diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/Utils.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/Utils.java index 6079da3656..1e39d99c3d 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/Utils.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/Utils.java @@ -171,7 +171,7 @@ public class Utils implements Serializable { public static List getCommunityIdList(String baseURL) throws IOException { return getValidCommunities(baseURL) .stream() - .map(community -> community.getId()) + .map(CommunityModel::getId) .collect(Collectors.toList()); } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep1.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep1.java index aede9ef05b..764390442d 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep1.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep1.java @@ -3,11 +3,14 @@ package eu.dnetlib.dhp.resulttocommunityfromsemrel; import static eu.dnetlib.dhp.PropagationConstant.*; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; +import static java.lang.String.join; import java.io.IOException; import java.util.Arrays; +import java.util.Collections; import java.util.List; +import eu.dnetlib.dhp.schema.common.ModelConstants; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.sql.*; @@ -34,7 +37,8 @@ public class PrepareResultCommunitySetStep1 { * relation */ // TODO - private static final String RESULT_CONTEXT_QUERY_TEMPLATE = "select target resultId, community_context " + private static final String RESULT_CONTEXT_QUERY_TEMPLATE = + "select target resultId, community_context " + "from (select id, collect_set(co.id) community_context " + " from result " + " lateral view explode (context) c as co " @@ -45,7 +49,7 @@ public class PrepareResultCommunitySetStep1 { /** * a dataset for example could be linked to more than one publication. For each publication linked to that dataset - * the previous query will produce a row: targetId set of community context the target could possibly inherit with + * the previous query will produce a row: targetId, set of community context the target could possibly inherit. With * the following query there will be a single row for each result linked to more than one result of the result type * currently being used */ @@ -56,6 +60,27 @@ public class PrepareResultCommunitySetStep1 { + "where length(co) > 0 " + "group by resultId"; + private static final String RESULT_CONTEXT_QUERY_TEMPLATE_IS_RELATED_TO = + "select target as resultId, community_context " + + "from resultWithContext rwc " + + "join relatedToRelations r " + + "join patents p " + + "on rwc.id = r.source and r.target = p.id"; + + private static final String RESULT_WITH_CONTEXT = "select id, collect_set(co.id) community_context \n" + + " from result " + + " lateral view explode (context) c as co " + + " where lower(co.id) IN %s" + + " group by id"; + + private static final String RESULT_PATENT = "select id " + + " from result " + + " where array_contains(instance.instancetype.classname, 'Patent')"; + + private static final String IS_RELATED_TO_RELATIONS = "select source, target " + + " from relation " + + " where lower(relClass) = 'isrelatedto' and datainfo.deletedbyinference = false"; + public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils .toString( @@ -82,14 +107,17 @@ public class PrepareResultCommunitySetStep1 { SparkConf conf = new SparkConf(); conf.set("hive.metastore.uris", parser.get("hive_metastore_uris")); - final List allowedsemrel = Arrays.asList(parser.get("allowedsemrels").split(";")); - log.info("allowedSemRel: {}", new Gson().toJson(allowedsemrel)); + final String allowedsemrel ="(" + join(",", + Arrays.asList(parser.get("allowedsemrels").split(";")).stream().map(value -> "'" + value.toLowerCase() + "'") + .toArray(String[]::new)) + ")"; + log.info("allowedSemRel: {}", allowedsemrel); final String baseURL = parser.get("baseURL"); log.info("baseURL: {}", baseURL); - final List communityIdList = getCommunityList(baseURL); - log.info("communityIdList: {}", new Gson().toJson(communityIdList)); + final String communityIdList = "(" + join(",", getCommunityList(baseURL).stream() + .map(value -> "'" + value.toLowerCase() + "'") + .toArray(String[]::new)) + ")"; final String resultType = resultClassName.substring(resultClassName.lastIndexOf(".") + 1).toLowerCase(); log.info("resultType: {}", resultType); @@ -118,10 +146,10 @@ public class PrepareResultCommunitySetStep1 { SparkSession spark, String inputPath, String outputPath, - List allowedsemrel, + String allowedsemrel, Class resultClazz, String resultType, - List communityIdList) { + String communityIdList) { final String inputResultPath = inputPath + "/" + resultType; log.info("Reading Graph table from: {}", inputResultPath); @@ -132,28 +160,42 @@ public class PrepareResultCommunitySetStep1 { Dataset relation = readPath(spark, inputRelationPath, Relation.class); relation.createOrReplaceTempView("relation"); - Dataset result = readPath(spark, inputResultPath, resultClazz); + Dataset result = readPath(spark, inputResultPath, resultClazz) + .where("datainfo.deletedbyinference != true AND datainfo.invisible != true"); result.createOrReplaceTempView("result"); final String outputResultPath = outputPath + "/" + resultType; log.info("writing output results to: {}", outputResultPath); + String resultContextQuery = String .format( RESULT_CONTEXT_QUERY_TEMPLATE, - getConstraintList(" lower(co.id) = '", communityIdList), - getConstraintList(" lower(relClass) = '", allowedsemrel)); - + "AND lower(co.id) IN " + communityIdList, + "AND lower(relClass) IN " + allowedsemrel); Dataset result_context = spark.sql(resultContextQuery); + + Dataset rwc = spark.sql(String.format(RESULT_WITH_CONTEXT, communityIdList)); + Dataset patents = spark.sql(RESULT_PATENT); + Dataset relatedToRelations = spark.sql(IS_RELATED_TO_RELATIONS); + + rwc.createOrReplaceTempView("resultWithContext"); + patents.createOrReplaceTempView("patents"); + relatedToRelations.createOrReplaceTempView("relatedTorelations"); + + + result_context = result_context.unionAll( spark.sql(RESULT_CONTEXT_QUERY_TEMPLATE_IS_RELATED_TO)); + result_context.createOrReplaceTempView("result_context"); spark - .sql(RESULT_COMMUNITY_LIST_QUERY) - .as(Encoders.bean(ResultCommunityList.class)) - .write() - .option("compression", "gzip") - .mode(SaveMode.Overwrite) - .json(outputResultPath); + .sql(RESULT_COMMUNITY_LIST_QUERY) + .as(Encoders.bean(ResultCommunityList.class)) + .write() + .option("compression", "gzip") + .mode(SaveMode.Append) + .json(outputResultPath); + } public static List getCommunityList(final String baseURL) throws IOException { diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep2.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep2.java index a53d3dfe32..9bebc36e58 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep2.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep2.java @@ -4,6 +4,7 @@ package eu.dnetlib.dhp.resulttocommunityfromsemrel; import static eu.dnetlib.dhp.PropagationConstant.*; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; +import java.util.ArrayList; import java.util.HashSet; import java.util.Set; @@ -76,22 +77,13 @@ public class PrepareResultCommunitySetStep2 { if (b == null) { return a; } - Set community_set = new HashSet<>(); - a.getCommunityList().stream().forEach(aa -> community_set.add(aa)); - b - .getCommunityList() - .stream() - .forEach( - aa -> { - if (!community_set.contains(aa)) { - a.getCommunityList().add(aa); - community_set.add(aa); - } - }); + Set community_set = new HashSet<>(a.getCommunityList()); + community_set.addAll(b.getCommunityList()); + a.setCommunityList(new ArrayList<>(community_set)); return a; }) .map(Tuple2::_2) - .map(r -> OBJECT_MAPPER.writeValueAsString(r)) + .map(OBJECT_MAPPER::writeValueAsString) .saveAsTextFile(outputPath, GzipCodec.class); } diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/ResultToCommunityJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/ResultToCommunityJobTest.java index 0d5b12c808..c1fcff4d99 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/ResultToCommunityJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/ResultToCommunityJobTest.java @@ -6,8 +6,11 @@ import static org.apache.spark.sql.functions.desc; import java.io.IOException; import java.nio.file.Files; import java.nio.file.Path; +import java.util.ArrayList; import java.util.List; +import java.util.stream.Collectors; +import