From 34172455d1057f947d299a9d8799684fce6991db Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 24 May 2023 09:56:23 +0200 Subject: [PATCH 01/12] [BulkTag] Adding remove constraints to specify when a community must not appear in the context of a result. --- .../dhp/bulktag/community/Community.java | 9 + .../community/CommunityConfiguration.java | 15 + .../CommunityConfigurationFactory.java | 14 + .../dhp/bulktag/community/ResultTagger.java | 23 +- .../resources/eu/dnetlib/dhp/bulktag/query.xq | 3 + .../dnetlib/dhp/bulktag/BulkTagJobTest.java | 49 +- .../tagging_conf_remove.xml | 1555 +++++++++++++++++ .../dataset_10.json | 4 +- 8 files changed, 1665 insertions(+), 7 deletions(-) create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf_remove.xml diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Community.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Community.java index c218b0c2bf..b44376e225 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Community.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Community.java @@ -15,6 +15,7 @@ public class Community implements Serializable { private List providers = new ArrayList<>(); private List zenodoCommunities = new ArrayList<>(); private SelectionConstraints constraints = new SelectionConstraints(); + private SelectionConstraints removeConstraints = new SelectionConstraints(); public String toJson() { final Gson g = new Gson(); @@ -67,4 +68,12 @@ public class Community implements Serializable { public void setConstraints(SelectionConstraints constraints) { this.constraints = constraints; } + + public SelectionConstraints getRemoveConstraints() { + return removeConstraints; + } + + public void setRemoveConstraints(SelectionConstraints removeConstraints) { + this.removeConstraints = removeConstraints; + } } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfiguration.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfiguration.java index a30e1cbbb7..6896288694 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfiguration.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfiguration.java @@ -28,6 +28,8 @@ public class CommunityConfiguration implements Serializable { private Map selectionConstraintsMap = new HashMap<>(); // map eosc datasource -> communityid private Map>> eoscDatasourceMap = new HashMap<>(); + //map communityid -> remove constraints + private Map removeConstraintsMap = new HashMap<>(); public Map>> getEoscDatasourceMap() { return eoscDatasourceMap; @@ -71,6 +73,14 @@ public class CommunityConfiguration implements Serializable { this.selectionConstraintsMap = selectionConstraintsMap; } + public Map getRemoveConstraintsMap() { + return removeConstraintsMap; + } + + public void setRemoveConstraintsMap(Map removeConstraintsMap) { + this.removeConstraintsMap = removeConstraintsMap; + } + CommunityConfiguration(final Map communities) { this.communities = communities; init(); @@ -90,6 +100,9 @@ public class CommunityConfiguration implements Serializable { if (selectionConstraintsMap == null) { selectionConstraintsMap = Maps.newHashMap(); } + if (removeConstraintsMap == null) { + removeConstraintsMap = Maps.newHashMap(); + } for (Community c : getCommunities().values()) { // get subjects @@ -111,6 +124,8 @@ public class CommunityConfiguration implements Serializable { zenodocommunityMap); } selectionConstraintsMap.put(id, c.getConstraints()); + + removeConstraintsMap.put(id, c.getRemoveConstraints()); } } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfigurationFactory.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfigurationFactory.java index da144fb7bb..695bbc3637 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfigurationFactory.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfigurationFactory.java @@ -86,6 +86,7 @@ public class CommunityConfigurationFactory { c.setProviders(parseDatasources(node)); c.setZenodoCommunities(parseZenodoCommunities(node)); c.setConstraints(parseConstrains(node)); + c.setRemoveConstraints(parseRemoveConstrains(node)); return c; } @@ -102,6 +103,19 @@ public class CommunityConfigurationFactory { return selectionConstraints; } + private static SelectionConstraints parseRemoveConstrains(Node node) { + Node constsNode = node.selectSingleNode("./removeConstraints"); + if (constsNode == null || StringUtils.isBlank(StringUtils.trim(constsNode.getText()))) { + return new SelectionConstraints(); + } + SelectionConstraints selectionConstraints = new Gson() + .fromJson(constsNode.getText(), SelectionConstraints.class); + + selectionConstraints.setSelection(resolver); + log.info("number of selection constraints set " + selectionConstraints.getCriteria().size()); + return selectionConstraints; + } + private static List parseSubjects(final Node node) { final List subjects = Lists.newArrayList(); diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java index 3f0954f385..0be2f59a95 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java @@ -79,6 +79,23 @@ public class ResultTagger implements Serializable { break; } + // communities contains all the communities to be not added to the context + final Set removeCommunities = new HashSet<>(); + + conf + .getRemoveConstraintsMap() + .keySet() + .forEach(communityId -> { + if (conf.getRemoveConstraintsMap().get(communityId).getCriteria() != null && + conf + .getRemoveConstraintsMap() + .get(communityId) + .getCriteria() + .stream() + .anyMatch(crit -> crit.verifyCriteria(param))) + removeCommunities.add(communityId); + }); + // communities contains all the communities to be added as context for the result final Set communities = new HashSet<>(); @@ -164,7 +181,8 @@ public class ResultTagger implements Serializable { .getSelectionConstraintsMap() .keySet() .forEach(communityId -> { - if (conf.getSelectionConstraintsMap().get(communityId).getCriteria() != null && + if (!removeCommunities.contains(communityId) && + conf.getSelectionConstraintsMap().get(communityId).getCriteria() != null && conf .getSelectionConstraintsMap() .get(communityId) @@ -175,6 +193,9 @@ public class ResultTagger implements Serializable { }); communities.addAll(aconstraints); + + communities.removeAll(removeCommunities); + if (aconstraints.size() > 0) log.info("Found {} for advancedConstraints ", aconstraints.size()); diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/query.xq b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/query.xq index a9c0d9e3f1..052037efbd 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/query.xq +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/query.xq @@ -10,6 +10,9 @@ where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] and $x//con return { $x//CONFIGURATION/context/@id} + +{$x//CONFIGURATION/context/param[./@name='removeConstraints']/text() } + {$x//CONFIGURATION/context/param[./@name='advancedConstraints']/text() } diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java index 4432210f1d..aff5ee5fbf 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java @@ -39,8 +39,10 @@ public class BulkTagJobTest { + " \"contributor\" : \"$['contributor'][*]['value']\"," + " \"description\" : \"$['description'][*]['value']\", " + " \"subject\" :\"$['subject'][*]['value']\" , " + - "\"fos\" : \"$['subject'][?(@['qualifier']['classid']=='FOS')].value\"" + - "} "; + "\"fos\" : \"$['subject'][?(@['qualifier']['classid']=='FOS')].value\"," + + "\"sdg\" : \"$['subject'][?