From e653756e3d855ae7c838afdb8c09b61cfb17d749 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 4 Oct 2021 18:40:07 +0200 Subject: [PATCH] applied some suggestiond from Sonar Lint --- .../dnetlib/dhp/oa/graph/dump/Constants.java | 27 ++-- .../dhp/oa/graph/dump/DumpProducts.java | 5 +- .../eu/dnetlib/dhp/oa/graph/dump/MakeTar.java | 12 +- .../oa/graph/dump/QueryInformationSystem.java | 4 +- .../dhp/oa/graph/dump/ResultMapper.java | 122 +++++++++--------- .../dhp/oa/graph/dump/SaveCommunityMap.java | 8 +- .../dhp/oa/graph/dump/SendToZenodoHDFS.java | 23 +--- .../graph/dump/community/CommunitySplit.java | 8 +- .../community/SparkPrepareResultProject.java | 6 +- .../dump/complete/CreateContextRelation.java | 3 +- .../dhp/oa/graph/dump/complete/Extractor.java | 43 +++--- .../dhp/oa/graph/dump/complete/Process.java | 5 +- .../dump/complete/QueryInformationSystem.java | 18 ++- .../dump/complete/SparkDumpRelationJob.java | 33 +++-- .../complete/SparkOrganizationRelation.java | 3 +- .../SparkSelectValidRelationsJob.java | 1 - .../dump/exceptions/MyRuntimeException.java | 30 +++++ .../NoAvailableEntityTypeException.java | 29 +++++ .../funderresults/SparkDumpFunderResults.java | 3 - .../SparkResultLinkedToProject.java | 3 - .../dump/PrepareResultProjectJobTest.java | 91 +++++++------ ...DumpOrganizationProjectDatasourceTest.java | 5 +- .../dhp/oa/graph/hostedbymap/TestApply.scala | 2 +- .../complete/organization/organization.json | 4 +- 24 files changed, 274 insertions(+), 214 deletions(-) create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/exceptions/MyRuntimeException.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/exceptions/NoAvailableEntityTypeException.java diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java index 6dca09b63..61167639c 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java @@ -5,37 +5,40 @@ import java.util.Map; import com.google.common.collect.Maps; +import eu.dnetlib.dhp.schema.common.ModelConstants; + public class Constants { - public static final Map accessRightsCoarMap = Maps.newHashMap(); - public static final Map coarCodeLabelMap = Maps.newHashMap(); + protected static final Map accessRightsCoarMap = Maps.newHashMap(); + protected static final Map coarCodeLabelMap = Maps.newHashMap(); public static final String INFERRED = "Inferred by OpenAIRE"; + public static final String CABF2 = "c_abf2"; public static final String HARVESTED = "Harvested"; public static final String DEFAULT_TRUST = "0.9"; public static final String USER_CLAIM = "Linked by user"; - public static String COAR_ACCESS_RIGHT_SCHEMA = "http://vocabularies.coar-repositories.org/documentation/access_rights/"; + public static final String COAR_ACCESS_RIGHT_SCHEMA = "http://vocabularies.coar-repositories.org/documentation/access_rights/"; - public static String ZENODO_COMMUNITY_PREFIX = "https://zenodo.org/communities/"; + public static final String ZENODO_COMMUNITY_PREFIX = "https://zenodo.org/communities/"; - public static String RESEARCH_COMMUNITY = "Research Community"; + public static final String RESEARCH_COMMUNITY = "Research Community"; - public static String RESEARCH_INFRASTRUCTURE = "Research Infrastructure/Initiative"; + public static final String RESEARCH_INFRASTRUCTURE = "Research Infrastructure/Initiative"; static { - accessRightsCoarMap.put("OPEN", "c_abf2"); + accessRightsCoarMap.put(ModelConstants.ACCESS_RIGHT_OPEN, CABF2); accessRightsCoarMap.put("RESTRICTED", "c_16ec"); - accessRightsCoarMap.put("OPEN SOURCE", "c_abf2"); - accessRightsCoarMap.put("CLOSED", "c_14cb"); - accessRightsCoarMap.put("EMBARGO", "c_f1cf"); + accessRightsCoarMap.put("OPEN SOURCE", CABF2); + accessRightsCoarMap.put(ModelConstants.ACCESS_RIGHT_CLOSED, "c_14cb"); + accessRightsCoarMap.put(ModelConstants.ACCESS_RIGHT_EMBARGO, "c_f1cf"); } static { - coarCodeLabelMap.put("c_abf2", "OPEN"); + coarCodeLabelMap.put(CABF2, ModelConstants.ACCESS_RIGHT_OPEN); coarCodeLabelMap.put("c_16ec", "RESTRICTED"); - coarCodeLabelMap.put("c_14cb", "CLOSED"); + coarCodeLabelMap.put("c_14cb", ModelConstants.ACCESS_RIGHT_CLOSED); coarCodeLabelMap.put("c_f1cf", "EMBARGO"); } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java index d09e584a3..68e1e8402 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java @@ -17,6 +17,7 @@ import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; +import eu.dnetlib.dhp.oa.graph.dump.exceptions.NoAvailableEntityTypeException; import eu.dnetlib.dhp.schema.oaf.*; /** @@ -66,7 +67,7 @@ public class DumpProducts implements Serializable { private static O execMap(I value, CommunityMap communityMap, - String dumpType) { + String dumpType) throws NoAvailableEntityTypeException { Optional odInfo = Optional.ofNullable(value.getDataInfo()); if (odInfo.isPresent()) { @@ -94,7 +95,7 @@ public class DumpProducts implements Serializable { } return null; }).filter(Objects::nonNull).collect(Collectors.toList()); - if (toDumpFor.size() == 0) { + if (toDumpFor.isEmpty()) { return null; } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/MakeTar.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/MakeTar.java index 0d2df11fe..b56849a3a 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/MakeTar.