eu.dnetlib.dhp.resulttocommunityfromorganization.ResultCommunityList; import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; @@ -25,6 +28,7 @@ import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.schema.oaf.Dataset; +import scala.collection.Seq; public class ResultToCommunityJobTest { @@ -271,4 +275,57 @@ public class ResultToCommunityJobTest { .get(0) .getString(0)); } + + @Test + public void prepareStep1Test() throws Exception { + /* + + + final String allowedsemrel = join(",", Arrays.stream(parser.get("allowedsemrels").split(";")) + .map(value -> "'" + value.toLowerCase() + "'") + .toArray(String[]::new)); + + log.info("allowedSemRel: {}", new Gson().toJson(allowedsemrel)); + + final String baseURL = parser.get("baseURL"); + log.info("baseURL: {}", baseURL); + */ + PrepareResultCommunitySetStep1 + .main( + new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", getClass() + .getResource("/eu/dnetlib/dhp/resulttocommunityfromsemrel/graph") + .getPath(), + "-hive_metastore_uris", "", + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", + "-outputPath", workingDir.toString() + "/preparedInfo", + "-allowedsemrels","issupplementto;issupplementedby", + "-baseURL","https://dev-openaire.d4science.org/openaire/community/" + }); + + + org.apache.spark.sql.Dataset resultCommunityList = spark.read().schema(Encoders.bean(ResultCommunityList.class).schema()) + .json(workingDir.toString() + "/preparedInfo/publication") + .as(Encoders.bean(ResultCommunityList.class)); + + Assertions.assertEquals(2, resultCommunityList.count()); + Assertions.assertEquals(1,resultCommunityList.filter("resultId = '50|dedup_wf_001::06e51d2bf295531b2d2e7a1b55500783'").count()); + Assertions.assertEquals(1,resultCommunityList.filter("resultId = '50|pending_org_::82f63b2d21ae88596b9d8991780e9888'").count()); + + ArrayList communities = resultCommunityList + .filter("resultId = '50|dedup_wf_001::06e51d2bf295531b2d2e7a1b55500783'") + .first().getCommunityList(); + Assertions.assertEquals(2, communities.size()); + Assertions.assertTrue(communities.stream().anyMatch(cid -> "beopen".equals(cid))); + Assertions.assertTrue(communities.stream().anyMatch(cid -> "dh-ch".equals(cid))); + + communities = resultCommunityList + .filter("resultId = '50|pending_org_::82f63b2d21ae88596b9d8991780e9888'") + .first().getCommunityList(); + Assertions.assertEquals(1, communities.size()); + Assertions.assertEquals("dh-ch", communities.get(0)); + } + + } diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttocommunityfromsemrel/graph/publication/part-00000.json b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttocommunityfromsemrel/graph/publication/part-00000.json new file mode 100644 index 0000000000..ae9083c655 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttocommunityfromsemrel/graph/publication/part-00000.json @@ -0,0 +1,13 @@ +{"author":[{"fullname":"Tanouayi, Gnon","name":"Gnon","pid":[],"rank":1,"surname":"Tanouayi"},{"fullname":"GNANDI, Kissao","name":"Kissao","pid":[],"rank":2,"surname":"Gnandi"},{"fullname":"Ouro-Sama, Kamilou","name":"Kamilou","pid":[],"rank":3,"surname":"Ouro-Sama"},{"fullname":"Ahoudi, Housséni","name":"Housséni","pid":[],"rank":4,"surname":"Ahoudi"},{"fullname":"Solitoke, Hodabalo Dhéoulaba","name":"Hodabalo Dhéoulaba","pid":[],"rank":5,"surname":"Solitoke"},{"fullname":"Badassan, Tchaa Esso-Essinam","name":"Tchaa Esso-Essinam","pid":[],"rank":6,"surname":"Badassan"},{"fullname":"Nyametso, A. Yawovi","name":"A. Yawovi","pid":[],"rank":7,"surname":"Nyametso"},{"fullname":"Agbéko, Aduayi-Akué Adoté","name":"Aduayi-Akué Adoté","pid":[],"rank":8,"surname":"Agbéko"}],"bestaccessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"collectedfrom":[{"key":"10|eurocrisdris::fe4903425d9040f680d8610d9079ea14","value":"Episciences"}],"context":[],"contributor":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"Importer of dst articles previously hosted by inist Eid system account"}],"country":[],"coverage":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"dateofacceptance":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"2017-05-01"},"dateofcollection":"2022-03-01T00:17:08.896Z","dateoftransformation":"2022-03-01T02:57:50.566Z","description":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"This