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[stats wf] indicators across stats dbs & updates in the org ids #248

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dimitris.pierrakos wants to merge 1742 commits from beta into beta2master_sept_2022
pull from: beta
merge into: D-Net:beta2master_sept_2022
Conversation 3 Commits 1742 Files Changed 1525 +136 -50
7 changed files with 136 additions and 50 deletions
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Showing only changes of commit 1b79c0ee79 - Show all commits

21
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java
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@ -27,8 +27,11 @@ public class GraphCleaningFunctions extends CleaningFunctions {
public static final int ORCID_LEN = 19; public static final int ORCID_LEN = 19;
public static final String CLEANING_REGEX = "(?:\\n|\\r|\\t)"; public static final String CLEANING_REGEX = "(?:\\n|\\r|\\t)";
public static final String INVALID_AUTHOR_REGEX = ".*deactivated.*"; public static final String INVALID_AUTHOR_REGEX = ".*deactivated.*";
public static final String TITLE_FILTER_REGEX = "[.*test.*\\W\\d]";
public static final int TITLE_FILTER_RESIDUAL_LENGTH = 10; public static final String TITLE_TEST = "test";
public static final String TITLE_FILTER_REGEX = String.format("(%s)|\\W|\\d", TITLE_TEST);
public static final int TITLE_FILTER_RESIDUAL_LENGTH = 5;
public static <T extends Oaf> T fixVocabularyNames(T value) { public static <T extends Oaf> T fixVocabularyNames(T value) {
if (value instanceof Datasource) { if (value instanceof Datasource) {
@ -195,10 +198,16 @@ public class GraphCleaningFunctions extends CleaningFunctions {
final String title = sp final String title = sp
.getValue() .getValue()
.toLowerCase(); .toLowerCase();
final String residual = Unidecode final String decoded = Unidecode.decode(title);
.decode(title)
.replaceAll(TITLE_FILTER_REGEX, ""); if (StringUtils.contains(decoded, TITLE_TEST)) {
return residual.length() > TITLE_FILTER_RESIDUAL_LENGTH; return decoded
.replaceAll(TITLE_FILTER_REGEX, "")
.length() > TITLE_FILTER_RESIDUAL_LENGTH;
}
return !decoded
.replaceAll("\\W|\\d", "")
.isEmpty();
}) })
.map(GraphCleaningFunctions::cleanValue) .map(GraphCleaningFunctions::cleanValue)
.collect(Collectors.toList())); .collect(Collectors.toList()));

15
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java
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@ -8,6 +8,7 @@ import java.io.IOException;
import java.util.Collection; import java.util.Collection;
import java.util.List; import java.util.List;
import java.util.Set; import java.util.Set;
import java.util.stream.Collectors;
import java.util.stream.Stream; import java.util.stream.Stream;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
@ -137,9 +138,21 @@ public class GraphCleaningFunctionsTest {
.stream() .stream()
.anyMatch(s -> s.getValue().equals("10.1009/qwerty"))); .anyMatch(s -> s.getValue().equals("10.1009/qwerty")));
assertEquals(5, p_out.getTitle().size());
Publication p_cleaned = GraphCleaningFunctions.cleanup(p_out); Publication p_cleaned = GraphCleaningFunctions.cleanup(p_out);
assertEquals(1, p_cleaned.getTitle().size()); assertEquals(3, p_cleaned.getTitle().size());
List<String> titles = p_cleaned
.getTitle()
.stream()
.map(StructuredProperty::getValue)
.collect(Collectors.toList());
assertTrue(titles.contains("omic"));
assertTrue(
titles.contains("Optical response of strained- and unstrained-silicon cold-electron bolometers test"));
assertTrue(titles.contains("｢マキャベリ的知性と心の理論の進化論｣ リチャード・バーン， アンドリュー・ホワイトゥン 編／藤田和生， 山下博志， 友永雅巳 監訳"));
assertEquals("CLOSED", p_cleaned.getBestaccessright().getClassid()); assertEquals("CLOSED", p_cleaned.getBestaccessright().getClassid());
assertNull(p_out.getPublisher()); assertNull(p_out.getPublisher());