(@['qualifier']['classid']=='SDG')].value\"," + + "\"hostedby\" : \"$['instance'][*]['hostedby']['key']\" , " + + "\"collectedfrom\" : \"$['instance'][*]['collectedfrom']['key']\"} "; private static SparkSession spark; @@ -56,7 +58,7 @@ public class BulkTagJobTest { .toString( BulkTagJobTest.class .getResourceAsStream( - "/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf_dth.xml")); + "/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf_remove.xml")); } catch (IOException e) { e.printStackTrace(); } @@ -1525,4 +1527,43 @@ public class BulkTagJobTest { .count()); } -} + + @Test + void removeTest() throws Exception { + final String pathMap = BulkTagJobTest.pathMap; + SparkBulkTagJob + .main( + new String[]{ + "-isTest", Boolean.TRUE.toString(), + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", + getClass().getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/update_datasourcewithconstraints").getPath(), + "-taggingConf", taggingConf, + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset", + "-outputPath", workingDir.toString() + "/dataset", + "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, + "-pathMap", pathMap + }); + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/dataset") + .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); + + Assertions.assertEquals(12, tmp.count()); + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(Dataset.class)); + + verificationDataset.createOrReplaceTempView("dataset"); + String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name " + + "from dataset " + + "lateral view explode(context) c as MyT " + + "lateral view explode(MyT.datainfo) d as MyD " + + "where MyD.inferenceprovenance = 'bulktagging'"; + + org.apache.spark.sql.Dataset idExplodeCommunity = spark.sql(query); + + idExplodeCommunity.show(false); + } + + } diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf_remove.xml b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf_remove.xml new file mode 100644 index 0000000000..edd6c7e0af --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf_remove.xml @@ -0,0 +1,1555 @@ + + + + + + + zenodo + + + + + + + + + + + + + + + + + + + + + + re3data_____::a507cdacc5bbcc08761c92185dee5cab + + + + + + + + + + + + rda + + + + + + + + SDG13 - Climate action + SDG8 - Decent work and economic growth + SDG15 - Life on land + SDG2 - Zero hunger + SDG17 - Partnerships for the goals + SDG10 - Reduced inequalities + SDG5 - Gender equality + SDG12 - Responsible consumption and production + SDG14 - Life below water + SDG6 - Clean water and sanitation + SDG11 - Sustainable cities and communities + SDG1 - No poverty + SDG3 - Good health and well being + SDG7 - Affordable and clean energy + SDG4 - Quality education + SDG9 - Industry innovation and infrastructure + SDG16 - Peace justice and strong institutions + + + + + + + + modern art + monuments + europeana data model + sites + field walking + frescoes + LIDO metadata schema + art history + excavation + Arts and Humanities General + cities + coins + temples + numismatics + lithics + roads + environmental archaeology + digital cultural heritage + archaeological reports + history + CRMba + churches + cultural heritage + archaeological stratigraphy + religious art + buidings + digital humanities + survey + archaeological sites + linguistic studies + bioarchaeology + architectural orders + palaeoanthropology + fine arts + europeana + CIDOC CRM + decorations + classic art + stratigraphy + digital archaeology + intangible cultural heritage + walls + humanities + chapels + CRMtex + Language and Literature + paintings + archaeology + fair data + mosaics + burials + architecture + medieval art + castles + CARARE metadata schema + statues + natural language processing + inscriptions + CRMsci + vaults + contemporary art + Arts and Humanities + CRMarchaeo + pottery + site + architectural + vessels + + + + re3data_____::9ebe127e5f3a0bf401875690f3bb6b81 + + + + doajarticles::c6cd4b532e12868c1d760a8d7cda6815 + + + + doajarticles::a6de4499bb87bf3c01add0a9e2c9ed0b + + + + doajarticles::6eb31d13b12bc06bbac06aef63cf33c9 + + + + doajarticles::0da84e9dfdc8419576169e027baa8028 + + + + re3data_____::84e123776089ce3c7a33db98d9cd15a8 + + + + openaire____::c5502a43e76feab55dd00cf50f519125 + + + + re3data_____::a48f09c562b247a9919acfe195549b47 + + + + opendoar____::97275a23ca44226c9964043c8462be96 + + + + + + storm + + + + crosscult + + + + wholodance_eu + + + + digcur2013 + + + + gravitate + + + + dipp2014 + + + + digitalhumanities + + + + dimpo + + + + adho + + + + chc + + + + wahr + + + + ibe + + + + ariadne + + + + parthenos-hub + + + + parthenos-training + + + + gandhara + + + + cmsouthasia + + + + nilgirihills + + + + shamsa_mustecio + + + + bodhgaya + + + + oac_dh-ch + + + + 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{"verb":"not_contains_caseinsensitive","field":"subject","value":"marine"}, + {"verb":"not_contains_caseinsensitive","field":"subject","value":"avionics"}, + {"verb":"not_contains_caseinsensitive","field":"subject","value":"battery"} + ]}, + {"constraint":[ + {"verb":"contains_caseinsensitive","field":"title","value":"Human Digital Twins"} + ]}, + {"constraint":[ + {"verb":"contains_caseinsensitive","field":"description","value":"Human Digital Twins"} + ]}, + {"constraint":[ + {"verb":"equals_caseinsensitive","field":"subject","value":"Human Digital Twins"} + ]}, + {"constraint":[ + {"verb":"contains_caseinsensitive","field":"title","value":"Virtual Human Twin"} + ]}, + {"constraint":[ + {"verb":"contains_caseinsensitive","field":"description","value":"Virtual Human Twin"} + ]}, + {"constraint":[ + {"verb":"equals_caseinsensitive","field":"subject","value":"Virtual Human Twin"} + ]}, + {"constraint":[ + {"verb":"equals_caseinsensitive","field":"subject","value":"digital twin"}, + 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El formato es al estilo inglés, similar al de la Oxford Union, donde algunos jóvenes se reunían a debatir sobre temas de la más candente actualidad y polemizaban con la intención de formarse en tan valoradas habilidades.\n\nLa Liga de Debate CICAE-UCJC es una ocasión única para los alumnos de ponerse en contacto con herramientas tan útiles como la oratoria y la comunicación efectiva. Pero, sobre todo, una oportunidad de fomentar el pensamiento crítico y la socialización entre alumnos con espíritu emprendedor. La Liga de Debate CICAE - Universidad Camilo José Cela se diferencia del resto de torneos en que potenciamos que sea eminentemente formativa. Alumnos y profesores reciben formación en comunicación, oratoria y debate por parte de alguno de los expertos en debate españoles más reconocidos en la escena internacional.