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/MakeTar.java @@ -57,16 +57,16 @@ public class MakeTar implements Serializable { public static void makeTArArchive(FileSystem fileSystem, String inputPath, String outputPath, int gBperSplit) throws IOException { - RemoteIterator dir_iterator = fileSystem.listLocatedStatus(new Path(inputPath)); + RemoteIterator dirIterator = fileSystem.listLocatedStatus(new Path(inputPath)); - while (dir_iterator.hasNext()) { - LocatedFileStatus fileStatus = dir_iterator.next(); + while (dirIterator.hasNext()) { + LocatedFileStatus fileStatus = dirIterator.next(); Path p = fileStatus.getPath(); - String p_string = p.toString(); - String entity = p_string.substring(p_string.lastIndexOf("/") + 1); + String pathString = p.toString(); + String entity = pathString.substring(pathString.lastIndexOf("/") + 1); - MakeTarArchive.tarMaxSize(fileSystem, p_string, outputPath + "/" + entity, entity, gBperSplit); + MakeTarArchive.tarMaxSize(fileSystem, pathString, outputPath + "/" + entity, entity, gBperSplit); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystem.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystem.java index 4d0c59955..b972de6e9 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystem.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystem.java @@ -40,10 +40,10 @@ public class QueryInformationSystem { "{$x//CONFIGURATION/context/@label}" + ""; - public CommunityMap getCommunityMap(boolean singleCommunity, String community_id) + public CommunityMap getCommunityMap(boolean singleCommunity, String communityId) throws ISLookUpException, DocumentException, SAXException { if (singleCommunity) - return getMap(isLookUp.quickSearchProfile(XQUERY_CI.replace("%s", "'" + community_id + "'"))); + return getMap(isLookUp.quickSearchProfile(XQUERY_CI.replace("%s", "'" + communityId + "'"))); return getMap(isLookUp.quickSearchProfile(XQUERY_ALL)); } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java index 988a8c7a4..0f3192c25 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java @@ -6,9 +6,8 @@ import java.util.*; import java.util.stream.Collectors; import org.apache.commons.lang3.StringUtils; -import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.sql.Encoders; +import eu.dnetlib.dhp.oa.graph.dump.exceptions.NoAvailableEntityTypeException; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.dump.oaf.*; import eu.dnetlib.dhp.schema.dump.oaf.AccessRight; @@ -29,7 +28,7 @@ import eu.dnetlib.dhp.schema.oaf.*; public class ResultMapper implements Serializable { public static Result map( - E in, Map communityMap, String dumpType) { + E in, Map communityMap, String dumpType) throws NoAvailableEntityTypeException { Result out; if (Constants.DUMPTYPE.COMPLETE.getType().equals(dumpType)) { @@ -136,6 +135,8 @@ public class ResultMapper implements Serializable { out.setType(ModelConstants.ORP_DEFAULT_RESULTTYPE.getClassname()); break; + default: + throw new NoAvailableEntityTypeException(); } Optional> mes = Optional.ofNullable(input.getMeasures()); @@ -156,17 +157,15 @@ public class ResultMapper implements Serializable { // I do not map Access Right UNKNOWN or OTHER Optional oar = Optional.ofNullable(input.getBestaccessright()); - if (oar.isPresent()) { - if (Constants.accessRightsCoarMap.containsKey(oar.get().getClassid())) { - String code = Constants.accessRightsCoarMap.get(oar.get().getClassid()); - out - .setBestaccessright( - AccessRight - .newInstance( - code, - Constants.coarCodeLabelMap.get(code), - Constants.COAR_ACCESS_RIGHT_SCHEMA)); - } + if (oar.isPresent() && Constants.accessRightsCoarMap.containsKey(oar.get().getClassid())) { + String code = Constants.accessRightsCoarMap.get(oar.get().getClassid()); + out + .setBestaccessright( + AccessRight + .newInstance( + code, + Constants.coarCodeLabelMap.get(code), + Constants.COAR_ACCESS_RIGHT_SCHEMA)); } final List contributorList = new ArrayList<>(); @@ -263,7 +262,7 @@ public class ResultMapper implements Serializable { .stream() .filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("main title")) .collect(Collectors.toList()); - if (iTitle.size() > 0) { + if (!iTitle.isEmpty()) { out.setMaintitle(iTitle.get(0).getValue()); } @@ -272,7 +271,7 @@ public class ResultMapper implements Serializable { .stream() .filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("subtitle")) .collect(Collectors.toList()); - if (iTitle.size() > 0) { + if (!iTitle.isEmpty()) { out.setSubtitle(iTitle.get(0).getValue()); } @@ -301,9 +300,8 @@ public class ResultMapper implements Serializable { Optional .ofNullable(input.getSource()) - .ifPresent(value -> out.setSource(value.stream().map(s -> s.getValue()).collect(Collectors.toList()))); - // value.stream().forEach(s -> sourceList.add(s.getValue()))); - // out.setSource(input.getSource().stream().map(s -> s.getValue()).collect(Collectors.toList())); + .ifPresent(value -> out.setSource(value.stream().map(Field::getValue).collect(Collectors.toList()))); + List subjectList = new ArrayList<>(); Optional .ofNullable(input.getSubject()) @@ -334,14 +332,14 @@ public class ResultMapper implements Serializable { value -> value .stream() .map(c -> { - String community_id = c.getId(); - if (community_id.indexOf("::") > 0) { - community_id = community_id.substring(0, community_id.indexOf("::")); + String communityId = c.getId(); + if (communityId.contains("::")) { + communityId = communityId.substring(0, communityId.indexOf("::")); } - if (communities.contains(community_id)) { + if (communities.contains(communityId)) { Context context = new Context(); - context.setCode(community_id); - context.setLabel(communityMap.get(community_id)); + context.setCode(communityId); + context.setLabel(communityMap.get(communityId)); Optional> dataInfo = Optional.ofNullable(c.getDataInfo()); if (dataInfo.isPresent()) { List provenance = new ArrayList<>(); @@ -361,7 +359,11 @@ public class ResultMapper implements Serializable { .filter(Objects::nonNull) .collect(Collectors.toSet())); - context.setProvenance(getUniqueProvenance(provenance)); + try { + context.setProvenance(getUniqueProvenance(provenance)); + } catch (NoAvailableEntityTypeException e) { + e.printStackTrace(); + } } return context; } @@ -371,7 +373,7 @@ public class ResultMapper implements Serializable { .collect(Collectors.toList())) .orElse(new ArrayList<>()); - if (contextList.size() > 0) { + if (!contextList.isEmpty()) { Set hashValue = new HashSet<>(); List remainigContext = new ArrayList<>(); contextList.forEach(c -> { @@ -417,35 +419,34 @@ public class ResultMapper implements Serializable { private static void setCommonValue(eu.dnetlib.dhp.schema.oaf.Instance i, I instance) { Optional opAr = Optional.ofNullable(i.getAccessright()); - if (opAr.isPresent()) { - if (Constants.accessRightsCoarMap.containsKey(opAr.get().getClassid())) { - String code = Constants.accessRightsCoarMap.get(opAr.get().getClassid()); + if (opAr.isPresent() && Constants.accessRightsCoarMap.containsKey(opAr.get().getClassid())) { + String code = Constants.accessRightsCoarMap.get(opAr.get().getClassid()); - instance - .setAccessright( - AccessRight - .newInstance( - code, - Constants.coarCodeLabelMap.get(code), - Constants.COAR_ACCESS_RIGHT_SCHEMA)); - if (opAr.get().getOpenAccessRoute() != null) { - switch (opAr.get().getOpenAccessRoute()) { - case hybrid: - instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.hybrid); - break; - case gold: - instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.gold); - break; - case green: - instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.green); - break; - case bronze: - instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.bronze); - break; + instance + .setAccessright( + AccessRight + .newInstance( + code, + Constants.coarCodeLabelMap.get(code), + Constants.COAR_ACCESS_RIGHT_SCHEMA)); + if (opAr.get().getOpenAccessRoute() != null) { + switch (opAr.get().getOpenAccessRoute()) { + case hybrid: + instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.hybrid); + break; + case gold: + instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.gold); + break; + case green: + instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.green); + break; + case bronze: + instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.bronze); + break; - } } } + } Optional @@ -498,7 +499,8 @@ public class ResultMapper implements Serializable { } - private static List getUniqueProvenance(List provenance) { + private static List getUniqueProvenance(List provenance) + throws NoAvailableEntityTypeException { Provenance iProv = new Provenance(); Provenance hProv = new Provenance(); @@ -520,6 +522,8 @@ public class ResultMapper implements Serializable { case Constants.USER_CLAIM: lProv = getHighestTrust(lProv, p); break; + default: + throw new NoAvailableEntityTypeException(); } } @@ -599,19 +603,19 @@ public class ResultMapper implements Serializable { } private static Pid getOrcid(List p) { - List pid_list = p.stream().map(pid -> { + List pidList = p.stream().map(pid -> { if (pid.getQualifier().getClassid().equals(ModelConstants.ORCID) || (pid.getQualifier().getClassid().equals(ModelConstants.ORCID_PENDING))) { return pid; } return null; - }).filter(pid -> pid != null).collect(Collectors.toList()); + }).filter(Objects::nonNull).collect(Collectors.toList()); - if (pid_list.size() == 1) { - return getAuthorPid(pid_list.get(0)); + if (pidList.size() == 1) { + return getAuthorPid(pidList.get(0)); } - List orcid = pid_list + List orcid = pidList .stream() .filter( ap -> ap @@ -622,7 +626,7 @@ public class ResultMapper implements Serializable { if (orcid.size() == 1) { return getAuthorPid(orcid.get(0)); } - orcid = pid_list + orcid = pidList .stream() .filter( ap -> ap diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SaveCommunityMap.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SaveCommunityMap.java index 971324744..1eff99892 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SaveCommunityMap.