From e5b04e61ff8f7f7b1d80f607e0fcb4da7c7c9f37 Mon Sep 17 00:00:00 2001 From: Miriam Baglioni Date: Thu, 21 Nov 2024 10:20:12 +0100 Subject: [PATCH 1/5] [CommunityPatents] extends the community propagation considering also the results of type patents linked with a isrelatedto semantcis --- .../main/java/eu/dnetlib/dhp/api/Utils.java | 2 +- .../PrepareResultCommunitySetStep1.java | 51 ++++++++++++++++--- .../PrepareResultCommunitySetStep2.java | 18 ++----- 3 files changed, 49 insertions(+), 22 deletions(-) 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 6079da365..1e39d99c3 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 aede9ef05..ff496bb87 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.*; @@ -45,7 +48,7 @@ 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 +59,16 @@ public class PrepareResultCommunitySetStep1 { + "where length(co) > 0 " + "group by resultId"; + private static final String RESULT_CONTEXT_QUERY_TEMPLATE_IS_RELATED_TO = "select target resultId, community_context " + + "from (select id, collect_set(co.id) community_context " + + " from result " + + " lateral view explode (context) c as co " + + " where datainfo.deletedbyinference = false %s " + + " and array_contains(instance.instancetype.classname, 'Patent') group by id) p " + + " JOIN " + + " (select source, target from relation " + + " where datainfo.deletedbyinference = false %s ) r ON p.id = r.source"; + public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils .toString( @@ -82,15 +95,20 @@ 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(";")); + 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); - 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)); + log.info("communityIdList: {}", new Gson().toJson(communityIdList)); final String resultType = resultClassName.substring(resultClassName.lastIndexOf(".") + 1).toLowerCase(); log.info("resultType: {}", resultType); @@ -118,10 +136,10 @@ 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); @@ -141,8 +159,15 @@ public class PrepareResultCommunitySetStep1 { String resultContextQuery = String .format( RESULT_CONTEXT_QUERY_TEMPLATE, - getConstraintList(" lower(co.id) = '", communityIdList), - getConstraintList(" lower(relClass) = '", allowedsemrel)); + " lower(co.id) IN " + communityIdList, + " AND lower(relClass) IN " + allowedsemrel); + + String resultContextQueryIsRelatedTo = String + .format( + RESULT_CONTEXT_QUERY_TEMPLATE_IS_RELATED_TO, + " AND lower(co.id) IN " + communityIdList, + "AND lower(relClass) = '"+ + ModelConstants.IS_RELATED_TO.toLowerCase() + "'"); Dataset result_context = spark.sql(resultContextQuery); result_context.createOrReplaceTempView("result_context"); @@ -154,6 +179,16 @@ public class PrepareResultCommunitySetStep1 { .option("compression", "gzip") .mode(SaveMode.Overwrite) .json(outputResultPath); + + result_context = spark.sql(resultContextQueryIsRelatedTo); + result_context.createOrReplaceTempView("result_context"); + spark + .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 a53d3dfe3..9bebc36e5 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); } -- 2.17.1 From 821700299a31e5201f616fd4235dcd599018d19b Mon Sep 17 00:00:00 2001 From: Miriam Baglioni Date: Fri, 22 Nov 2024 17:21:58 +0100 Subject: [PATCH 2/5] [patents] added test and resources --- .../PrepareResultCommunitySetStep1.java | 93 +++++++++++-------- .../ResultToCommunityJobTest.java | 55 +++++++++++ .../graph/publication/part-00000.json | 13 +++ .../graph/relation/part-00000.json | 24 +++++ 4 files changed, 147 insertions(+), 38 deletions(-) create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttocommunityfromsemrel/graph/publication/part-00000.json create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttocommunityfromsemrel/graph/relation/part-00000.json 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 ff496bb87..8f23a4cfd 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 @@ -37,7 +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 " @@ -59,15 +60,26 @@ public class PrepareResultCommunitySetStep1 { + "where length(co) > 0 " + "group by resultId"; - private static final String RESULT_CONTEXT_QUERY_TEMPLATE_IS_RELATED_TO = "select target resultId, community_context " - + "from (select id, collect_set(co.id) community_context " - + " from result " - + " lateral view explode (context) c as co " - + " where datainfo.deletedbyinference = false %s " - + " and array_contains(instance.instancetype.classname, 'Patent') group by id) p " - + " JOIN " - + " (select source, target from relation " - + " where datainfo.deletedbyinference = false %s ) r ON p.id = r.source"; + 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 datainfo.deletedbyinference = false AND 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 @@ -95,20 +107,18 @@ public class PrepareResultCommunitySetStep1 { SparkConf conf = new SparkConf(); conf.set("hive.metastore.uris", parser.get("hive_metastore_uris")); - 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 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 String communityIdList = join(",", getCommunityList(baseURL).stream() + final String communityIdList = "(" + join(",", getCommunityList(baseURL).stream() .map(value -> "'" + value.toLowerCase() + "'") - .toArray(String[]::new)); + .toArray(String[]::new)) + ")"; - log.info("communityIdList: {}", new Gson().toJson(communityIdList)); final String resultType = resultClassName.substring(resultClassName.lastIndexOf(".") + 1).toLowerCase(); log.info("resultType: {}", resultType); @@ -156,32 +166,38 @@ public class