\n\nDatos de la III Liga de Debate CICAE - UCJC http://ligacicae.ucjc.edu/","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2018-10-23","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":null,"embargoenddate":null,"source":[],"fulltext":[],"format":[],"contributor":[{"value":"Universidad 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"dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "value": "Routledge"}, "eoscifguidelines": [], "language": {"classid": "eng", "classname": "English", "schemeid": "dnet:languages", "schemename": "dnet:languages"}, "resulttype": {"classid": "publication", "classname": "publication", "schemeid": "dnet:result_typologies", "schemename": "dnet:result_typologies"}, "country": [{"classid": "QA", "classname": "Qatar", "dataInfo": {"provenanceaction": {"classid": "country:instrepos", "classname": "Inferred by OpenAIRE", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": "propagation", "invisible": false, "trust": "0.85"}, "schemeid": "dnet:countries", "schemename": "dnet:countries"}], "extraInfo": [], "originalId": ["50|od______1664::602656670df91ab0bcaa3cef70797101", "oai:qspace.qu.edu.qa:10576/17266"], "source": [], "dateofacceptance": {"dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "value": "2020-12-01"}, "title": [{"dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "qualifier": {"classid": "main title", "classname": "main title", "schemeid": "dnet:dataCite_title", "schemename": "dnet:dataCite_title"}, "value": "Human digital thought clones: the Holy Grail of artificial intelligence for big data"}]} \ No newline at end of file From 9567c13bc37d8c32c0b8b5763206b502c12ea02c Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 24 May 2023 16:20:05 +0200 Subject: [PATCH 02/12] refactoring --- .../community/CommunityConfiguration.java | 2 +- .../CommunityConfigurationFactory.java | 2 +- .../dhp/bulktag/community/ResultTagger.java | 26 +++++----- .../dnetlib/dhp/bulktag/BulkTagJobTest.java | 47 ++++++++++--------- 4 files changed, 39 insertions(+), 38 deletions(-) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfiguration.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfiguration.java index 6896288694..e061ccd5ea 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfiguration.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfiguration.java @@ -28,7 +28,7 @@ public class CommunityConfiguration implements Serializable { private Map selectionConstraintsMap = new HashMap<>(); // map eosc datasource -> communityid private Map>> eoscDatasourceMap = new HashMap<>(); - //map communityid -> remove constraints + // map communityid -> remove constraints private Map removeConstraintsMap = new HashMap<>(); public Map>> getEoscDatasourceMap() { diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfigurationFactory.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfigurationFactory.java index 695bbc3637..7b9e03ef60 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfigurationFactory.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfigurationFactory.java @@ -109,7 +109,7 @@ public class CommunityConfigurationFactory { return new SelectionConstraints(); } SelectionConstraints selectionConstraints = new Gson() - .fromJson(constsNode.getText(), SelectionConstraints.class); + .fromJson(constsNode.getText(), SelectionConstraints.class); selectionConstraints.setSelection(resolver); log.info("number of selection constraints set " + selectionConstraints.getCriteria().size()); diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java index 0be2f59a95..5f62c10f4b 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java @@ -83,18 +83,18 @@ public class ResultTagger implements Serializable { final Set removeCommunities = new HashSet<>(); conf - .getRemoveConstraintsMap() - .keySet() - .forEach(communityId -> { - if (conf.getRemoveConstraintsMap().get(communityId).getCriteria() != null && - conf - .getRemoveConstraintsMap() - .get(communityId) - .getCriteria() - .stream() - .anyMatch(crit -> crit.verifyCriteria(param))) - removeCommunities.add(communityId); - }); + .getRemoveConstraintsMap() + .keySet() + .forEach(communityId -> { + if (conf.getRemoveConstraintsMap().get(communityId).getCriteria() != null && + conf + .getRemoveConstraintsMap() + .get(communityId) + .getCriteria() + .stream() + .anyMatch(crit -> crit.verifyCriteria(param))) + removeCommunities.add(communityId); + }); // communities contains all the communities to be added as context for the result final Set communities = new HashSet<>(); @@ -182,7 +182,7 @@ public class ResultTagger implements Serializable { .keySet() .forEach(communityId -> { if (!removeCommunities.contains(communityId) && - conf.getSelectionConstraintsMap().get(communityId).getCriteria() != null && + conf.getSelectionConstraintsMap().get(communityId).getCriteria() != null && conf .getSelectionConstraintsMap() .get(communityId) diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java index aff5ee5fbf..a63e624712 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java @@ -40,9 +40,9 @@ public class BulkTagJobTest { + " \"description\" : \"$['description'][*]['value']\", " + " \"subject\" :\"$['subject'][*]['value']\" , " + "\"fos\" : \"$['subject'][?(@['qualifier']['classid']=='FOS')].value\"," + - "\"sdg\" : \"$['subject'][?(@['qualifier']['classid']=='SDG')].value\"," + + "\"sdg\" : \"$['subject'][?(@['qualifier']['classid']=='SDG')].value\"," + "\"hostedby\" : \"$['instance'][*]['hostedby']['key']\" , " + - "\"collectedfrom\" : \"$['instance'][*]['collectedfrom']['key']\"} "; + "\"collectedfrom\" : \"$['instance'][*]['collectedfrom']['key']\"} "; private static SparkSession spark; @@ -1527,43 +1527,44 @@ public class BulkTagJobTest { .count()); } - @Test void removeTest() throws Exception { final String pathMap = BulkTagJobTest.pathMap; SparkBulkTagJob - .main( - new String[]{ - "-isTest", Boolean.TRUE.toString(), - "-isSparkSessionManaged", Boolean.FALSE.toString(), - "-sourcePath", - getClass().getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/update_datasourcewithconstraints").getPath(), - "-taggingConf", taggingConf, - "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset", - "-outputPath", workingDir.toString() + "/dataset", - "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, - "-pathMap", pathMap - }); + .main( + new String[] { + "-isTest", Boolean.TRUE.toString(), + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", + getClass() + .getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/update_datasourcewithconstraints") + .getPath(), + "-taggingConf", taggingConf, + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset", + "-outputPath", workingDir.toString() + "/dataset", + "-isLookUpUrl", MOCK_IS_LOOK_UP_URL, + "-pathMap", pathMap + }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/dataset") - .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); + .textFile(workingDir.toString() + "/dataset") + .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); Assertions.assertEquals(12, tmp.count()); org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(Dataset.class)); + .createDataset(tmp.rdd(), Encoders.bean(Dataset.class)); verificationDataset.createOrReplaceTempView("dataset"); String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name " - + "from dataset " - + "lateral view explode(context) c as MyT " - + "lateral view explode(MyT.datainfo) d as MyD " - + "where MyD.inferenceprovenance = 'bulktagging'"; + + "from dataset " + + "lateral view explode(context) c as MyT " + + "lateral view explode(MyT.datainfo) d as MyD " + + "where MyD.inferenceprovenance = 'bulktagging'"; org.apache.spark.sql.Dataset idExplodeCommunity = spark.sql(query); idExplodeCommunity.show(false); } - } +} From 9097e718533da9f38fda55efd56aa4b99e2d34fa Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 24 May 2023 16:30:53 +0200 Subject: [PATCH 03/12] Added assertion in test --- .../src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java index a63e624712..2997315201 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java @@ -1564,7 +1564,8 @@ public class BulkTagJobTest { org.apache.spark.sql.Dataset idExplodeCommunity = spark.sql(query); - idExplodeCommunity.show(false); + Assertions.assertEquals(3, idExplodeCommunity.filter("community = 'dth'").count()); + } } From d6102dd576c78b1f823262344bdb520493184d4f Mon Sep 17 00:00:00 2001 From: dimitrispie Date: Thu, 25 May 2023 14:52:34 +0300 Subject: [PATCH 04/12] Update step16-createIndicatorsTables.sql - Add org names to indi_project_collab_org - Add indi_pub_bronze_oa - Changes to indi_pub_hybrid_oa_with_cc --- .../scripts/step16-createIndicatorsTables.sql | 51 ++++++++++++++++--- 1 file changed, 45 insertions(+), 6 deletions(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql index 4fd941e5da..7e560684bf 100755 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql @@ -119,12 +119,16 @@ drop table tmp purge; ANALYZE TABLE indi_result_org_country_collab COMPUTE STATISTICS; +create TEMPORARY TABLE AS +select o.id organization, o.name, ro.project as project from organization o + join organization_projects ro on o.id=ro.id; + create table if not exists indi_project_collab_org stored as parquet as -select o1.id org1,o2.id org2, count(distinct o1.project) as collaborations -from organization_projects as o1 - join organization_projects as o2 on o1.project=o2.project -where o1.id!