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stats DB for monitor #99

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claudio.atzori merged 15 commits from :master into master 2021-03-03 10:29:09 +01:00
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3 changed files with 167 additions and 0 deletions
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24
dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/monitor.sh Normal file
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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
export SCRIPT_PATH=$4
echo "Getting file from " $4
hdfs dfs -copyToLocal $4
echo "Creating monitor database"
cat step21-createMonitorDB.sql | sed s/SOURCE/$1/g | sed s/TARGET/$2/g1 | impala-shell -f -
echo "Impala shell finished"
echo "Updating shadow monitor database"
impala-shell -d $3 -q "show tables" --delimited | sed 's/^/drop view if exists $3./' | sed 's/$/;/' | impala-shell -f -
impala-shell -d $2 -q "show tables" --delimited | sed 's/\(.*\)/create view $3.\1 as select * from $2.\1;/' | impala-shell -f -
echo "Shadow db ready!"

121
dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step21-createMonitorDB.sql Normal file
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drop database if exists TARGET cascade;
create database if not exists TARGET;
create view if not exists TARGET.category as select * from SOURCE.category;
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.roarmap as select * from SOURCE.roarmap;
create table TARGET.result as
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)
union all
select * from SOURCE.result r where exists (select 1 from SOURCE.result_concepts rc where rc.id=r.id) ) foo;
compute stats TARGET.result;
create table TARGET.result_affiliated_country as select * from SOURCE.result_affiliated_country rac where exists (select 1 from TARGET.result r where r.id=rac.id);
compute stats TARGET.result_affiliated_country;
create table TARGET.result_citations as select * from SOURCE.result_citations orig where exists (select 1 from TARGET.result r where r.id=orig.id);
compute stats TARGET.result_citations;
create table TARGET.result_classifications as select * from SOURCE.result_classifications orig where exists (select 1 from TARGET.result r where r.id=orig.id);
compute stats TARGET.result_classifications;
create table TARGET.result_concepts as select * from SOURCE.result_concepts orig where exists (select 1 from TARGET.result r where r.id=orig.id);
compute stats TARGET.result_concepts;
create table TARGET.result_datasources as select * from SOURCE.result_datasources orig where exists (select 1 from TARGET.result r where r.id=orig.id);
compute stats TARGET.result_datasources;
create table TARGET.result_deposited_country as select * from SOURCE.result_deposited_country orig where exists (select 1 from TARGET.result r where r.id=orig.id);
compute stats TARGET.result_deposited_country;
create table TARGET.result_fundercount as select * from SOURCE.result_fundercount orig where exists (select 1 from TARGET.result r where r.id=orig.id);
compute stats TARGET.result_fundercount;
create table TARGET.result_gold as select * from SOURCE.result_gold orig where exists (select 1 from TARGET.result r where r.id=orig.id);
compute stats TARGET.result_gold;
create table TARGET.result_greenoa as select * from SOURCE.result_greenoa orig where exists (select 1 from TARGET.result r where r.id=orig.id);
compute stats TARGET.result_greenoa;
create table TARGET.result_languages as select * from SOURCE.result_languages orig where exists (select 1 from TARGET.result r where r.id=orig.id);
compute stats TARGET.result_languages;
create table TARGET.result_licences as select * from SOURCE.result_licenses orig where exists (select 1 from TARGET.result r where r.id=orig.id);
compute stats TARGET.result_licences;
create table TARGET.result_oids as select * from SOURCE.result_oids orig where exists (select 1 from TARGET.result r where r.id=orig.id);
compute stats TARGET.result_oids;
create table TARGET.result_organization as select * from SOURCE.result_organization orig where exists (select 1 from TARGET.result r where r.id=orig.id);
compute stats TARGET.result_organization;
create table TARGET.result_peerreviewed as select * from SOURCE.result_peerreviewed orig where exists (select 1 from TARGET.result r where r.id=orig.id);
compute stats TARGET.result_peerreviewed;
create table TARGET.result_pids as select * from SOURCE.result_pids orig where exists (select 1 from TARGET.result r where r.id=orig.id);
compute stats TARGET.result_pids;
create table TARGET.result_projectcount as select * from SOURCE.result_projectcount orig where exists (select 1 from TARGET.result r where r.id=orig.id);
compute stats TARGET.result_projectcount;
create table TARGET.result_projects as select * from SOURCE.result_projects orig where exists (select 1 from TARGET.result r where r.id=orig.id);
compute stats TARGET.result_projects;
create table TARGET.result_refereed as select * from SOURCE.result_refereed orig where exists (select 1 from TARGET.result r where r.id=orig.id);
compute stats TARGET.result_refereed;
create table TARGET.result_sources as select * from SOURCE.result_sources orig where exists (select 1 from TARGET.result r where r.id=orig.id);
compute stats TARGET.result_sources;
create table TARGET.result_topics as select * from SOURCE.result_topics orig where exists (select 1 from TARGET.result r where r.id=orig.id);
compute stats TARGET.result_topics;
-- 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 as select id as result, datasource as id from TARGET.result_datasources;
compute stats TARGET.datasource_results;
-- 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 table TARGET.project_results as select id as result, project as id from TARGET.result_projects;
compute stats TARGET.project_results;
--denorm
alter table TARGET.result rename to TARGET.res_tmp;
create table TARGET.result_denorm as
select distinct r.*, rp.project, p.acronym as pacronym, p.title as ptitle, p.funder as pfunder, p.funding_lvl0 as pfunding_lvl0, rd.datasource, d.name as dname, d.type as dtype
from TARGET.res_tmp r
join TARGET.result_projects rp on rp.id=r.id
join TARGET.result_datasources rd on rd.id=r.id
join TARGET.project p on p.id=rp.project
join TARGET.datasource d on d.id=rd.datasource;
compute stats TARGET.result_denorm;
alter table TARGET.result_denorm rename to TARGET.result;
drop table TARGET.res_tmp;
--- done!

22
dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml
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@ -17,6 +17,14 @@
<name>stats_db_shadow_name</name>
<description>the name of the shadow schema</description>
</property>
<property>
<name>monitor_db_name</name>
<description>the target monitor db name</description>
</property>
<property>
<name>monitor_db_shadow_name</name>
<description>the name of the shadow monitor db</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 update.</description>
@ -303,6 +311,20 @@
<argument>${stats_tool_api_url}</argument>
<file>updateCache.sh</file>
</shell>
<ok to="step21-createMonitorDB"/>
<error to="Kill"/>
</action>
<action name="step21-createMonitorDB">
<shell xmlns="uri:oozie:shell-action:0.1">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<exec>monitor.sh</exec>
<argument>${stats-db-name}</argument>
<argument>${monitor-db-name}</argument>
<argument>${wf:appPath()}/scripts/step21-createMonitorDB.sql</argument>
<file>monitor.sh</file>
</shell>
<ok to="End"/>
<error to="Kill"/>
</action>