Bug fixes

dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/monitor-post.sh

@@ -11,11 +11,11 @@ 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 -
+#impala-shell -d ${TARGET} -q "show tables" --delimited | sed "s/\(.*\)/compute stats ${TARGET}.\1;/" | impala-shell -f -
-echo "Impala shell finished"
+#echo "Impala shell finished"
-
+#
-echo "Updating shadow monitor database"
+#echo "Updating shadow monitor database"
-impala-shell -q "create database if not exists ${SHADOW}"
+#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 ${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 -
+#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!"
+#echo "Shadow db ready!"

dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/scripts/createMonitorDB.sql

@@ -0,0 +1,149 @@
+DROP TABLE IF EXISTS TARGET.result_new;
+
+create table TARGET.result_new stored as parquet 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)
+        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 (
+--              'openorgs____::b8b8ca674452579f3f593d9f5e557483',  -- University College Cork
+             'openorgs____::38d7097854736583dde879d12dacafca'	-- Brown University
+        ) )) foo;
+
+ANALYZE TABLE TARGET.result_new COMPUTE STATISTICS;
+
+INSERT INTO TARGET.result select * from TARGET.result_new;
+
+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_citations COMPUTE STATISTICS;
+
+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_references_oc COMPUTE STATISTICS;
+
+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_citations_oc COMPUTE STATISTICS;
+
+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_classifications COMPUTE STATISTICS;
+
+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_apc COMPUTE STATISTICS;
+
+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_concepts COMPUTE STATISTICS;
+
+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_datasources COMPUTE STATISTICS;
+
+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_fundercount COMPUTE STATISTICS;
+
+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_gold COMPUTE STATISTICS;
+
+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_greenoa COMPUTE STATISTICS;
+
+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_languages COMPUTE STATISTICS;
+
+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.result_licenses COMPUTE STATISTICS;
+
+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;
+
+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;
+
+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;
+
+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;
+
+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;
+
+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;
+
+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;
+
+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;
+
+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;
+
+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;
+
+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 TARGET.result_result rr where rr.target in (select id from TARGET.result_new);
+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.foo2;
+ANALYZE TABLE TARGET.result_result COMPUTE STATISTICS;
+
+
+-- indicators
+-- Sprint 1 ----
+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;
+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;
+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;
+-- Sprint 2 ----
+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;
+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;
+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;
+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;
+---- Sprint 3 ----
+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;
+---- Sprint 4 ----
+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;
+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;
+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;
+---- Sprint 5 ----
+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;
+---- Sprint 6 ----
+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;
+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;
+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;
+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;
+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;
+---- Sprint 7 ----
+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;
+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;
+
+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);
+ANALYZE TABLE TARGET.indi_pub_has_preprint COMPUTE STATISTICS;
+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);
+ANALYZE TABLE TARGET.indi_pub_in_subscribed COMPUTE STATISTICS;
+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);
+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);
+--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);
+--compute stats TARGET.indi_software_gold_oa;
+DROP TABLE TARGET.result_new;

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

@@ -89,17 +89,5 @@
         <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"/>
-        <error to="Kill"/>
-    </action>
-
     <end name="End"/>
 </workflow-app>