=o2.id -group by o1.id, o2.id; +select o1.organization org1,o1.name orgname1, o2.organization org2, o2.name orgname2, count(distinct o1.project) as collaborations +from tmp as o1 + join tmp as o2 on o1.project=o2.project +where o1.organization<>o2.organization and o1.name<>o2.name +group by o1.name,o2.name, o1.organization, o2.organization; ANALYZE TABLE indi_project_collab_org COMPUTE STATISTICS; @@ -245,10 +249,45 @@ FROM publication_datasources pd 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 - where cc.has_cc_license=1) tmp on pd.id=tmp.id; + JOIN indi_pub_gold_oa ga on pd.id=ga.id + where cc.has_cc_license=1 and ga.is_gold=0) tmp on pd.id=tmp.id; 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_downloads stored as parquet as SELECT result_id, sum(downloads) no_downloads from openaire_prod_usage_stats.usage_stats join publication on result_id=id From ebe586b1d14a8f49c01354fe09b496e7cb206c44 Mon Sep 17 00:00:00 2001 From: dimitrispie Date: Fri, 26 May 2023 10:25:28 +0300 Subject: [PATCH 05/12] Impact indicators/Unpaywall - Added Impact indicators - Added unpaywall open access colours --- .../oa/graph/stats/oozie_app/scripts/step14.sql | 6 +++++- .../scripts/step16-createIndicatorsTables.sql | 8 ++++++++ .../oozie_app/scripts/step20-createMonitorDB.sql | 16 +++++++++++++--- 3 files changed, 26 insertions(+), 4 deletions(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql index 47a6f84c26..dc9e6c1f9a 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql @@ -46,4 +46,8 @@ FROM ( LEFT OUTER JOIN ( SELECT substr(d.id, 4) id from ${openaire_db_name}.datasource d - WHERE d.datainfo.deletedbyinference=false and d.datainfo.invisible = FALSE) d on o.datasource = d.id; \ No newline at end of file + 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 +lateral view explode (instance.accessright.openaccessroute) openaccessroute as accessroute; diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql index 7e560684bf..ef573916f4 100755 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql @@ -772,3 +772,11 @@ from result p on p.id= tmp.id; 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; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql index bc72b6c15d..86b5c7ca11 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql @@ -64,9 +64,12 @@ create table TARGET.result stored as parquet as 'openorgs____::38d7097854736583dde879d12dacafca' -- Brown University 'openorgs____::57784c9e047e826fefdb1ef816120d92', --Arts et Métiers ParisTech 'openorgs____::2530baca8a15936ba2e3297f2bce2e7e', -- University of Cape Town - 'openorgs____::d11f981828c485cd23d93f7f24f24db1', -- Technological University Dublin - 'openorgs____::5e6bf8962665cdd040341171e5c631d8', -- Delft University of Technology - 'openorgs____::846cb428d3f52a445f7275561a7beb5d' -- University of Manitoba + 'openorgs____::d11f981828c485cd23d93f7f24f24db1', -- Technological University Dublin + 'openorgs____::5e6bf8962665cdd040341171e5c631d8', -- Delft University of Technology + 'openorgs____::846cb428d3f52a445f7275561a7beb5d', -- University of Manitoba + 'openorgs____::eb391317ed0dc684aa81ac16265de041', -- Universitat Rovira i Virgili + 'openorgs____::66aa9fc2fceb271423dfabcc38752dc0', -- Lund University + 'openorgs____::3cff625a4370d51e08624cc586138b2f' -- IMT Atlantique ) )) foo; ANALYZE TABLE TARGET.result COMPUTE STATISTICS; @@ -140,6 +143,9 @@ ANALYZE TABLE TARGET.result_topics COMPUTE STATISTICS; 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); ANALYZE TABLE TARGET.result_fos COMPUTE STATISTICS; +create table TARGET.result_accessroute stored as parquet as select * from SOURCE.result_accessroute orig where exists (select 1 from TARGET.result r where r.id=orig.id); +ANALYZE TABLE TARGET.result_accessroute COMPUTE STATISTICS; + create view TARGET.foo1 as select * from SOURCE.result_result rr where rr.source in (select id from TARGET.result); create view TARGET.foo2 as select * from SOURCE.result_result rr where rr.target in (select id from TARGET.result); create table TARGET.result_result STORED AS PARQUET as select distinct * from (select * from TARGET.foo1 union all select * from TARGET.foo2) foufou; @@ -213,6 +219,8 @@ ANALYZE TABLE TARGET.indi_result_no_of_copies COMPUTE STATISTICS; ---- 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); ANALYZE TABLE TARGET.indi_pub_hybrid_oa_with_cc COMPUTE STATISTICS; +create table TARGET.indi_pub_bronze_oa stored as parquet as select * from SOURCE.indi_pub_bronze_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id); +ANALYZE TABLE TARGET.indi_pub_bronze_oa COMPUTE STATISTICS; 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); ANALYZE TABLE TARGET.indi_pub_downloads COMPUTE STATISTICS; 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); @@ -241,3 +249,5 @@ create table TARGET.indi_pub_in_subscribed stored as parquet as select * from SO 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_impact_measures stored as parquet as select * from SOURCE.indi_impact_measures orig where exists (select 1 from TARGET.result r where r.id=orig.id); +ANALYZE TABLE TARGET.indi_impact_measures COMPUTE STATISTICS; From e45777e7e12256669ce541ad50b6820c0d945cec Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Fri, 26 May 2023 11:33:42 +0200 Subject: [PATCH 06/12] [aggregator graph] added validation for URLs mapped from oaf:fulltext --- .../raw/AbstractMdRecordToOafMapper.java | 20 ++++++++++++------- .../dhp/oa/graph/raw/OafToOafMapper.java | 8 +++++++- .../dhp/oa/graph/raw/OdfToOafMapper.java | 7 ++++++- .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 19 ++++++++++-------- pom.xml | 2 +- 5 files changed, 38 insertions(+), 18 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index 504c9dd4c9..efb860d44d 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -5,8 +5,6 @@ import static eu.dnetlib.dhp.schema.common.ModelConstants.*; import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.*; import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.createOpenaireId; -import java.net.MalformedURLException; -import java.net.URL; import java.util.