result_has_cc_licence select * from TARGET.indi_result_has_cc_licence orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
ANALYZE TABLE TARGET.indi_result_has_cc_licence COMPUTE STATISTICS; COMPUTE STATS TARGET.indi_result_has_cc_licence;
create table TARGET.indi_result_has_cc_licence_url stored as parquet as select * from SOURCE.indi_result_has_cc_licence_url orig where exists (select 1 from TARGET.result r where r.id=orig.id); INSERT INTO TARGET.indi_result_has_cc_licence_url select * from TARGET.indi_result_has_cc_licence_url orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
ANALYZE TABLE TARGET.indi_result_has_cc_licence_url COMPUTE STATISTICS; COMPUTE STATS TARGET.indi_result_has_cc_licence_url;
create table TARGET.indi_pub_has_abstract stored as parquet as select * from SOURCE.indi_pub_has_abstract orig where exists (select 1 from TARGET.result r where r.id=orig.id); INSERT INTO TARGET.indi_pub_has_abstract select * from TARGET.indi_pub_has_abstract orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
ANALYZE TABLE TARGET.indi_pub_has_abstract COMPUTE STATISTICS; COMPUTE STATS TARGET.indi_pub_has_abstract;
create table TARGET.indi_result_with_orcid stored as parquet as select * from SOURCE.indi_result_with_orcid orig where exists (select 1 from TARGET.result r where r.id=orig.id); INSERT INTO TARGET.indi_result_with_orcid select * from TARGET.indi_result_with_orcid orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
ANALYZE TABLE TARGET.indi_result_with_orcid COMPUTE STATISTICS; COMPUTE STATS TARGET.indi_result_with_orcid;
---- Sprint 3 ---- ---- Sprint 3 ----
create table TARGET.indi_funded_result_with_fundref stored as parquet as select * from SOURCE.indi_funded_result_with_fundref orig where exists (select 1 from TARGET.result r where r.id=orig.id); INSERT INTO TARGET.indi_funded_result_with_fundref select * from TARGET.indi_funded_result_with_fundref orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
ANALYZE TABLE TARGET.indi_funded_result_with_fundref COMPUTE STATISTICS; COMPUTE STATS TARGET.indi_funded_result_with_fundref;
create view TARGET.indi_result_org_collab as select * from SOURCE.indi_result_org_collab;
create view TARGET.indi_result_org_country_collab as select * from SOURCE.indi_result_org_country_collab;
create view TARGET.indi_project_collab_org as select * from SOURCE.indi_project_collab_org;
create view TARGET.indi_project_collab_org_country as select * from SOURCE.indi_project_collab_org_country;
create view TARGET.indi_funder_country_collab as select * from SOURCE.indi_funder_country_collab;
create view TARGET.indi_result_country_collab as select * from SOURCE.indi_result_country_collab;
---- Sprint 4 ---- ---- Sprint 4 ----
create table TARGET.indi_pub_diamond stored as parquet as select * from SOURCE.indi_pub_diamond orig where exists (select 1 from TARGET.result r where r.id=orig.id); INSERT INTO TARGET.indi_pub_diamond select * from TARGET.indi_pub_diamond orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
ANALYZE TABLE TARGET.indi_pub_diamond COMPUTE STATISTICS; COMPUTE STATS TARGET.indi_pub_diamond;
create table TARGET.indi_pub_in_transformative stored as parquet as select * from SOURCE.indi_pub_in_transformative orig where exists (select 1 from TARGET.result r where r.id=orig.id); INSERT INTO TARGET.indi_pub_in_transformative select * from TARGET.indi_pub_in_transformative orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
ANALYZE TABLE TARGET.indi_pub_in_transformative COMPUTE STATISTICS; COMPUTE STATS TARGET.indi_pub_in_transformative;
create table TARGET.indi_pub_closed_other_open stored as parquet as select * from SOURCE.indi_pub_closed_other_open orig where exists (select 1 from TARGET.result r where r.id=orig.id); INSERT INTO TARGET.indi_pub_closed_other_open select * from TARGET.indi_pub_closed_other_open orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
ANALYZE TABLE TARGET.indi_pub_closed_other_open COMPUTE STATISTICS; COMPUTE STATS TARGET.indi_pub_closed_other_open;
---- Sprint 5 ---- ---- Sprint 5 ----
create table TARGET.indi_result_no_of_copies stored as parquet as select * from SOURCE.indi_result_no_of_copies orig where exists (select 1 from TARGET.result r where r.id=orig.id); INSERT INTO TARGET.indi_result_no_of_copies select * from TARGET.indi_result_no_of_copies orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
ANALYZE TABLE TARGET.indi_result_no_of_copies COMPUTE STATISTICS; COMPUTE STATS TARGET.indi_result_no_of_copies;
---- Sprint 6 ---- ---- Sprint 6 ----
create table TARGET.indi_pub_hybrid_oa_with_cc stored as parquet as select * from SOURCE.indi_pub_hybrid_oa_with_cc orig where exists (select 1 from TARGET.result r where r.id=orig.id); INSERT INTO TARGET.indi_pub_hybrid_oa_with_cc select * from TARGET.indi_pub_hybrid_oa_with_cc orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
ANALYZE TABLE TARGET.indi_pub_hybrid_oa_with_cc COMPUTE STATISTICS; COMPUTE STATS TARGET.indi_pub_hybrid_oa_with_cc;
create table TARGET.indi_pub_downloads stored as parquet as select * from SOURCE.indi_pub_downloads orig where exists (select 1 from TARGET.result r where r.id=orig.result_id); INSERT INTO TARGET.indi_pub_downloads select * from TARGET.indi_pub_downloads orig where exists (select 1 from TARGET.result_new r where r.id=orig.result_id);