study is a contribution to the development of adsorption techniques for the removal of fluoride in natural waters. The work is carried out on a laboratory scale using local geo-materials sorbents, on the one hand the residues from the treatment of natural phosphorite of Hahotoé-Kpogamé and on the other hand the attapulgite clay mineral from the costal basin of Togo. The work carried out concerns the adsorption of fluoride on those sorbents. The following parameters are batch tested on synthetic fluoride solutions: time, solution pH, geo-material dose and fluoride concentration. The fluoride is analyzed by absorption spectrometry. The adsorption yields on the phosphorite treatment residues for aqueous fluoride solutions at an initial concentration of 10 mg/L and an adsorbent concentration of 10 g/L are 49 % at pH 6.5 and 66 % at pH 4.0. In the same experimental conditions, the yields on clay minerals are 28.2 % and 36.3 %. These yields are logically improved by increasing the adsorbent dosage (from 2 to 30 g/L). Additional tests are carried out on natural water at an initial fluoride concentration of 3.76 mg/L."},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"Cette étude est une contribution au développement de techniques d’adsorption pour l’élimination du fluor dans les eaux naturelles. Les travaux ont été réalisés à l’échelle du laboratoire en utilisant comme sorbants des géo-matériaux locaux, d’une part les résidus du traitement des phosphates naturels de Hahotoé-Kpogamé et d’autre part l’argilite feuilletée du bassin sédimentaire côtier du Togo. Les travaux réalisés concernent l’adsorption du fluor sur les sorbants considérés. Les paramètres suivants ont été testés en batch sur des solutions synthétiques de fluor : le temps, le pH de la solution, la dose du géo-matériau et la concentration du fluor. Le fluor a été dosé par spectromètrie d’absorption. Les rendements d’adsorption sur les résidus de traitement des phosphates pour des solutions aqueuses de fluor à concentration initiale de 10 mg/L et une concentration en adsorbant de 10 g/L ont été de 49 % à pH 6,5 et 66 % à pH de 4,0. Dans les mêmes conditions expérimentales, les rendements sur les argilites ont été de 28,2 % et 36,3 %. Ces rendements ont logiquement été améliorés en augmentant le dosage en adsorbant (de 2 à 30 g/L). Des essais complémentaires ont été réalisés sur une eau naturelle à une concentration initiale en fluor de 3,76 mg/L."}],"externalReference":[],"extraInfo":[],"format":[],"fulltext":[],"id":"50|06cdd3ff4700::49ec404cee4e1452808aabeaffbd3072","instance":[{"accessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"alternateIdentifier":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"doi","classname":"Digital Object 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Hydrolysates of lignocellulosic biomass, used as substrates for the sustainable production of fuels and chemicals often contain high amounts of phenolic compounds inhibiting the production microbiota. Quantification of these inhibitor compounds may help to understand possible difficulties in bioprocessing and further the development of more efficient, robust and tolerable processes. A separation method based on capillary electrophoresis with UV detection was developed for the simultaneous quantification of 10 phenolic compounds that may have inhibitor properties. Intraday relative standard deviations were less than 0.7% for migration times and between 2.6% and 6.4% for peak areas. Interday relative standard deviations were less than 3.0% for migration times and between 5.0% and 7.2% for peak areas. The method was applied to demonstrate that Saccharomyces cerevisiae was able to decrease the concentrations of vanillin, coniferyl aldehyde, syringaldehyde, acetoguaiacone and cinnamic acid during the cultivation, whereas the concentrations of phenols increased.

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Ex situ analyses of the tiles were performed by secondary ion mass spectrometry.
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The deposition rate for carbon by plasma was also calculated in long term experiment. 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