3
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/resolution/ResolveEntitiesTest.scala
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@ -52,8 +52,6 @@ class ResolveEntitiesTest extends Serializable {
} }
def generateUpdates(spark:SparkSession):Unit = { def generateUpdates(spark:SparkSession):Unit = {
val template = Source.fromInputStream(this.getClass.getResourceAsStream("updates")).mkString val template = Source.fromInputStream(this.getClass.getResourceAsStream("updates")).mkString
@ -152,7 +150,6 @@ class ResolveEntitiesTest extends Serializable {
val pubDS:Dataset[Result] = spark.read.text(s"$workingDir/work/resolvedGraph/publication").as[String].map(s => SparkResolveEntities.deserializeObject(s, EntityType.publication)) val pubDS:Dataset[Result] = spark.read.text(s"$workingDir/work/resolvedGraph/publication").as[String].map(s => SparkResolveEntities.deserializeObject(s, EntityType.publication))
val t = pubDS.filter(p => p.getTitle!=null && p.getSubject!=null).filter(p => p.getTitle.asScala.exists(t => t.getValue.equalsIgnoreCase("FAKETITLE"))).count() val t = pubDS.filter(p => p.getTitle!=null && p.getSubject!=null).filter(p => p.getTitle.asScala.exists(t => t.getValue.equalsIgnoreCase("FAKETITLE"))).count()

68
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json
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@ -864,7 +864,7 @@
"schemeid": "dnet:dataCite_title", "schemeid": "dnet:dataCite_title",
"schemename": "dnet:dataCite_title" "schemename": "dnet:dataCite_title"
}, },
"value": "Optical response of strained- and unstrained-silicon cold-electron bolometers" "value": "Optical response of strained- and unstrained-silicon cold-electron bolometers test"
}, },
{ {
"dataInfo": { "dataInfo": {
@ -887,6 +887,72 @@
"schemename": "dnet:dataCite_title" "schemename": "dnet:dataCite_title"
}, },
"value": "test test 123 test" "value": "test test 123 test"
},
{
"dataInfo": {
"deletedbyinference": false,
"inferenceprovenance": "",
"inferred": false,
"invisible": false,
"provenanceaction": {
"classid": "sysimport:crosswalk:datasetarchive",
"classname": "sysimport:crosswalk:datasetarchive",
"schemeid": "dnet:provenanceActions",
"schemename": "dnet:provenanceActions"
},
"trust": "0.9"
},
"qualifier": {
"classid": "main title",
"classname": "main title",
"schemeid": "dnet:dataCite_title",
"schemename": "dnet:dataCite_title"
},
"value": "omic"
},
{
"dataInfo": {
"deletedbyinference": false,
"inferenceprovenance": "",
"inferred": false,
"invisible": false,
"provenanceaction": {
"classid": "sysimport:crosswalk:datasetarchive",
"classname": "sysimport:crosswalk:datasetarchive",
"schemeid": "dnet:provenanceActions",
"schemename": "dnet:provenanceActions"
},
"trust": "0.9"
},
"qualifier": {
"classid": "main title",
"classname": "main title",
"schemeid": "dnet:dataCite_title",
"schemename": "dnet:dataCite_title"
},
"value": "｢マキャベリ的知性と心の理論の進化論｣ リチャード・バーン， アンドリュー・ホワイトゥン 編／藤田和生， 山下博志， 友永雅巳 監訳"
},
{
"dataInfo": {
"deletedbyinference": false,
"inferenceprovenance": "",
"inferred": false,
"invisible": false,
"provenanceaction": {
"classid": "sysimport:crosswalk:datasetarchive",
"classname": "sysimport:crosswalk:datasetarchive",
"schemeid": "dnet:provenanceActions",
"schemename": "dnet:provenanceActions"
},
"trust": "0.9"
},
"qualifier": {
"classid": "main title",
"classname": "main title",
"schemeid": "dnet:dataCite_title",
"schemename": "dnet:dataCite_title"
},
"value": "-"
} }
] ]
} }

6
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/resolution/dataset
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File diff suppressed because one or more lines are too long