ANALYZE TABLE TARGET.indi_pub_downloads COMPUTE STATISTICS; COMPUTE STATS TARGET.indi_pub_downloads;
create table TARGET.indi_pub_downloads_datasource stored as parquet as select * from SOURCE.indi_pub_downloads_datasource orig where exists (select 1 from TARGET.result r where r.id=orig.result_id); INSERT INTO TARGET.indi_pub_downloads_datasource select * from TARGET.indi_pub_downloads_datasource orig where exists (select 1 from TARGET.result_new r where r.id=orig.result_id);
ANALYZE TABLE TARGET.indi_pub_downloads_datasource COMPUTE STATISTICS; COMPUTE STATS TARGET.indi_pub_downloads_datasource;
create table TARGET.indi_pub_downloads_year stored as parquet as select * from SOURCE.indi_pub_downloads_year orig where exists (select 1 from TARGET.result r where r.id=orig.result_id); INSERT INTO TARGET.indi_pub_downloads_year select * from TARGET.indi_pub_downloads_year orig where exists (select 1 from TARGET.result_new r where r.id=orig.result_id);
ANALYZE TABLE TARGET.indi_pub_downloads_year COMPUTE STATISTICS; COMPUTE STATS TARGET.indi_pub_downloads_year;
create table TARGET.indi_pub_downloads_datasource_year stored as parquet as select * from SOURCE.indi_pub_downloads_datasource_year orig where exists (select 1 from TARGET.result r where r.id=orig.result_id); INSERT INTO TARGET.indi_pub_downloads_datasource_year select * from TARGET.indi_pub_downloads_datasource_year orig where exists (select 1 from TARGET.result_new r where r.id=orig.result_id);
ANALYZE TABLE TARGET.indi_pub_downloads_datasource_year COMPUTE STATISTICS; COMPUTE STATS TARGET.indi_pub_downloads_datasource_year;
---- Sprint 7 ---- ---- Sprint 7 ----
create table TARGET.indi_pub_gold_oa stored as parquet as select * from SOURCE.indi_pub_gold_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id); INSERT INTO TARGET.indi_pub_gold_oa select * from TARGET.indi_pub_gold_oa orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
ANALYZE TABLE TARGET.indi_pub_gold_oa COMPUTE STATISTICS; COMPUTE STATS TARGET.indi_pub_gold_oa;
create table TARGET.indi_pub_hybrid stored as parquet as select * from SOURCE.indi_pub_hybrid orig where exists (select 1 from TARGET.result r where r.id=orig.id); INSERT INTO TARGET.indi_pub_hybrid select * from TARGET.indi_pub_hybrid orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
ANALYZE TABLE TARGET.indi_pub_hybrid COMPUTE STATISTICS; COMPUTE STATS TARGET.indi_pub_hybrid;
create view TARGET.indi_org_fairness as select * from SOURCE.indi_org_fairness;
create view TARGET.indi_org_fairness_pub_pr as select * from SOURCE.indi_org_fairness_pub_pr; INSERT INTO TARGET.indi_pub_has_preprint select * from TARGET.indi_pub_has_preprint orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
create view TARGET.indi_org_fairness_pub_year as select * from SOURCE.indi_org_fairness_pub_year; COMPUTE STATS TARGET.indi_pub_has_preprint;
create view TARGET.indi_org_fairness_pub as select * from SOURCE.indi_org_fairness_pub; INSERT INTO TARGET.indi_pub_in_subscribed select * from TARGET.indi_pub_in_subscribed orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
create view TARGET.indi_org_fairness_year as select * from SOURCE.indi_org_fairness_year; COMPUTE STATS TARGET.indi_pub_in_subscribed;
create view TARGET.indi_org_findable_year as select * from SOURCE.indi_org_findable_year; INSERT INTO TARGET.indi_result_with_pid select * from TARGET.indi_result_with_pid orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
create view TARGET.indi_org_findable as select * from SOURCE.indi_org_findable; COMPUTE STATS TARGET.indi_result_with_pid;
create view TARGET.indi_org_openess as select * from SOURCE.indi_org_openess;
create view TARGET.indi_org_openess_year as select * from SOURCE.indi_org_openess_year;
create table TARGET.indi_pub_has_preprint stored as parquet as select * from SOURCE.indi_pub_has_preprint orig where exists (select 1 from TARGET.result r where r.id=orig.id);
ANALYZE TABLE TARGET.indi_pub_has_preprint COMPUTE STATISTICS;
create table TARGET.indi_pub_in_subscribed stored as parquet as select * from SOURCE.indi_pub_in_subscribed orig where exists (select 1 from TARGET.result r where r.id=orig.id);
ANALYZE TABLE TARGET.indi_pub_in_subscribed COMPUTE STATISTICS;
create table TARGET.indi_result_with_pid stored as parquet as select * from SOURCE.indi_result_with_pid orig where exists (select 1 from TARGET.result r where r.id=orig.id);
ANALYZE TABLE TARGET.indi_result_with_pid COMPUTE STATISTICS;
--create table TARGET.indi_datasets_gold_oa stored as parquet as select * from SOURCE.indi_datasets_gold_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id); --create table TARGET.indi_datasets_gold_oa stored as parquet as select * from SOURCE.indi_datasets_gold_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id);
--compute stats TARGET.indi_datasets_gold_oa; --compute stats TARGET.indi_datasets_gold_oa;
--create table TARGET.indi_software_gold_oa stored as parquet as select * from SOURCE.indi_software_gold_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id); --create table TARGET.indi_software_gold_oa stored as parquet as select * from SOURCE.indi_software_gold_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id);
--compute stats TARGET.indi_software_gold_oa; --compute stats TARGET.indi_software_gold_oa;
DROP TABLE TARGET.result_new;

