diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java index 040c897829..76c8ec7fae 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java @@ -95,7 +95,7 @@ public class SparkAtomicActionScoreJob implements Serializable { return projectScores.map((MapFunction) bipProjectScores -> { Project project = new Project(); - project.setId(bipProjectScores.getProjectId()); + //project.setId(bipProjectScores.getProjectId()); project.setMeasures(bipProjectScores.toMeasures()); return project; }, Encoders.bean(Project.class)) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/Action.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/Action.java new file mode 100644 index 0000000000..6c9e7694f3 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/Action.java @@ -0,0 +1,38 @@ +package eu.dnetlib.dhp.bulktag.actions; + +import java.io.Serializable; +import java.util.List; + +/** + * @author miriam.baglioni + * @Date 22/01/24 + */ +public class Action implements Serializable { + private String clazz; + private String method; + private List params; + + public String getClazz() { + return clazz; + } + + public void setClazz(String clazz) { + this.clazz = clazz; + } + + public String getMethod() { + return method; + } + + public void setMethod(String method) { + this.method = method; + } + + public List getParams() { + return params; + } + + public void setParams(List params) { + this.params = params; + } +} diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/ExecSubstringAction.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/ExecSubstringAction.java new file mode 100644 index 0000000000..fd3091fd0f --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/ExecSubstringAction.java @@ -0,0 +1,54 @@ +package eu.dnetlib.dhp.bulktag.actions; + +import java.io.Serializable; + +/** + * @author miriam.baglioni + * @Date 19/01/24 + */ +public class ExecSubstringAction implements Serializable { + + private String value; + private String from; + private String to; + + public String getValue() { + return value; + } + + public void setValue(String value) { + this.value = value; + } + + public String getFrom() { + return from; + } + + public void setFrom(String from) { + this.from = from; + } + + public String getTo() { + return to; + } + + public void setTo(String to) { + this.to = to; + } + + public String execSubstring(){ + int to = Integer.valueOf(this.to); + int from = Integer.valueOf(this.from); + + if(to < from || from > this.value.length()) + return ""; + + if(from < 0) + from = 0; + if (to > this.value.length()) + to = this.value.length(); + + return this.value.substring(from, to); + + } +} diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/MapModel.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/MapModel.java new file mode 100644 index 0000000000..ef3eb43ccb --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/MapModel.java @@ -0,0 +1,30 @@ +package eu.dnetlib.dhp.bulktag.actions; + +import java.io.Serializable; + +/** + * @author miriam.baglioni + * @Date 22/01/24 + */ +public class MapModel implements Serializable { + + private String path; + private Action action; + + + public String getPath() { + return path; + } + + public void setPath(String path) { + this.path = path; + } + + public Action getAction() { + return action; + } + + public void setAction(Action action) { + this.action = action; + } +} diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/Parameters.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/Parameters.java new file mode 100644 index 0000000000..d23634605b --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/Parameters.java @@ -0,0 +1,28 @@ +package eu.dnetlib.dhp.bulktag.actions; + +import java.io.Serializable; + +/** + * @author miriam.baglioni + * @Date 22/01/24 + */ +public class Parameters implements Serializable { + private String paramName; + private String paramValue; + + public String getParamName() { + return paramName; + } + + public void setParamName(String paramName) { + this.paramName = paramName; + } + + public String getParamValue() { + return paramValue; + } + + public void setParamValue(String paramValue) { + this.paramValue = paramValue; + } +} diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ProtoMap.