PrepareResultCommunitySetStep1 { final String outputResultPath = outputPath + "/" + resultType; log.info("writing output results to: {}", outputResultPath); + String resultContextQuery = String .format( RESULT_CONTEXT_QUERY_TEMPLATE, - " lower(co.id) IN " + communityIdList, - " AND lower(relClass) IN " + allowedsemrel); - - String resultContextQueryIsRelatedTo = String - .format( - RESULT_CONTEXT_QUERY_TEMPLATE_IS_RELATED_TO, - " AND lower(co.id) IN " + communityIdList, - "AND lower(relClass) = '"+ - ModelConstants.IS_RELATED_TO.toLowerCase() + "'"); - + "AND lower(co.id) IN " + communityIdList, + "AND lower(relClass) IN " + allowedsemrel); Dataset result_context = spark.sql(resultContextQuery); + //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); + + 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); - - result_context = spark.sql(resultContextQueryIsRelatedTo); - result_context.createOrReplaceTempView("result_context"); spark .sql(RESULT_COMMUNITY_LIST_QUERY) .as(Encoders.bean(ResultCommunityList.class)) @@ -189,6 +205,7 @@ public class PrepareResultCommunitySetStep1 { .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/test/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/ResultToCommunityJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/ResultToCommunityJobTest.java index 0d5b12c80..4361b6f39 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 +275,55 @@ 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 000000000..7957bcfd5 --- /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). 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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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+{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"isAuthorInstitutionOf","relType":"resultOrganization","source":"20|pending_org_::c522a7c935f9fd9578122e60eeec282c","subRelType":"affiliation","target":"50|dedup_wf_001::12206bf78aabd7d52132477182d19147","validated":false} +{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional 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8f23a4cfd..5af2bf481 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 @@ -173,24 +173,13 @@ public class PrepareResultCommunitySetStep1 { "AND lower(co.id) IN " + communityIdList, "AND lower(relClass) IN " + allowedsemrel); Dataset result_context = spark.sql(resultContextQuery); - //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); 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"); 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 4361b6f39..c1fcff4d9 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 @@ -326,4 +326,6 @@ public class ResultToCommunityJobTest { Assertions.assertEquals(1, communities.size()); Assertions.assertEquals("dh-ch", communities.get(0)); } + + } -- 2.17.1 From ee84db7a6a5ff1e271f5d6a0cfdfcc07e1a59ac9 Mon Sep 17 00:00:00 2001 From: Miriam Baglioni Date: Fri, 6 Dec 2024 12:20:13 +0100 Subject: [PATCH 4/5] [communityfromsemrelpropagation] added filtering to remove the deletedbyinference and invisible results --- .../PrepareResultCommunitySetStep1.java | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) 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 5af2bf481..764390442 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 @@ -70,7 +70,7 @@ public class PrepareResultCommunitySetStep1 { 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 datainfo.deletedbyinference = false AND lower(co.id) IN %s" + + " where lower(co.id) IN %s" + " group by id"; private static final String RESULT_PATENT = "select id " + @@ -160,7 +160,8 @@ 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; -- 2.17.1 From 666155bafaa04db7153c98d91b911d88e9cb2f01 Mon Sep 17 00:00:00 2001 From: Miriam Baglioni Date: Fri, 6 Dec 2024 12:26:41 +0100 Subject: [PATCH 5/5] [communityfromsemrelpropagation] changed resource to have deletedbyinference = false. --- .../graph/publication/part-00000.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 index 7957bcfd5..ae9083c65 100644 --- 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 @@ -7,7 +7,7 @@ {"author":[{"fullname":"Turkia, Heidi","name":"Heidi","pid":[],"rank":1,"surname":"Turkia"},{"fullname":"Sirén, Heli","name":"Heli","pid":[],"rank":2,"surname":"Sirén"},{"fullname":"Penttilä, Merja","name":"Merja","pid":[],"rank":3,"surname":"Penttilä"},{"fullname":"Pitkänen, Juha Pekka","name":"Juha Pekka","pid":[],"rank":4,"surname":"Pitkänen"}],"bestaccessright":{"classid":"CLOSED","classname":"Closed 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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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Results include drying rates for 1.5 mm thick birch veneers as well as 1.5 mm and 2.6 mm thick spruce veneers of both heartwood and sapwood. Based on the test results, material parameter values for a simplified drying model are assessed. The model is based on the use of an effective diffusion coefficient and an effective surface emission coefficient, which values are calibrated to fit to the experimental results. It is observed, that separate model parameter sets are needed for the two different species but also for occurrence of heartwood or sapwood (spruce) and different thickness values of veneers."}],"externalReference":[],"extraInfo":[],"format":[],"fulltext":[],"id":"50|dedup_wf_001::08d6f2001319c86d0e69b0f83ad75df2","instance":[{"accessright":{"classid":"CLOSED","classname":"Closed 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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