69
dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql
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@ -11,7 +11,7 @@ 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.fundref as select * from SOURCE.fundref;
create view if not exists TARGET.rndexpenditure as select * from SOURCE.rndexpediture; create view if not exists TARGET.rndexpenditure as select * from SOURCE.rndexpediture;
create table TARGET.result as 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
@ -21,61 +21,62 @@ create table TARGET.result as
'openorgs____::759d59f05d77188faee99b7493b46805', 'openorgs____::759d59f05d77188faee99b7493b46805',
'openorgs____::b84450f9864182c67b8611b5593f4250', 'openorgs____::b84450f9864182c67b8611b5593f4250',
'openorgs____::d41cf6bd4ab1b1362a44397e0b95c975', 'openorgs____::d41cf6bd4ab1b1362a44397e0b95c975',
'openorgs____::eadc8da90a546e98c03f896661a2e4d4') )) foo; 'openorgs____::eadc8da90a546e98c03f896661a2e4d4',
'openorgs____::d2a09b9d5eabb10c95f9470e172d05d2') )) foo;
compute stats TARGET.result; compute stats TARGET.result;
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); 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);
compute stats TARGET.result_citations; 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); 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);
compute stats TARGET.result_classifications; 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); 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);
compute stats TARGET.result_concepts; 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); 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);
compute stats TARGET.result_datasources; compute stats TARGET.result_datasources;
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); 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);
compute stats TARGET.result_fundercount; 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); 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);
compute stats TARGET.result_gold; 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); 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);
compute stats TARGET.result_greenoa; 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); 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);
compute stats TARGET.result_languages; 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); create table TARGET.result_licences stored as parquet 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; 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); 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);
compute stats TARGET.result_oids; 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); 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);
compute stats TARGET.result_organization; 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); 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);
compute stats TARGET.result_peerreviewed; 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); 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);
compute stats TARGET.result_pids; 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); 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);
compute stats TARGET.result_projectcount; 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); 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);
compute stats TARGET.result_projects; 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); 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);
compute stats TARGET.result_refereed; 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); 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);
compute stats TARGET.result_sources; 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); 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);
compute stats TARGET.result_topics; compute stats TARGET.result_topics;
-- datasources -- datasources
@ -84,7 +85,7 @@ create view if not exists TARGET.datasource_oids as select * from SOURCE.datasou
create view if not exists TARGET.datasource_organizations as select * from SOURCE.datasource_organizations; 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 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; create table TARGET.datasource_results stored as parquet as select id as result, datasource as id from TARGET.result_datasources;
compute stats TARGET.datasource_results; compute stats TARGET.datasource_results;
-- organizations -- organizations
@ -100,7 +101,7 @@ create view if not exists TARGET.project_oids as select * from SOURCE.project_oi
create view if not exists TARGET.project_organizations as select * from SOURCE.project_organizations; 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_resultcount as select * from SOURCE.project_resultcount;
create table TARGET.project_results as select id as result, project as id from TARGET.result_projects; create table TARGET.project_results stored as parquet as select id as result, project as id from TARGET.result_projects;