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ProtoMap.java index fd74817199..15b4d10b74 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ProtoMap.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ProtoMap.java @@ -1,10 +1,12 @@ package eu.dnetlib.dhp.bulktag.community; +import eu.dnetlib.dhp.bulktag.actions.MapModel; + import java.io.Serializable; import java.util.HashMap; -public class ProtoMap extends HashMap implements Serializable { +public class ProtoMap extends HashMap implements Serializable { public ProtoMap() { super(); 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 98c46cf003..67422c2adb 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 @@ -5,9 +5,14 @@ import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.*; import static eu.dnetlib.dhp.schema.common.ModelConstants.*; import java.io.Serializable; +import java.lang.reflect.InvocationTargetException; +import java.lang.reflect.Method; import java.util.*; import java.util.stream.Collectors; +import com.jayway.jsonpath.PathNotFoundException; +import eu.dnetlib.dhp.bulktag.actions.MapModel; +import eu.dnetlib.dhp.bulktag.actions.Parameters; import org.apache.commons.lang3.StringUtils; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -35,27 +40,55 @@ public class ResultTagger implements Serializable { return (tmp != clist.size()); } - private Map> getParamMap(final Result result, Map params) { + private Map> getParamMap(final Result result, Map params) throws NoSuchMethodException, InvocationTargetException { Map> param = new HashMap<>(); String json = new Gson().toJson(result, Result.class); DocumentContext jsonContext = JsonPath.parse(json); + if (params == null) { params = new HashMap<>(); } for (String key : params.keySet()) { + MapModel mapModel = params.get(key); + try { - param.put(key, jsonContext.read(params.get(key))); - } catch (com.jayway.jsonpath.PathNotFoundException e) { + String path = mapModel.getPath(); + Object obj = jsonContext.read(path); + List pathValue ; + if(obj instanceof java.lang.String) + pathValue = Arrays.asList((String)obj); + else + pathValue = (List)obj; + if(Optional.ofNullable(mapModel.getAction()).isPresent()){ + Class c = Class.forName(mapModel.getAction().getClazz()); + Object class_instance = c.newInstance(); + Method setField = c.getMethod("setValue", String.class); + setField.invoke(class_instance, pathValue.get(0)); + for(Parameters p : mapModel.getAction().getParams()){ + setField = c.getMethod("set" + p.getParamName(), String.class); + setField.invoke(class_instance, p.getParamValue()); + } + + param.put(key,Arrays.asList((String)c.getMethod(mapModel.getAction().getMethod()).invoke(class_instance))); + + } + + else{ + param.put(key, pathValue); + } + + } catch (PathNotFoundException | ClassNotFoundException | InstantiationException | IllegalAccessException e) { param.put(key, new ArrayList<>()); } } return param; + } public R enrichContextCriteria( - final R result, final CommunityConfiguration conf, final Map criteria) { + final R result, final CommunityConfiguration conf, final Map criteria) throws InvocationTargetException, NoSuchMethodException { + - final Map> param = getParamMap(result, criteria); // Verify if the entity is deletedbyinference. In case verify if to clean the context list // from all the zenodo communities @@ -64,6 +97,8 @@ public class ResultTagger implements Serializable { return result; } + final Map> param = getParamMap(result, criteria); + // Execute the EOSCTag for the services switch (result.getResulttype().getClassid()) { case PUBLICATION_RESULTTYPE_CLASSID: diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/GreatThanVerb.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/GreatThanVerb.java new file mode 100644 index 0000000000..f771208007 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/GreatThanVerb.java @@ -0,0 +1,34 @@ + +package eu.dnetlib.dhp.bulktag.criteria; + +import java.io.Serializable; + +/** + * @author miriam.baglioni + * @Date 11/11/22 + */ +@VerbClass("greater_than") +public class GreatThanVerb implements Selection, Serializable { + + private String param; + + public GreatThanVerb() { + } + + public GreatThanVerb(final String param) { + this.param = param; + } + + @Override + public boolean apply(String value) { + return value.compareTo(param) > 0; + } + + public String getParam() { + return param; + } + + public void setParam(String param) { + this.param = param; + } +} diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/LessThanVerb.