*; import java.util.stream.Collectors; @@ -17,7 +15,6 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; import com.google.common.collect.Lists; -import com.google.common.collect.Maps; import com.google.common.collect.Sets; import eu.dnetlib.dhp.common.Constants; @@ -27,12 +24,13 @@ import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory; import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; -import eu.dnetlib.dhp.schema.oaf.utils.PidType; public abstract class AbstractMdRecordToOafMapper { protected final VocabularyGroup vocs; + protected static final UrlValidator URL_VALIDATOR = UrlValidator.getInstance(); + private final boolean invisible; private final boolean shouldHashId; @@ -393,7 +391,7 @@ public abstract class AbstractMdRecordToOafMapper { r.setPublisher(preparePublisher(doc, info)); r.setEmbargoenddate(prepareField(doc, "//oaf:embargoenddate", info)); r.setSource(prepareSources(doc, info)); - r.setFulltext(prepareListFields(doc, "//oaf:fulltext", info)); + r.setFulltext(prepareListURL(doc, "//oaf:fulltext", info)); r.setFormat(prepareFormats(doc, info)); r.setContributor(prepareContributors(doc, info)); r.setResourcetype(prepareResourceType(doc, info)); @@ -672,6 +670,14 @@ public abstract class AbstractMdRecordToOafMapper { qualifier(paClassId, paClassName, paSchemeId, paSchemeName), trust); } + protected List> prepareListURL(final Node node, final String xpath, final DataInfo info) { + return listFields( + info, prepareListString(node, xpath) + .stream() + .filter(URL_VALIDATOR::isValid) + .collect(Collectors.toList())); + } + protected Field prepareField(final Node node, final String xpath, final DataInfo info) { return field(node.valueOf(xpath), info); } @@ -695,13 +701,13 @@ public abstract class AbstractMdRecordToOafMapper { } protected Set validateUrl(Collection url) { - UrlValidator urlValidator = UrlValidator.getInstance(); + if (Objects.isNull(url)) { return new HashSet<>(); } return url .stream() - .filter(u -> urlValidator.isValid(u)) + .filter(URL_VALIDATOR::isValid) .collect(Collectors.toCollection(HashSet::new)); } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java index 30f3935f5f..2271a0fff8 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java @@ -140,7 +140,7 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper { final List alternateIdentifier = prepareResultPids(doc, info); final List pid = IdentifierFactory.getPids(alternateIdentifier, collectedfrom); - final Set pids = pid.stream().collect(Collectors.toCollection(HashSet::new)); + final Set pids = new HashSet<>(pid); instance .setAlternateIdentifier( @@ -158,6 +158,12 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper { instance .setProcessingchargecurrency(field(doc.valueOf("//oaf:processingchargeamount/@currency"), info)); + prepareListURL(doc, "//oaf:fulltext", info) + .stream() + .findFirst() + .map(Field::getValue) + .ifPresent(instance::setFulltext); + final List nodes = Lists.newArrayList(doc.selectNodes("//dc:identifier")); final List url = nodes .stream() diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java index 39c77bd37f..1faa2fe9b8 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java @@ -144,7 +144,7 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { final List alternateIdentifier = prepareResultPids(doc, info); final List pid = IdentifierFactory.getPids(alternateIdentifier, collectedfrom); - final Set pids = pid.stream().collect(Collectors.toCollection(HashSet::new)); + final Set pids = new HashSet<>(pid); instance .setAlternateIdentifier( @@ -161,6 +161,11 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { instance.setProcessingchargeamount(field(doc.valueOf("//oaf:processingchargeamount"), info)); instance .setProcessingchargecurrency(field(doc.valueOf("//oaf:processingchargeamount/@currency"), info)); + prepareListURL(doc, "//oaf:fulltext", info) + .stream() + .findFirst() + .map(Field::getValue) + .ifPresent(instance::setFulltext); final Set url = new HashSet<>(); for (final Object o : doc diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index a5a2774701..894ed33f77 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -27,7 +27,6 @@ import eu.dnetlib.dhp.common.Constants; import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.*; -import eu.dnetlib.dhp.schema.oaf.utils.GraphCleaningFunctions; import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory; import eu.dnetlib.dhp.schema.oaf.utils.PidType; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; @@ -52,7 +51,7 @@ class MappersTest { } @Test - void testPublication() throws IOException, DocumentException { + void testPublication() throws IOException { final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("oaf_record.xml"))); @@ -112,13 +111,17 @@ class MappersTest { assertNotNull(i.getAccessright()); assertEquals("OPEN", i.getAccessright().getClassid()); }); - assertEquals("0001", p.getInstance().get(0).getRefereed().getClassid()); - assertNotNull(p.getInstance().get(0).getPid()); - assertTrue(p.getInstance().get(0).getPid().isEmpty()); + final Instance instance = p.getInstance().get(0); + assertEquals("0001", instance.getRefereed().getClassid()); + assertNotNull(instance.getPid()); + assertTrue(instance.getPid().isEmpty()); - assertTrue(!p.getInstance().get(0).getAlternateIdentifier().isEmpty()); - assertEquals("doi", p.getInstance().get(0).getAlternateIdentifier().get(0).getQualifier().getClassid()); - assertEquals("10.3897/oneeco.2.e13718", p.getInstance().get(0).getAlternateIdentifier().get(0).getValue()); + assertFalse(instance.getAlternateIdentifier().isEmpty()); + assertEquals("doi", instance.getAlternateIdentifier().get(0).getQualifier().getClassid()); + assertEquals("10.3897/oneeco.2.e13718", instance.getAlternateIdentifier().get(0).getValue()); + + assertNotNull(instance.getFulltext()); + assertEquals("https://oneecosystem.pensoft.net/article/13718/", instance.getFulltext()); assertNotNull(p.getBestaccessright()); assertEquals("OPEN", p.getBestaccessright().getClassid()); diff --git a/pom.xml b/pom.xml index 8a9f1dea8b..63d871039e 100644 --- a/pom.xml +++ b/pom.xml @@ -807,7 +807,7 @@ 3.3.3 3.4.2 [2.12,3.0) - [3.16.0] + [3.17.1-SNAPSHOT] [4.0.3] [6.0.5] [3.1.6] From 23246707141163f90c53e6c4f983b000dea38c11 Mon Sep 17 00:00:00 2001 From: dimitrispie Date: Fri, 2 Jun 2023 13:34:16 +0300 Subject: [PATCH 07/12] Split Monitor DBs-Interdisciplinarity indicators - Split DBs Monitor for faster rendering of visualizations - Add interdisciplinarity indicators from result_fos --- .../oozie_app/copyDataToImpalaCluster.sh | 12 +- .../stats/oozie_app/finalizeImpalaCluster.sh | 11 ++ .../dhp/oa/graph/stats/oozie_app/monitor.sh | 80 +++++++++- .../scripts/step16-createIndicatorsTables.sql | 16 +- .../scripts/step20-createMonitorDB.sql | 137 ++++++++++-------- .../scripts/step20-createMonitorDB_RIs.sql | 15 ++ .../step20-createMonitorDB_RIs_tail.sql | 15 ++ .../scripts/step20-createMonitorDB_funded.sql | 9 ++ .../step20-createMonitorDB_institutions.sql | 56 +++++++ .../dhp/oa/graph/stats/oozie_app/workflow.xml | 30 ++-- 10 files changed, 302 insertions(+), 79 deletions(-) create mode 100644 dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_RIs.sql create mode 100644 dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_RIs_tail.sql create mode 100644 dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_funded.sql create mode 100644 dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_institutions.sql diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/copyDataToImpalaCluster.sh b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/copyDataToImpalaCluster.sh index 66783c2343..b937eea25a 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/copyDataToImpalaCluster.sh +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/copyDataToImpalaCluster.sh @@ -68,6 +68,16 @@ copydb $USAGE_STATS_DB copydb $PROD_USAGE_STATS_DB