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

@ -1,4 +0,0 @@
#!/usr/bin/env bash
curl --request GET $1/cache/updateCache
sleep 6h

28
dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/workflow.xml
View File

@ -66,37 +66,9 @@
<exec>monitor.sh</exec> <exec>monitor.sh</exec>
<argument>${stats_db_name}</argument> <argument>${stats_db_name}</argument>
<argument>${monitor_db_name}</argument> <argument>${monitor_db_name}</argument>
<argument>${monitor_db_shadow_name}</argument>
<argument>${wf:appPath()}/scripts/createMonitorDB.sql</argument> <argument>${wf:appPath()}/scripts/createMonitorDB.sql</argument>
<file>monitor.sh</file> <file>monitor.sh</file>
</shell> </shell>
<ok to="Step2-createMonitorDB-post"/>
<error to="Kill"/>
</action>
<action name="Step2-createMonitorDB-post">
<shell xmlns="uri:oozie:shell-action:0.1">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<exec>monitor-post.sh</exec>
<argument>${stats_db_name}</argument>
<argument>${monitor_db_name}</argument>
<argument>${monitor_db_shadow_name}</argument>
<file>monitor-post.sh</file>
</shell>
<ok to="Step3-updateCache"/>
<error to="Kill"/>
</action>
<action name="Step3-updateCache">
<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>

3
dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql
View File

@ -60,7 +60,8 @@ create table TARGET.result stored as parquet as
'openorgs____::235d7f9ad18ecd7e6dc62ea4990cb9db', -- Bilkent University 'openorgs____::235d7f9ad18ecd7e6dc62ea4990cb9db', -- Bilkent University
'openorgs____::31f2fa9e05b49d4cf40a19c3fed8eb06', -- Saints Cyril and Methodius University of Skopje 'openorgs____::31f2fa9e05b49d4cf40a19c3fed8eb06', -- Saints Cyril and Methodius University of Skopje
'openorgs____::db7686f30f22cbe73a4fde872ce812a6', -- University of Milan 'openorgs____::db7686f30f22cbe73a4fde872ce812a6', -- University of Milan
'openorgs____::b8b8ca674452579f3f593d9f5e557483' -- University College Cork 'openorgs____::b8b8ca674452579f3f593d9f5e557483', -- University College Cork
'openorgs____::38d7097854736583dde879d12dacafca' -- Brown University
) )) foo; ) )) foo;
compute stats TARGET.result; compute stats TARGET.result;