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SaveCommunityMap.java @@ -31,9 +31,9 @@ import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; public class SaveCommunityMap implements Serializable { private static final Logger log = LoggerFactory.getLogger(SaveCommunityMap.class); - private final QueryInformationSystem queryInformationSystem; + private final transient QueryInformationSystem queryInformationSystem; - private final BufferedWriter writer; + private final transient BufferedWriter writer; public SaveCommunityMap(String hdfsPath, String hdfsNameNode, String isLookUpUrl) throws IOException { final Configuration conf = new Configuration(); @@ -84,12 +84,12 @@ public class SaveCommunityMap implements Serializable { } - private void saveCommunityMap(boolean singleCommunity, String community_id) + private void saveCommunityMap(boolean singleCommunity, String communityId) throws ISLookUpException, IOException, DocumentException, SAXException { writer .write( Utils.OBJECT_MAPPER - .writeValueAsString(queryInformationSystem.getCommunityMap(singleCommunity, community_id))); + .writeValueAsString(queryInformationSystem.getCommunityMap(singleCommunity, communityId))); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SendToZenodoHDFS.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SendToZenodoHDFS.java index 09e301572..a19a3a5b6 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SendToZenodoHDFS.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SendToZenodoHDFS.java @@ -5,15 +5,13 @@ import java.io.Serializable; import java.util.Optional; import org.apache.commons.io.IOUtils; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.fs.*; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.api.MissingConceptDoiException; import eu.dnetlib.dhp.common.api.ZenodoAPIClient; -import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; +import eu.dnetlib.dhp.oa.graph.dump.exceptions.NoAvailableEntityTypeException; public class SendToZenodoHDFS implements Serializable { @@ -21,8 +19,6 @@ public class SendToZenodoHDFS implements Serializable { private static final String VERSION = "version"; // to be used to upload a new version of a published deposition private static final String UPDATE = "update"; // to upload content to an open deposition not published - private static final Log log = LogFactory.getLog(SendToZenodoHDFS.class); - public static void main(final String[] args) throws Exception, MissingConceptDoiException { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils @@ -48,15 +44,12 @@ public class SendToZenodoHDFS implements Serializable { .orElse(false); final String depositionId = Optional.ofNullable(parser.get("depositionId")).orElse(null); - // final String communityMapPath = parser.get("communityMapPath"); Configuration conf = new Configuration(); conf.set("fs.defaultFS", hdfsNameNode); FileSystem fileSystem = FileSystem.get(conf); - // CommunityMap communityMap = Utils.readCommunityMap(fileSystem, communityMapPath); - RemoteIterator fileStatusListIterator = fileSystem .listFiles( new Path(hdfsPath), true); @@ -77,19 +70,17 @@ public class SendToZenodoHDFS implements Serializable { } zenodoApiClient.uploadOpenDeposition(depositionId); break; + default: + throw new NoAvailableEntityTypeException(); } while (fileStatusListIterator.hasNext()) { LocatedFileStatus fileStatus = fileStatusListIterator.next(); Path p = fileStatus.getPath(); - String p_string = p.toString(); - if (!p_string.endsWith("_SUCCESS")) { - String name = p_string.substring(p_string.lastIndexOf("/") + 1); -// log.info("Sending information for community: " + name); -// if (communityMap.containsKey(name.substring(0, name.lastIndexOf(".")))) { -// name = communityMap.get(name.substring(0, name.lastIndexOf("."))).replace(" ", "_") + ".tar"; -// } + String pString = p.toString(); + if (!pString.endsWith("_SUCCESS")) { + String name = pString.substring(pString.lastIndexOf("/") + 1); FSDataInputStream inputStream = fileSystem.open(p); zenodoApiClient.uploadIS(inputStream, name, fileStatus.getLen()); @@ -101,7 +92,7 @@ public class SendToZenodoHDFS implements Serializable { zenodoApiClient.sendMretadata(metadata); } - if (publish) { + if (Boolean.TRUE.equals(publish)) { zenodoApiClient.publish(); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java index 6abca2255..ee6341f84 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java @@ -5,7 +5,6 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.io.Serializable; import java.util.Optional; -import java.util.Set; import java.util.stream.Collectors; import org.apache.spark.SparkConf; @@ -16,6 +15,7 @@ import org.apache.spark.sql.SparkSession; import eu.dnetlib.dhp.oa.graph.dump.Utils; import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; +import eu.dnetlib.dhp.schema.dump.oaf.community.Context; /** * This class splits the dumped results according to the research community - research initiative/infrastructure they @@ -56,10 +56,10 @@ public class CommunitySplit implements Serializable { } private static void printResult(String c, Dataset result, String outputPath) { - Dataset community_products = result + Dataset communityProducts = result .filter((FilterFunction) r -> containsCommunity(r, c)); - community_products + communityProducts .write() .option("compression", "gzip") .mode(SaveMode.Overwrite) @@ -72,7 +72,7 @@ public class CommunitySplit implements Serializable { return r .getContext() .stream() - .map(con -> con.getCode()) + .map(Context::getCode) .collect(Collectors.toList()) .contains(c); } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java index 3508e4126..87ac20948 