copydb $EXT_DB copydb $STATS_DB -copydb $MONITOR_DB +#copydb $MONITOR_DB copydb $OBSERVATORY_DB +copydb $MONITOR_DB'_funded' +copydb $MONITOR_DB'_institutions' +copydb $MONITOR_DB'_RIs_tail' + +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'` + copydb ${MONITOR_DB}'_'${tmp} +done \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/finalizeImpalaCluster.sh b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/finalizeImpalaCluster.sh index 5914b95f80..a77b5a1139 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/finalizeImpalaCluster.sh +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/finalizeImpalaCluster.sh @@ -29,3 +29,14 @@ createShadowDB $STATS_DB $STATS_DB_SHADOW createShadowDB $MONITOR_DB $MONITOR_DB_SHADOW createShadowDB $OBSERVATORY_DB $OBSERVATORY_DB_SHADOW createShadowDB USAGE_STATS_DB USAGE_STATS_DB_SHADOW + +createShadowDB $MONITOR_DB'_funded' $MONITOR_DB'_funded_shadow' +createShadowDB $MONITOR_DB'_institutions' $MONITOR_DB'_institutions_shadow' +createShadowDB $MONITOR_DB'_RIs_tail' $MONITOR_DB'_RIs_tail_shadow' + +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'` + createShadowDB ${MONITOR_DB}'_'${tmp} ${MONITOR_DB}'_'${tmp}'_shadow' +done \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/monitor.sh b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/monitor.sh index 440aac7704..08f4c9232d 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/monitor.sh +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/monitor.sh @@ -10,16 +10,88 @@ export SOURCE=$1 export TARGET=$2 export SHADOW=$3 export SCRIPT_PATH=$4 +export SCRIPT_PATH2=$5 +export SCRIPT_PATH3=$6 +export SCRIPT_PATH4=$7 +export SCRIPT_PATH5=$8 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" export HADOOP_USER_NAME="oozie" -echo "Getting file from " $SCRIPT_PATH -hdfs dfs -copyToLocal $SCRIPT_PATH +echo "Getting file from " $4 +hdfs dfs -copyToLocal $4 + +echo "Getting file from " $5 +hdfs dfs -copyToLocal $5 + +echo "Getting file from " $6 +hdfs dfs -copyToLocal $6 + +echo "Getting file from " $7 +hdfs dfs -copyToLocal $7 + +echo "Getting file from " $8 +hdfs dfs -copyToLocal $8 echo "Creating monitor database" -#cat step20-createMonitorDB.sql | sed s/SOURCE/$1/g | sed s/TARGET/$2/g1 > foo -cat step20-createMonitorDB.sql | sed "s/TARGET/${TARGET}/g" | sed "s/SOURCE/${SOURCE}/g1" > foo +cat step20-createMonitorDB_funded.sql | sed "s/SOURCE/$1/g" | sed "s/TARGET/$2_funded/g1" > foo hive $HIVE_OPTS -f foo +cat step20-createMonitorDB.sql | sed "s/SOURCE/$1/g" | sed "s/TARGET/$2_funded/g1" > foo +hive $HIVE_OPTS -f foo +# +cat step20-createMonitorDB_institutions.sql | sed "s/SOURCE/$1/g" | sed "s/TARGET/$2_institutions/g1" > foo +hive $HIVE_OPTS -f foo +cat step20-createMonitorDB.sql | sed "s/SOURCE/$1/g" | sed "s/TARGET/$2_institutions/g1" > foo +hive $HIVE_OPTS -f foo + +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'` + tmp2=`echo "$i" |sed 's/:.*//' ` + cat step20-createMonitorDB_RIs.sql | sed "s/SOURCE/$1/g" | sed "s/TARGET/$2_$tmp/g1" | sed "s/CONTEXT/\'%$tmp2%\'/g" > foo + hive $HIVE_OPTS -f foo + cat step20-createMonitorDB.sql | sed "s/SOURCE/$1/g" | sed "s/TARGET/$2_$tmp/g1" > foo + hive $HIVE_OPTS -f foo +done + + +cat step20-createMonitorDB_RIs_tail.sql | sed "s/SOURCE/$1/g" | sed "s/TARGET/$2_RIs_tail/g1" | sed "s/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'\"/g" > foo +hive $HIVE_OPTS -f foo +cat step20-createMonitorDB.sql | sed "s/SOURCE/$1/g" | sed "s/TARGET/$2_RIs_tail/g1" > foo +hive $HIVE_OPTS -f foo + echo "Hive shell finished" +echo "Updating shadow monitor funded database" +hive -e "drop database if exists ${SHADOW}_funded cascade" +hive -e "create database if not exists ${SHADOW}_funded" +hive $HIVE_OPTS --database ${2}_funded -e "show tables" | grep -v WARN | sed "s/\(.*\)/create view ${SHADOW}_funded.\1 as select * from ${2}_funded.\1;/" > foo +hive -f foo +echo "Updated shadow monitor funded database" + +echo "Updating shadow monitor insitutions database" +hive -e "drop database if exists ${SHADOW}_institutions cascade" +hive -e "create database if not exists ${SHADOW}_institutions" +hive $HIVE_OPTS --database ${2}_institutions -e "show tables" | grep -v WARN | sed "s/\(.*\)/create view ${SHADOW}_institutions.\1 as select * from ${2}_institutions.\1;/" > foo +hive -f foo +echo "Shadow db monitor insitutions ready!" + +echo "Updating shadow monitor RIs database" +for i in $contexts +do + tmp=`echo "$i" | sed 's/'-'/'_'/g' | sed 's/'::'/'_'/g'` + hive -e "drop database if exists ${SHADOW}_${tmp} cascade" + hive -e "create database if not exists ${SHADOW}_${tmp}" + hive $HIVE_OPTS --database ${2}_${tmp} -e "show tables" | grep -v WARN | sed "s/\(.*\)/create view ${SHADOW}_${tmp}.\1 as select * from ${2}_${tmp}.\1;/" > foo + hive -f foo +done +echo "Shadow db monitor RIs ready!" + +echo "Updating shadow monitor RIs tail database" +hive -e "drop database if exists ${SHADOW}_ris_tail cascade" +hive -e "create database if not exists ${SHADOW}_ris_tail" +hive $HIVE_OPTS --database ${2}_ris_tail -e "show tables" | grep -v WARN | sed "s/\(.*\)/create view ${SHADOW}_ris_tail.\1 as select * from ${2}_ris_tail.\1;/" > foo +hive -f foo +echo "Shadow db monitor RIs tail ready!" diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql index ef573916f4..e358e0ef07 100755 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql @@ -779,4 +779,18 @@ cast(measures_ids.unit.value[0] as decimal(6,3)) score_dec, measures_ids.unit.va 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; \ No newline at end of file +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 +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; + +ANALYZE TABLE indi_pub_interdisciplinarity COMPUTE STATISTICS; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql index 86b5c7ca11..9744d5aae2 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql @@ -1,5 +1,78 @@ -drop database if exists TARGET cascade; -create database if not exists TARGET; +--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.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 * 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____::b84450f9864182c67b8611b5593f4250', --"Athena Research and Innovation Center In Information Communication & Knowledge Technologies', --ARC" +-- 'openorgs____::d41cf6bd4ab1b1362a44397e0b95c975', --National Research Council +-- '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 +-- 'openorgs____::38d7097854736583dde879d12dacafca' -- Brown University +-- 'openorgs____::57784c9e047e826fefdb1ef816120d92', --Arts et Métiers ParisTech +-- 'openorgs____::2530baca8a15936ba2e3297f2bce2e7e', -- University of Cape Town +-- 'openorgs____::d11f981828c485cd23d93f7f24f24db1', -- Technological University Dublin +-- 'openorgs____::5e6bf8962665cdd040341171e5c631d8', -- Delft University of Technology +-- 'openorgs____::846cb428d3f52a445f7275561a7beb5d', -- University of Manitoba +-- 'openorgs____::eb391317ed0dc684aa81ac16265de041', -- Universitat Rovira i Virgili +-- 'openorgs____::66aa9fc2fceb271423dfabcc38752dc0', -- Lund University +-- 'openorgs____::3cff625a4370d51e08624cc586138b2f' -- IMT Atlantique +-- ) )) foo; +-- +--ANALYZE TABLE TARGET.result COMPUTE STATISTICS; create view if not exists TARGET.category as select * from SOURCE.category; create view if not exists TARGET.concept as select * from SOURCE.concept; @@ -16,64 +89,6 @@ create view if not exists TARGET.totalresearchers as select * from SOURCE.totalr 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 * 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____::b84450f9864182c67b8611b5593f4250', --"Athena Research and Innovation Center In Information Communication & Knowledge Technologies', --ARC" - 'openorgs____::d41cf6bd4ab1b1362a44397e0b95c975', --National Research Council - '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 - 'openorgs____::38d7097854736583dde879d12dacafca' -- Brown University - 'openorgs____::57784c9e047e826fefdb1ef816120d92', --Arts et Métiers ParisTech - 'openorgs____::2530baca8a15936ba2e3297f2bce2e7e', -- University of Cape Town - 'openorgs____::d11f981828c485cd23d93f7f24f24db1', -- Technological University Dublin - 'openorgs____::5e6bf8962665cdd040341171e5c631d8', -- Delft University of Technology - 'openorgs____::846cb428d3f52a445f7275561a7beb5d', -- University of Manitoba - 'openorgs____::eb391317ed0dc684aa81ac16265de041', -- Universitat Rovira i Virgili - 'openorgs____::66aa9fc2fceb271423dfabcc38752dc0', -- Lund University - 'openorgs____::3cff625a4370d51e08624cc586138b2f' -- IMT Atlantique - ) )) foo; - -ANALYZE TABLE TARGET.result COMPUTE STATISTICS; - 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); ANALYZE TABLE TARGET.result_citations COMPUTE STATISTICS; @@ -251,3 +266,5 @@ create table TARGET.indi_result_with_pid stored as parquet as select * from SOUR ANALYZE TABLE TARGET.indi_result_with_pid COMPUTE STATISTICS; create table TARGET.indi_impact_measures stored as parquet as select * from SOURCE.indi_impact_measures orig where exists (select 1 from TARGET.result r where r.id=orig.id); ANALYZE TABLE TARGET.indi_impact_measures COMPUTE STATISTICS; +create table TARGET.indi_pub_interdisciplinarity stored as parquet as select * from SOURCE.indi_pub_interdisciplinarity orig where exists (select 1 from TARGET.result r where r.id=orig.id); +ANALYZE TABLE TARGET.indi_pub_interdisciplinarity COMPUTE STATISTICS; diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_RIs.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_RIs.sql new file mode 100644 index 0000000000..92b40405d4 --- /dev/null +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_RIs.sql @@ -0,0 +1,15 @@ +drop database if exists TARGET cascade; +create database if not exists TARGET; + +create table TARGET.result stored as parquet as + select distinct * from ( + select * from SOURCE.result r where exists + (select 1 + from SOURCE.result_concepts rc + join SOURCE.concept conc on conc.id=rc.concept + join SOURCE.category cat on cat.id=conc.category + join SOURCE.context cont on cont.id=cat.context +-- join SOURCE.result + where rc.id=r.id and conc.category like CONTEXT) +) foo; +ANALYZE TABLE TARGET.result COMPUTE STATISTICS; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_RIs_tail.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_RIs_tail.sql new file mode 100644 index 0000000000..ef6d08d797 --- /dev/null +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_RIs_tail.sql @@ -0,0 +1,15 @@ +drop database if exists TARGET cascade; +create database if not exists TARGET; + +create table TARGET.result stored as parquet as + select distinct * from ( + select * from SOURCE.result r where exists + (select 1 + from SOURCE.result_concepts rc + join SOURCE.concept conc on conc.id=rc.concept + join SOURCE.category cat on cat.id=conc.category + join SOURCE.context cont on cont.id=cat.context +-- join SOURCE.result + where rc.id=r.id and conc.category not in (CONTEXTS)) +) foo; +ANALYZE TABLE TARGET.result COMPUTE STATISTICS; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_funded.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_funded.sql new file mode 100644 index 0000000000..8d8739c743 --- /dev/null +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_funded.sql @@ -0,0 +1,9 @@ +drop database if exists TARGET cascade; +create database if not exists TARGET; + +create table TARGET.result 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) + ) foo; + +ANALYZE TABLE TARGET.result COMPUTE STATISTICS; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_institutions.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_institutions.sql new file mode 100644 index 0000000000..121ee6e7f4 --- /dev/null +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_institutions.sql @@ -0,0 +1,56 @@ +drop database if exists TARGET cascade; +create database if not exists TARGET; + +create table TARGET.result stored as parquet as + select distinct * from ( + 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____::d41cf6bd4ab1b1362a44397e0b95c975', --National Research Council + '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 + 'openorgs____::38d7097854736583dde879d12dacafca' -- Brown University + 'openorgs____::57784c9e047e826fefdb1ef816120d92', --Arts et Métiers ParisTech + 'openorgs____::2530baca8a15936ba2e3297f2bce2e7e', -- University of Cape Town + 'openorgs____::d11f981828c485cd23d93f7f24f24db1', -- Technological University Dublin + 'openorgs____::5e6bf8962665cdd040341171e5c631d8', -- Delft University of Technology + 'openorgs____::846cb428d3f52a445f7275561a7beb5d', -- University of Manitoba + 'openorgs____::eb391317ed0dc684aa81ac16265de041', -- Universitat Rovira i Virgili + 'openorgs____::66aa9fc2fceb271423dfabcc38752dc0', -- Lund University + 'openorgs____::3cff625a4370d51e08624cc586138b2f' -- IMT Atlantique + ))) foo; + +ANALYZE TABLE TARGET.result COMPUTE STATISTICS; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml index 68ef4595ef..2ab50fb29f 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml @@ -374,25 +374,29 @@ ${monitor_db_name} ${monitor_db_shadow_name} ${wf:appPath()}/scripts/step20-createMonitorDB.sql + ${wf:appPath()}/scripts/step20-createMonitorDB_funded.sql + ${wf:appPath()}/scripts/step20-createMonitorDB_institutions.sql + ${wf:appPath()}/scripts/step20-createMonitorDB_RIs.sql + ${wf:appPath()}/scripts/step20-createMonitorDB_RIs_tail.sql monitor.sh - - - - - - - ${jobTracker} - ${nameNode} - monitor-post.sh - ${monitor_db_name} - ${monitor_db_shadow_name} - monitor-post.sh - + + + + + + + + + + + + + ${jobTracker} From ad07fbf0538aedd4dbb54673f45cac56586a36d8 Mon Sep 17 00:00:00 2001 From: dimitrispie Date: Fri, 2 Jun 2023 14:13:10 +0300 Subject: [PATCH 08/12] Add names to organizations for collaboration indicators --- .../scripts/step16-createIndicatorsTables.sql | 26 ++++++++++--------- 1 file changed, 14 insertions(+), 12 deletions(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql index e358e0ef07..f523b63d56 100755 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql @@ -92,28 +92,28 @@ ANALYZE TABLE indi_funded_result_with_fundref COMPUTE STATISTICS; -- -- compute stats indi_result_org_collab; -- -create TEMPORARY TABLE tmp AS SELECT ro.organization organization, ro.id from result_organization ro +create TEMPORARY TABLE tmp AS SELECT ro.organization organization, ro.id, o.name from result_organization ro join organization o on o.id=ro.organization where o.name is not null; create table if not exists indi_result_org_collab stored as parquet as -select o1.organization org1, o2.organization org2, count(o1.id) as collaborations +select o1.organization org1, o1.name org1name1, o2.organization org2, o2.name org2name2, count(o1.id) as collaborations from tmp as o1 -join tmp as o2 where o1.id=o2.id and o1.organization!=o2.organization -group by o1.organization, o2.organization; +join tmp as o2 where o1.id=o2.id and o1.organization!=o2.organization and o1.name!