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/LessThanVerb.java new file mode 100644 index 0000000000..4aa52bfae1 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/LessThanVerb.java @@ -0,0 +1,34 @@ + +package eu.dnetlib.dhp.bulktag.criteria; + +import java.io.Serializable; + +/** + * @author miriam.baglioni + * @Date 11/11/22 + */ +@VerbClass("lesser_than") +public class LessThanVerb implements Selection, Serializable { + + private String param; + + public LessThanVerb() { + } + + public LessThanVerb(final String param) { + this.param = param; + } + + @Override + public boolean apply(String value) { + return value.compareTo(param) < 0; + } + + public String getParam() { + return param; + } + + public void setParam(String param) { + this.param = param; + } +} 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 743e62b5f9..01be4d0a3a 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 @@ -13,6 +13,7 @@ import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.FilterFunction; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.Row; import org.apache.spark.sql.SparkSession; @@ -31,18 +32,26 @@ public class BulkTagJobTest { private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - public static final String pathMap = "{ \"author\" : \"$['author'][*]['fullname']\"," - + " \"title\" : \"$['title'][*]['value']\"," - + " \"orcid\" : \"$['author'][*]['pid'][*][?(@['key']=='ORCID')]['value']\"," - + " \"contributor\" : \"$['contributor'][*]['value']\"," - + " \"description\" : \"$['description'][*]['value']\", " - + " \"subject\" :\"$['subject'][*]['value']\" , " + - "\"fos\" : \"$['subject'][?(@['qualifier']['classid']=='FOS')].value\"," + - "\"sdg\" : \"$['subject'][?(@['qualifier']['classid']=='SDG')].value\"," + - "\"hostedby\" : \"$['instance'][*]['hostedby']['key']\" , " + - "\"collectedfrom\" : \"$['instance'][*]['collectedfrom']['key']\"," + - "\"publisher\":\"$['publisher'].value\"," + - "\"publicationyear\":\"$['dateofacceptance'].value\"} "; + public static final String pathMap = "{\"author\":{\"path\":\"$['author'][*]['fullname']\"}," + + " \"title\":{\"path\":\"$['title'][*]['value']\"}, "+ + " \"orcid\":{\"path\":\"$['author'][*]['pid'][*][?(@['qualifier']['classid']=='orcid')]['value']\"} , " + + " \"orcid_pending\":{\"path\":\"$['author'][*]['pid'][*][?(@['qualifier']['classid']=='orcid_pending')]['value']\"} ,"+ + "\"contributor\" : {\"path\":\"$['contributor'][*]['value']\"},"+ + " \"description\" : {\"path\":\"$['description'][*]['value']\"},"+ + " \"subject\" :{\"path\":\"$['subject'][*]['value']\"}, " + + " \"fos\" : {\"path\":\"$['subject'][?(@['qualifier']['classid']=='FOS')].value\"} , "+ + "\"sdg\" : {\"path\":\"$['subject'][?(@['qualifier']['classid']=='SDG')].value\"}," + + "\"journal\":{\"path\":\"$['journal'].name\"}," + + "\"hostedby\":{\"path\":\"$['instance'][*]['hostedby']['key']\"}," + + "\"collectedfrom\":{\"path\":\"$['instance'][*]['collectedfrom']['key']\"}," + + "\"publisher\":{\"path\":\"$['publisher'].value\"}," + + "\"publicationyear\":{\"path\":\"$['dateofacceptance'].value\", " + + " \"action\":{\"clazz\":\"eu.dnetlib.dhp.bulktag.actions.ExecSubstringAction\"," + + "\"method\":\"execSubstring\","+ + "\"params\":[" + + "{\"paramName\":\"From\", \"paramValue\":0}, " + + "{\"paramName\":\"To\",\"paramValue\":4}]}}}"; + private static SparkSession spark; @@ -1600,4 +1609,60 @@ public class BulkTagJobTest { Assertions.assertEquals(0, spark.sql(query).count()); } + + @Test + void pubdateTest() throws Exception { + + + final String pathMap = BulkTagJobTest.pathMap; + SparkBulkTagJob + .main( + new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", + getClass().getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/publicationyear/").getPath(), + "-taggingConf", + IOUtils + .toString( + BulkTagJobTest.class + .getResourceAsStream( + "/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf_publicationdate.xml")), + "-outputPath", workingDir.toString() + "/", + "-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(10, 