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java @@ -161,7 +161,7 @@ public class SparkPrepareResultProject implements Serializable { provenance.setTrust(di.get().getTrust()); p.setProvenance(provenance); } - if (relation.getValidated()) { + if (Boolean.TRUE.equals(relation.getValidated())) { p.setValidated(Validated.newInstance(relation.getValidated(), relation.getValidationDate())); } return p; @@ -179,8 +179,8 @@ public class SparkPrepareResultProject implements Serializable { f.setName(((Node) (doc.selectNodes("//funder/name").get(0))).getText()); f.setJurisdiction(((Node) (doc.selectNodes("//funder/jurisdiction").get(0))).getText()); for (Object o : doc.selectNodes("//funding_level_0")) { - List node = ((Node) o).selectNodes("./name"); - f.setFundingStream(((Node) node.get(0)).getText()); + List node = ((Node) o).selectNodes("./name"); + f.setFundingStream((node.get(0)).getText()); } return f; diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextRelation.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextRelation.java index 0c8f5dba4..a468e334d 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextRelation.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextRelation.java @@ -22,6 +22,7 @@ import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.graph.dump.Utils; +import eu.dnetlib.dhp.oa.graph.dump.exceptions.MyRuntimeException; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.dump.oaf.graph.*; import eu.dnetlib.dhp.schema.oaf.Datasource; @@ -120,7 +121,7 @@ public class CreateContextRelation implements Serializable { writer.write(Utils.OBJECT_MAPPER.writeValueAsString(r)); writer.newLine(); } catch (final Exception e) { - throw new RuntimeException(e); + throw new MyRuntimeException(e); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Extractor.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Extractor.java index 7e8ddfaf8..3e47ee664 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Extractor.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Extractor.java @@ -62,22 +62,7 @@ public class Extractor implements Serializable { .readPath(spark, inputPath, inputClazz) .flatMap((FlatMapFunction) value -> { List relationList = new ArrayList<>(); - Optional - .ofNullable(value.getInstance()) - .ifPresent(inst -> inst.forEach(instance -> { - Optional - .ofNullable(instance.getCollectedfrom()) - .ifPresent( - cf -> getRelatioPair( - value, relationList, cf, - ModelConstants.IS_PROVIDED_BY, ModelConstants.PROVIDES, hashCodes)); - Optional - .ofNullable(instance.getHostedby()) - .ifPresent( - hb -> getRelatioPair( - value, relationList, hb, - Constants.IS_HOSTED_BY, Constants.HOSTS, hashCodes)); - })); + extractRelationsFromInstance(hashCodes, value, relationList); Set communities = communityMap.keySet(); Optional .ofNullable(value.getContext()) @@ -136,8 +121,28 @@ public class Extractor implements Serializable { } + private void extractRelationsFromInstance(Set hashCodes, R value, + List relationList) { + Optional + .ofNullable(value.getInstance()) + .ifPresent(inst -> inst.forEach(instance -> { + Optional + .ofNullable(instance.getCollectedfrom()) + .ifPresent( + cf -> getRelatioPair( + value, relationList, cf, + ModelConstants.IS_PROVIDED_BY, ModelConstants.PROVIDES, hashCodes)); + Optional + .ofNullable(instance.getHostedby()) + .ifPresent( + hb -> getRelatioPair( + value, relationList, hb, + Constants.IS_HOSTED_BY, Constants.HOSTS, hashCodes)); + })); + } + private static void getRelatioPair(R value, List relationList, KeyValue cf, - String result_dtasource, String datasource_result, + String resultDatasource, String datasourceResult, Set hashCodes) { Provenance provenance = Optional .ofNullable(cf.getDataInfo()) @@ -162,7 +167,7 @@ public class Extractor implements Serializable { Relation r = getRelation( value.getId(), cf.getKey(), Constants.RESULT_ENTITY, Constants.DATASOURCE_ENTITY, - result_dtasource, ModelConstants.PROVISION, + resultDatasource, ModelConstants.PROVISION, provenance); if (!hashCodes.contains(r.hashCode())) { relationList @@ -173,7 +178,7 @@ public class Extractor implements Serializable { r = getRelation( cf.getKey(), value.getId(), Constants.DATASOURCE_ENTITY, Constants.RESULT_ENTITY, - datasource_result, ModelConstants.PROVISION, + datasourceResult, ModelConstants.PROVISION, provenance); if (!hashCodes.contains(r.hashCode())) { diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Process.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Process.java index b0b8b8acd..e1cb0e753 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Process.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Process.java @@ -9,6 +9,7 @@ import org.apache.commons.lang3.StringUtils; import eu.dnetlib.dhp.oa.graph.dump.Constants; import eu.dnetlib.dhp.oa.graph.dump.Utils; +import eu.dnetlib.dhp.oa.graph.dump.exceptions.MyRuntimeException; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.dump.oaf.Provenance; @@ -43,7 +44,7 @@ public class Process implements Serializable { return (R) ri; } catch (final Exception e) { - throw new RuntimeException(e); + throw new MyRuntimeException(e); } } @@ -91,7 +92,7 @@ public class Process implements Serializable { return relationList; } catch (final Exception e) { - throw new RuntimeException(e); + throw new MyRuntimeException(e); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystem.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystem.java index 88c92da53..fcc4bf39c 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystem.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystem.java @@ -13,7 +13,6 @@ import org.dom4j.io.SAXReader; import org.jetbrains.annotations.NotNull; import org.xml.sax.SAXException; -import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.utils.DHPUtils; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; @@ -94,9 +93,9 @@ public class QueryInformationSystem { Element root = doc.getRootElement(); cinfo.setId(root.attributeValue("id")); - Iterator it = root.elementIterator(); + Iterator it = root.elementIterator(); while (it.hasNext()) { - Element el = (Element) it.next(); + Element el = it.next(); if (el.getName().equals("category")) { String categoryId = el.attributeValue("id"); categoryId = categoryId.substring(categoryId.lastIndexOf("::") + 2); @@ -143,7 +142,7 @@ public class QueryInformationSystem { if (!prefix.equals(ModelSupport.entityIdPrefix.get("project"))) { return null; } - String funder = null; + String funder = ""; String grantId = null; String funding = null; for (Object node : el.selectNodes(".//param")) { @@ -158,9 +157,12 @@ public class QueryInformationSystem { case "CD_PROJECT_NUMBER": grantId = n.getText(); break; + default: + break; } } String nsp = null; + switch (funder.toLowerCase()) { case "ec": if (funding == null) { @@ -179,10 +181,12 @@ public class QueryInformationSystem { nsp = "dfgf________::"; break; default: - nsp = funder.toLowerCase(); + StringBuilder bld = new StringBuilder(); + bld.append(funder.toLowerCase()); for (int i = funder.length(); i < 12; i++) - nsp += "_"; - nsp += "::"; + bld.append("_"); + bld.append("::"); + nsp = bld.toString(); } return prefix + "|" + nsp + DHPUtils.md5(grantId); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkDumpRelationJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkDumpRelationJob.java index ab7e7e595..ddfd6592f 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkDumpRelationJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkDumpRelationJob.java @@ -71,22 +71,22 @@ public class SparkDumpRelationJob implements Serializable { Dataset relations = Utils.readPath(spark, inputPath, Relation.class); relations .map((MapFunction) relation -> { - eu.dnetlib.dhp.schema.dump.oaf.graph.Relation rel_new = new eu.dnetlib.dhp.schema.dump.oaf.graph.Relation(); - rel_new + eu.dnetlib.dhp.schema.dump.oaf.graph.Relation relNew = new eu.dnetlib.dhp.schema.dump.oaf.graph.Relation(); + relNew .setSource( Node .newInstance( relation.getSource(), ModelSupport.idPrefixEntity.get(relation.getSource().substring(0, 2)))); - rel_new + relNew .setTarget( Node .newInstance( relation.getTarget(), ModelSupport.idPrefixEntity.get(relation.getTarget().substring(0, 2)))); - rel_new + relNew .setReltype( RelType .newInstance( @@ -96,23 +96,22 @@ public class SparkDumpRelationJob implements Serializable { Optional odInfo = Optional.ofNullable(relation.getDataInfo()); if (odInfo.isPresent()) { DataInfo dInfo = odInfo.get(); - if (Optional.ofNullable(dInfo.getProvenanceaction()).isPresent()) { - if (Optional.ofNullable(dInfo.getProvenanceaction().getClassname()).isPresent()) { - rel_new - .setProvenance( - Provenance - .newInstance( - dInfo.getProvenanceaction().getClassname(), - dInfo.getTrust())); - } + if (Optional.ofNullable(dInfo.getProvenanceaction()).isPresent() && + Optional.ofNullable(dInfo.getProvenanceaction().getClassname()).isPresent()) { + relNew + .setProvenance( + Provenance + .newInstance( + dInfo.getProvenanceaction().getClassname(), + dInfo.getTrust())); } } - if (relation.getValidated()) { - rel_new.setValidated(relation.getValidated()); - rel_new.setValidationDate(relation.getValidationDate()); + if (Boolean.TRUE.equals(relation.getValidated())) { + relNew.setValidated(relation.getValidated()); + relNew.setValidationDate(relation.getValidationDate()); } - return rel_new; + return relNew; }, Encoders.bean(eu.dnetlib.dhp.schema.dump.oaf.graph.Relation.class)) .write() diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkOrganizationRelation.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkOrganizationRelation.java index 4365e861f..f9d2123e2 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkOrganizationRelation.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkOrganizationRelation.java @@ -58,7 +58,8 @@ public class SparkOrganizationRelation implements Serializable { final OrganizationMap organizationMap = new Gson() .fromJson(parser.get("organizationCommunityMap"), OrganizationMap.class); - log.info("organization map : {}", new Gson().toJson(organizationMap)); + final String serializedOrganizationMap = new Gson().toJson(organizationMap); + log.info("organization map : {}", serializedOrganizationMap); final String communityMapPath = parser.get("communityMapPath"); log.info("communityMapPath: {}", communityMapPath); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkSelectValidRelationsJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkSelectValidRelationsJob.java index e729e13df..20f3fc4a7 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkSelectValidRelationsJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkSelectValidRelationsJob.java @@ -131,7 +131,6 @@ public class SparkSelectValidRelationsJob implements Serializable { .option("compression", "gzip") .mode(SaveMode.Overwrite) .json(outputPath); - ; } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/exceptions/MyRuntimeException.