=o2.name +group by o1.organization, o2.organization, o1.name, o2.name; drop table tmp purge; ANALYZE TABLE indi_result_org_collab COMPUTE STATISTICS; create TEMPORARY TABLE tmp AS -select distinct ro.organization organization, ro.id, o.country from result_organization ro +select distinct ro.organization organization, ro.id, o.name, o.country from result_organization ro join organization o on o.id=ro.organization where country <> 'UNKNOWN' and o.name is not null; create table if not exists indi_result_org_country_collab stored as parquet as -select o1.organization org1,o2.country country2, count(o1.id) as collaborations +select o1.organization org1,o1.name org1name1, o2.country country2, count(o1.id) as collaborations from tmp as o1 join tmp as o2 on o1.id=o2.id where o1.id=o2.id and o1.country!=o2.country -group by o1.organization, o1.id, o2.country; +group by o1.organization, o1.id, o1.name, o2.country; drop table tmp purge; @@ -121,7 +121,7 @@ ANALYZE TABLE indi_result_org_country_collab COMPUTE STATISTICS; create TEMPORARY TABLE AS select o.id organization, o.name, ro.project as project from organization o - join organization_projects ro on o.id=ro.id; + join organization_projects ro on o.id=ro.id where o.name is not null; create table if not exists indi_project_collab_org stored as parquet as select o1.organization org1,o1.name orgname1, o2.organization org2, o2.name orgname2, count(distinct o1.project) as collaborations @@ -133,16 +133,16 @@ group by o1.name,o2.name, o1.organization, o2.organization; ANALYZE TABLE indi_project_collab_org COMPUTE STATISTICS; create TEMPORARY TABLE tmp AS -select o.id organization, o.country , ro.project as project from organization o +select o.id organization, o.name, o.country , ro.project as project from organization o join organization_projects ro on o.id=ro.id - and o.country <> 'UNKNOWN'; + and o.country <> 'UNKNOWN' and o.name is not null; create table if not exists indi_project_collab_org_country stored as parquet as -select o1.organization org1,o2.country country2, count(distinct o1.project) as collaborations +select o1.organization org1,o1.name org1name, o2.country country2, count(distinct o1.project) as collaborations from tmp as o1 join tmp as o2 on o1.project=o2.project where o1.organization<>o2.organization and o1.country<>o2.country -group by o1.organization, o2.country; +group by o1.organization, o2.country, o1.name; drop table tmp purge; @@ -793,4 +793,6 @@ 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; +drop table pub_fos_totals purge; + ANALYZE TABLE indi_pub_interdisciplinarity COMPUTE STATISTICS; \ No newline at end of file From d5be6a13e9167ee8b947b7ac657810e11dd93ed7 Mon Sep 17 00:00:00 2001 From: Alessia Bardi Date: Tue, 6 Jun 2023 14:43:32 +0200 Subject: [PATCH 09/12] Updated officialnmae of pangaea in hostedbymap for Datacite to avoid duplicate entries in the source filter of the portal --- .../main/resources/eu/dnetlib/dhp/datacite/hostedBy_map.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/hostedBy_map.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/hostedBy_map.json index ecae6811a1..9088d29600 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/hostedBy_map.json +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/hostedBy_map.json @@ -642,12 +642,12 @@ "PANGAEA.REPOSITORY": { "openaire_id": "re3data_____::r3d100010134", "datacite_name": "PANGAEA", - "official_name": "PANGAEA" + "official_name": "PANGAEA - Data Publisher for Earth and Environmental Science" }, "TIB.PANGAEA": { "openaire_id": "re3data_____::r3d100010134", "datacite_name": "PANGAEA", - "official_name": "PANGAEA" + "official_name": "PANGAEA - Data Publisher for Earth and Environmental Science" }, "NASAPDS.NASAPDS": { "openaire_id": "re3data_____::r3d100010121", From 28272c1b0e6435818a1e589d6f6597e910ca126c Mon Sep 17 00:00:00 2001 From: dimitrispie Date: Wed, 7 Jun 2023 15:34:01 +0300 Subject: [PATCH 10/12] Bug fix --- .../stats/oozie_app/scripts/step16-createIndicatorsTables.sql | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql index f523b63d56..15d28400e9 100755 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql @@ -119,7 +119,7 @@ drop table tmp purge; ANALYZE TABLE indi_result_org_country_collab COMPUTE STATISTICS; -create TEMPORARY TABLE AS +create TEMPORARY TABLE tmp AS select o.id organization, o.name, ro.project as project from organization o join organization_projects ro on o.id=ro.id where o.name is not null; @@ -130,6 +130,8 @@ from tmp as o1 where o1.organization<>o2.organization and o1.name<>o2.name group by o1.name,o2.name, o1.organization, o2.organization; +drop table tmp purge; + ANALYZE TABLE indi_project_collab_org COMPUTE STATISTICS; create TEMPORARY TABLE tmp AS From fa24e2e18fcac5244e22435167115ca95dd71e09 Mon Sep 17 00:00:00 2001 From: dimitrispie Date: Wed, 7 Jun 2023 17:43:37 +0300 Subject: [PATCH 11/12] Bug fix on indicators step indi_pub_gold_oa table was missing during the creation of other indicators --- .../scripts/step16-createIndicatorsTables.sql | 134 +++++++++--------- 1 file changed, 67 insertions(+), 67 deletions(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql index 15d28400e9..21d4efbf75 100755 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql @@ -223,73 +223,6 @@ select id, count(id) as number_of_copies from result_instance group by id; ANALYZE TABLE indi_result_no_of_copies COMPUTE STATISTICS; ---- Sprint 6 ---- -create table if not exists indi_pub_hybrid_oa_with_cc 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_hybrid_oa, 0) as is_hybrid_oa -FROM publication_datasources pd - LEFT OUTER JOIN ( - SELECT pd.id, 1 as is_hybrid_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 - where cc.has_cc_license=1 and ga.is_gold=0) tmp on pd.id=tmp.id; - -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_downloads stored as parquet as SELECT result_id, sum(downloads) no_downloads from openaire_prod_usage_stats.usage_stats join publication on result_id=id @@ -376,6 +309,73 @@ FROM ANALYZE TABLE indi_pub_gold_oa COMPUTE STATISTICS; +create table if not exists indi_pub_hybrid_oa_with_cc 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_hybrid_oa, 0) as is_hybrid_oa +FROM publication_datasources pd + LEFT OUTER JOIN ( + SELECT pd.id, 1 as is_hybrid_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 + where cc.has_cc_license=1 and ga.is_gold=0) tmp on pd.id=tmp.id; + +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, From c5f42c7f5bd0b2dcbae771e9e8e6ba46233e930c Mon Sep 17 00:00:00 2001 From: dimitrispie Date: Wed, 7 Jun 2023 18:18:23 +0300 Subject: [PATCH 12/12] Added memory to hive --- .../eu/dnetlib/dhp/oa/graph/stats/oozie_app/config-default.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/config-default.xml b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/config-default.xml index 63fc84d75e..98a1821751 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/config-default.xml +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/config-default.xml @@ -21,7 +21,7 @@ hive_jdbc_url - jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000/;UseNativeQuery=1;?spark.executor.memory=19166291558;spark.yarn.executor.memoryOverhead=3225;spark.driver.memory=11596411699;spark.yarn.driver.memoryOverhead=1228 + jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000/;UseNativeQuery=1;?spark.executor.memory=22166291558;spark.yarn.executor.memoryOverhead=3225;spark.driver.memory=15596411699;spark.yarn.driver.memoryOverhead=1228 oozie.wf.workflow.notification.url