compute stats TARGET.project_results; compute stats TARGET.project_results;
-- indicators -- indicators
@ -121,19 +122,19 @@ create view TARGET.indi_pub_avg_year_content_oa as select * from SOURCE.indi_pub
create view TARGET.indi_pub_avg_year_context_oa as select * from SOURCE.indi_pub_avg_year_context_oa orig; create view TARGET.indi_pub_avg_year_context_oa as select * from SOURCE.indi_pub_avg_year_context_oa orig;
create view TARGET.indi_pub_avg_year_country_oa as select * from SOURCE.indi_pub_avg_year_country_oa orig; create view TARGET.indi_pub_avg_year_country_oa as select * from SOURCE.indi_pub_avg_year_country_oa orig;
create table TARGET.indi_pub_green_oa as select * from SOURCE.indi_pub_green_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id); 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);
compute stats TARGET.indi_pub_green_oa; compute stats TARGET.indi_pub_green_oa;
create table TARGET.indi_pub_grey_lit as select * from SOURCE.indi_pub_grey_lit orig where exists (select 1 from TARGET.result r where r.id=orig.id); 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);
compute stats TARGET.indi_pub_grey_lit; compute stats TARGET.indi_pub_grey_lit;
create table TARGET.indi_pub_doi_from_crossref as select * from SOURCE.indi_pub_doi_from_crossref orig where exists (select 1 from TARGET.result r where r.id=orig.id); 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);
compute stats TARGET.indi_pub_doi_from_crossref; compute stats TARGET.indi_pub_doi_from_crossref;
create table TARGET.indi_pub_gold_oa as select * from SOURCE.indi_pub_gold_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id); 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);
compute stats TARGET.indi_pub_gold_oa; compute stats TARGET.indi_pub_gold_oa;
create table TARGET.indi_pub_has_abstract as select * from SOURCE.indi_pub_has_abstract orig where exists (select 1 from TARGET.result r where r.id=orig.id); 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);
compute stats TARGET.indi_pub_has_abstract; compute stats TARGET.indi_pub_has_abstract;
create table TARGET.indi_pub_has_cc_licence as select * from SOURCE.indi_pub_has_cc_licence orig where exists (select 1 from TARGET.result r where r.id=orig.id); create table TARGET.indi_pub_has_cc_licence stored as parquet as select * from SOURCE.indi_pub_has_cc_licence orig where exists (select 1 from TARGET.result r where r.id=orig.id);
compute stats TARGET.indi_pub_has_cc_licence; compute stats TARGET.indi_pub_has_cc_licence;
create table TARGET.indi_pub_has_cc_licence_url as select * from SOURCE.indi_pub_has_cc_licence_url orig where exists (select 1 from TARGET.result r where r.id=orig.id); create table TARGET.indi_pub_has_cc_licence_url stored as parquet as select * from SOURCE.indi_pub_has_cc_licence_url orig where exists (select 1 from TARGET.result r where r.id=orig.id);
compute stats TARGET.indi_pub_has_cc_licence_url; compute stats TARGET.indi_pub_has_cc_licence_url;
create view TARGET.indi_software_avg_year_content_oa as select * from SOURCE.indi_software_avg_year_content_oa orig; create view TARGET.indi_software_avg_year_content_oa as select * from SOURCE.indi_software_avg_year_content_oa orig;
@ -143,13 +144,13 @@ create view TARGET.indi_software_avg_year_country_oa as select * from SOURCE.ind
--denorm --denorm
alter table TARGET.result rename to TARGET.res_tmp; alter table TARGET.result rename to TARGET.res_tmp;
create table TARGET.result_denorm as create table TARGET.result_denorm stored as parquet 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 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 from TARGET.res_tmp r
join TARGET.result_projects rp on rp.id=r.id left outer join TARGET.result_projects rp on rp.id=r.id
join TARGET.result_datasources rd on rd.id=r.id left outer join TARGET.result_datasources rd on rd.id=r.id
join TARGET.project p on p.id=rp.project left outer join TARGET.project p on p.id=rp.project
join TARGET.datasource d on d.id=rd.datasource; left outer join TARGET.datasource d on d.id=rd.datasource;
compute stats TARGET.result_denorm; compute stats TARGET.result_denorm;
alter table TARGET.result_denorm rename to TARGET.result; alter table TARGET.result_denorm rename to TARGET.result;

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

@ -126,7 +126,7 @@ FROM ${stats_db_name}.otherresearchproduct_topics;
CREATE TABLE ${stats_db_name}.result_organization AS CREATE TABLE ${stats_db_name}.result_organization AS
SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS organization SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS organization
FROM ${openaire_db_name}.relation r FROM ${openaire_db_name}.relation r
WHERE r.reltype = 'resultOrganization' and r.relclass='hasAuthorInstitution' and r.subreltype='affiliation' WHERE r.reltype = 'resultOrganization'
and r.datainfo.deletedbyinference = false; and r.datainfo.deletedbyinference = false;
CREATE TABLE ${stats_db_name}.result_projects AS CREATE TABLE ${stats_db_name}.result_projects AS