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/exceptions/MyRuntimeException.java new file mode 100644 index 000000000..e325c4334 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/exceptions/MyRuntimeException.java @@ -0,0 +1,30 @@ + +package eu.dnetlib.dhp.oa.graph.dump.exceptions; + +public class MyRuntimeException extends RuntimeException { + + public MyRuntimeException() { + super(); + } + + public MyRuntimeException( + final String message, + final Throwable cause, + final boolean enableSuppression, + final boolean writableStackTrace) { + super(message, cause, enableSuppression, writableStackTrace); + } + + public MyRuntimeException(final String message, final Throwable cause) { + super(message, cause); + } + + public MyRuntimeException(final String message) { + super(message); + } + + public MyRuntimeException(final Throwable cause) { + super(cause); + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/exceptions/NoAvailableEntityTypeException.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/exceptions/NoAvailableEntityTypeException.java new file mode 100644 index 000000000..f3fbf740a --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/exceptions/NoAvailableEntityTypeException.java @@ -0,0 +1,29 @@ + +package eu.dnetlib.dhp.oa.graph.dump.exceptions; + +public class NoAvailableEntityTypeException extends Exception { + public NoAvailableEntityTypeException() { + super(); + } + + public NoAvailableEntityTypeException( + final String message, + final Throwable cause, + final boolean enableSuppression, + final boolean writableStackTrace) { + super(message, cause, enableSuppression, writableStackTrace); + } + + public NoAvailableEntityTypeException(final String message, final Throwable cause) { + super(message, cause); + } + + public NoAvailableEntityTypeException(final String message) { + super(message); + } + + public NoAvailableEntityTypeException(final Throwable cause) { + super(cause); + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java index 9cddba3c5..6aed9d7a8 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java @@ -10,7 +10,6 @@ import java.util.Optional; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.FilterFunction; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.*; import org.slf4j.Logger; @@ -18,10 +17,8 @@ import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; import eu.dnetlib.dhp.schema.dump.oaf.community.Project; -import eu.dnetlib.dhp.schema.oaf.Relation; /** * Splits the dumped results by funder and stores them in a folder named as the funder nsp (for all the funders, but the EC diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java index 156ae6d63..d89b9e86d 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java @@ -10,7 +10,6 @@ import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.api.java.function.MapGroupsFunction; -import org.apache.spark.sql.*; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SaveMode; @@ -19,13 +18,11 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.graph.dump.Constants; import eu.dnetlib.dhp.oa.graph.dump.Utils; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.Project; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.Result; -import scala.Tuple2; /** * Selects the results linked to projects. Only for these results the dump will be performed. diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java index a17861ad7..86d2f93c9 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java @@ -8,17 +8,14 @@ import java.nio.file.Files; import java.nio.file.Path; import org.apache.commons.io.FileUtils; - import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; - import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.Row; import org.apache.spark.sql.SparkSession; import org.junit.jupiter.api.AfterAll; - import org.junit.jupiter.api.BeforeAll; import org.junit.jupiter.api.Test; import org.slf4j.Logger; @@ -248,14 +245,14 @@ public class PrepareResultProjectJobTest { org.apache.spark.sql.Dataset verificationDataset = spark .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); - assertEquals(2, verificationDataset.count() ); + assertEquals(2, verificationDataset.count()); assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); + 1, + verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); assertEquals( - 1, - verificationDataset.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); + 1, + verificationDataset.