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 " + + "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 queryResult = spark.sql(query); + queryResult.show(false); + Assertions.assertEquals(5, queryResult.count()); + + Assertions.assertEquals(1, queryResult.filter((FilterFunction) r -> r.getAs("id").equals("50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529")).count()); + Assertions.assertEquals(1, queryResult.filter((FilterFunction) r -> r.getAs("id").equals("50|od______3989::2f4f3c820c450bd08dac08d07cc82dcf")).count()); + Assertions.assertEquals(1, queryResult.filter((FilterFunction) r -> r.getAs("id").equals("50|od______3989::7fcbe3a03280663cddebfd3cb9203177")).count()); + Assertions.assertEquals(1, queryResult.filter((FilterFunction) r -> r.getAs("id").equals("50|od______3989::d791339867bec6d3eb2104deeb4e4961")).count()); + Assertions.assertEquals(1, queryResult.filter((FilterFunction) r -> r.getAs("id").equals("50|od______3989::d90d3a1f64ad264b5ebed8a35b280343")).count()); + + + } + + + } diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf_publicationdate.xml b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf_publicationdate.xml new file mode 100644 index 0000000000..26f1ca8221 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf_publicationdate.xml @@ -0,0 +1,1431 @@ + + + + + + + zenodo + + + + + + + + + + + + + + + + + + + + + + 10|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 + + + + 10|re3data_____::9ebe127e5f3a0bf401875690f3bb6b81 + + + + 10|doajarticles::c6cd4b532e12868c1d760a8d7cda6815 + + + + 10|doajarticles::a6de4499bb87bf3c01add0a9e2c9ed0b + + + + 10|doajarticles::6eb31d13b12bc06bbac06aef63cf33c9 + + + + 10|doajarticles::0da84e9dfdc8419576169e027baa8028 + + + + 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 + + + + 10|openaire____::c5502a43e76feab55dd00cf50f519125 + + + + 10|re3data_____::a48f09c562b247a9919acfe195549b47 + + + + 10|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 + + + + + + + Stock Assessment + pelagic + Acoustic + Fish farming + Fisheries + Fishermen + maximum sustainable yield + trawler + Fishing vessel + Fisherman + Fishing gear + mackerel + RFMO + Fish Aggregating Device + Bycatch + Fishery + common fisheries policy + Fishing fleet + Aquaculture + + + + 10|doajarticles::8cec81178926caaca531afbd8eb5d64c + + + + 10|doajarticles::0f7a7f30b5400615cae1829f3e743982 + + + + 10|doajarticles::9740f7f5af3e506d2ad2c215cdccd51a + + + + 10|doajarticles::9f3fbaae044fa33cb7069b72935a3254 + + + + 10|doajarticles::cb67f33eb9819f5c624ce0313957f6b3 + + + + 10|doajarticles::e21c97cbb7a209afc75703681c462906 + + + + 10|doajarticles::554cde3be9e5c4588b4c4f9f503120cb + + + + 10|tubitakulakb::11e22f49e65b9fd11d5b144b93861a1b + + + + 10|doajarticles::57c5d3837da943e93b28ec4db82ec7a5 + + + + 10|doajarticles::a186f5ddb8e8c7ecc992ef51cf3315b1 + + + + 10|doajarticles::e21c97cbb7a209afc75703681c462906 + + + + 10|doajarticles::dca64612dfe0963fffc119098a319957 + + + + 10|doajarticles::dd70e44479f0ade25aa106aef3e87a0a + + + + + + discardless + + + + farfish2020 + + + + 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se están desarrollando en la Universidad Camilo José Cela (UCJC) sobre la cafeína y sus efectos cuando se realiza deporte. https://www.ucjc.edu/2016/08/la-bbc-s...\n\nJuan Del Coso, director del Laboratorio de Fisiología del Ejercicio de la Universidad Camilo José Cela, nos describe cómo está siendo la investigación que desarrolla con deportistas de alto rendimiento y el consumo de cafeína.\n\n\"Nuestra investigación se enmarca dentro del campo de la fisiología del ejercicio y el objetivo que tenemos es investigar los efectos que tiene la cafeína en los deportistas, principalmente saber si es una ayuda ergogénica en la mayor parte de los deportes, pero también conocer qué perjuicios existen para aquellos deportistas que la utilizan para incrementar el rendimiento deportivo\", explica Del Coso.\n\nY es que los datos son muy llamativos: tres de cada cuatro deportistas de alto rendimiento utilizan la cafeína antes de la competición y muchas veces se utiliza sin saber los perjuicios que 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