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); verificationDataset.createOrReplaceTempView("dataset"); @@ -269,59 +266,59 @@ public class PrepareResultProjectJobTest { assertEquals(3, resultExplodedProvenance.count()); assertEquals(3, resultExplodedProvenance.filter("validatedByFunder = true").count()); assertEquals( - 2, - resultExplodedProvenance - .filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") - .count()); + 2, + resultExplodedProvenance + .filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") - .count()); + 1, + resultExplodedProvenance + .filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") + .count()); assertEquals( - 2, - resultExplodedProvenance - .filter("project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6'") - .count()); + 2, + resultExplodedProvenance + .filter("project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " + - "and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " + - "and validatedByFunder = true " + - "and validationDate = '2021-08-06'") - .count()); + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " + + "and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " + + "and validatedByFunder = true " + + "and validationDate = '2021-08-06'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " + - "and resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80' " + - "and validatedByFunder = true and validationDate = '2021-08-04'") - .count()); + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " + + "and resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80' " + + "and validatedByFunder = true and validationDate = '2021-08-04'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter("project = '40|aka_________::03376222b28a3aebf2730ac514818d04'") - .count()); + 1, + resultExplodedProvenance + .filter("project = '40|aka_________::03376222b28a3aebf2730ac514818d04'") + .count()); assertEquals( - 1, - resultExplodedProvenance - .filter( - "project = '40|aka_________::03376222b28a3aebf2730ac514818d04' " + - "and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " + - "and validatedByFunder = true and validationDate = '2021-08-05'") - .count()); + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::03376222b28a3aebf2730ac514818d04' " + + "and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " + + "and validatedByFunder = true and validationDate = '2021-08-05'") + .count()); assertEquals( - 3, resultExplodedProvenance.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); + 3, resultExplodedProvenance.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpOrganizationProjectDatasourceTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpOrganizationProjectDatasourceTest.java index 89ecdfb2b..051141e18 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpOrganizationProjectDatasourceTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpOrganizationProjectDatasourceTest.java @@ -6,6 +6,7 @@ import java.nio.file.Files; import java.nio.file.Path; import java.util.HashMap; +import eu.dnetlib.dhp.oa.graph.dump.exceptions.NoAvailableEntityTypeException; import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; @@ -98,7 +99,7 @@ public class DumpOrganizationProjectDatasourceTest { } @Test - public void dumpProjectTest() { + public void dumpProjectTest() throws NoAvailableEntityTypeException { final String sourcePath = getClass() .getResource("/eu/dnetlib/dhp/oa/graph/dump/complete/project") @@ -127,7 +128,7 @@ public class DumpOrganizationProjectDatasourceTest { } @Test - public void dumpDatasourceTest() { + public void dumpDatasourceTest() throws NoAvailableEntityTypeException { final String sourcePath = getClass() .getResource("/eu/dnetlib/dhp/oa/graph/dump/complete/datasource") .getPath(); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/TestApply.scala b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/TestApply.scala index 1bdcb60aa..4613d5636 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/TestApply.scala +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/TestApply.scala @@ -54,7 +54,7 @@ class TestApply extends java.io.Serializable{ assertTrue(pa.getInstance().get(0).getHostedby.getValue.equals("Academic Therapy")) assertTrue(pa.getInstance().get(0).getAccessright.getClassid.equals("OPEN")) assertTrue(pa.getInstance().get(0).getAccessright.getClassname.equals("Open Access")) - assertTrue(pa.getInstance().get(0).getAccessright.getOpenAccessRoute.equals(OpenAccessRoute.hybrid)) + assertTrue(pa.getInstance().get(0).getAccessright.getOpenAccessRoute.equals(OpenAccessRoute.gold)) assertTrue(pa.getBestaccessright.getClassid.equals("OPEN")) assertTrue(pa.getBestaccessright.getClassname.equals("Open Access")) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/complete/organization/organization.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/complete/organization/organization.json index d172419bf..e141af787 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/complete/organization/organization.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/complete/organization/organization.json @@ -1,6 +1,5 @@ {"alternativeNames":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""},"trust":""},"value":"한국초등도덕교육학회"}],"collectedfrom":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""},"trust":""},"key":"10|openaire____::ff4a008470319a22d9cf3d14af485977","value":"GRID - Global Research Identifier Database"}],"country":{"classid":"KR","classname":"Korea (Republic 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