diff --git a/.gitignore b/.gitignore index 486eacee9..3f00d9729 100644 --- a/.gitignore +++ b/.gitignore @@ -18,4 +18,5 @@ /*/build /build spark-warehouse -/dhp-workflows/dhp-graph-mapper/job-override.properties +/*/*/job-override.properties + diff --git a/dhp-build/dhp-build-assembly-resources/pom.xml b/dhp-build/dhp-build-assembly-resources/pom.xml index f1dd5f631..834af77fa 100644 --- a/dhp-build/dhp-build-assembly-resources/pom.xml +++ b/dhp-build/dhp-build-assembly-resources/pom.xml @@ -17,6 +17,7 @@ org.apache.maven.plugins maven-compiler-plugin + ${maven.compiler.plugin.version} diff --git a/dhp-build/dhp-build-properties-maven-plugin/pom.xml b/dhp-build/dhp-build-properties-maven-plugin/pom.xml index d561ce5dc..4f99d5298 100644 --- a/dhp-build/dhp-build-properties-maven-plugin/pom.xml +++ b/dhp-build/dhp-build-properties-maven-plugin/pom.xml @@ -53,6 +53,7 @@ org.apache.maven.plugins maven-compiler-plugin + ${maven.compiler.plugin.version} org.apache.maven.plugins diff --git a/dhp-common/pom.xml b/dhp-common/pom.xml index 6fac06b68..43c2a3834 100644 --- a/dhp-common/pom.xml +++ b/dhp-common/pom.xml @@ -17,6 +17,10 @@ commons-cli commons-cli + + commons-io + commons-io + org.apache.commons commons-lang3 @@ -29,21 +33,15 @@ javax.persistence javax.persistence-api - com.fasterxml.jackson.core jackson-databind - com.rabbitmq amqp-client - - commons-io - commons-io - diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/application/ArgumentApplicationParser.java b/dhp-common/src/main/java/eu/dnetlib/dhp/application/ArgumentApplicationParser.java index a4970a928..cbfc5caf1 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/application/ArgumentApplicationParser.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/application/ArgumentApplicationParser.java @@ -2,17 +2,25 @@ package eu.dnetlib.dhp.application; import com.fasterxml.jackson.databind.ObjectMapper; import org.apache.commons.cli.*; +import org.apache.commons.codec.binary.Base64; +import org.apache.commons.io.IOUtils; +import java.io.ByteArrayInputStream; +import java.io.ByteArrayOutputStream; import java.io.Serializable; -import java.util.Arrays; -import java.util.HashMap; -import java.util.Map; +import java.io.StringWriter; +import java.util.*; +import java.util.zip.GZIPInputStream; +import java.util.zip.GZIPOutputStream; +import java.util.zip.Inflater; public class ArgumentApplicationParser implements Serializable { private final Options options = new Options(); private final Map objectMap = new HashMap<>(); + private final List compressedValues = new ArrayList<>(); + public ArgumentApplicationParser(final String json_configuration) throws Exception { final ObjectMapper mapper = new ObjectMapper(); final OptionsParameter[] configuration = mapper.readValue(json_configuration, OptionsParameter[].class); @@ -29,6 +37,9 @@ public class ArgumentApplicationParser implements Serializable { final Option o = new Option(conf.getParamName(), true, conf.getParamDescription()); o.setLongOpt(conf.getParamLongName()); o.setRequired(conf.isParamRequired()); + if (conf.isCompressed()) { + compressedValues.add(conf.getParamLongName()); + } return o; }).forEach(options::addOption); @@ -38,10 +49,32 @@ public class ArgumentApplicationParser implements Serializable { } + + public static String decompressValue(final String abstractCompressed) { + try { + byte[] byteArray = Base64.decodeBase64(abstractCompressed.getBytes()); + GZIPInputStream gis = new GZIPInputStream(new ByteArrayInputStream(byteArray)); + final StringWriter stringWriter = new StringWriter(); + IOUtils.copy(gis, stringWriter); + return stringWriter.toString(); + } catch (Throwable e) { + System.out.println("Wrong value to decompress:" + abstractCompressed); + throw new RuntimeException(e); + } + } + + public static String compressArgument(final String value) throws Exception{ + ByteArrayOutputStream out = new ByteArrayOutputStream(); + GZIPOutputStream gzip = new GZIPOutputStream(out); + gzip.write(value.getBytes()); + gzip.close(); + return java.util.Base64.getEncoder().encodeToString(out.toByteArray()); + } + public void parseArgument(final String[] args) throws Exception { CommandLineParser parser = new BasicParser(); CommandLine cmd = parser.parse(options, args); - Arrays.stream(cmd.getOptions()).forEach(it -> objectMap.put(it.getLongOpt(), it.getValue())); + Arrays.stream(cmd.getOptions()).forEach(it -> objectMap.put(it.getLongOpt(), compressedValues.contains(it.getLongOpt())? decompressValue(it.getValue()): it.getValue())); } public String get(final String key) { diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/application/OptionsParameter.java b/dhp-common/src/main/java/eu/dnetlib/dhp/application/OptionsParameter.java index 92079fce7..4e7c2826b 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/application/OptionsParameter.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/application/OptionsParameter.java @@ -7,6 +7,7 @@ public class OptionsParameter { private String paramLongName; private String paramDescription; private boolean paramRequired; + private boolean compressed; public OptionsParameter() { } @@ -26,4 +27,12 @@ public class OptionsParameter { public boolean isParamRequired() { return paramRequired; } + + public boolean isCompressed() { + return compressed; + } + + public void setCompressed(boolean compressed) { + this.compressed = compressed; + } } diff --git a/dhp-common/src/test/java/eu/dnetlib/dhp/application/ArgumentApplicationParserTest.java b/dhp-common/src/test/java/eu/dnetlib/dhp/application/ArgumentApplicationParserTest.java index 2033919b9..fdea3c2d4 100644 --- a/dhp-common/src/test/java/eu/dnetlib/dhp/application/ArgumentApplicationParserTest.java +++ b/dhp-common/src/test/java/eu/dnetlib/dhp/application/ArgumentApplicationParserTest.java @@ -3,6 +3,10 @@ package eu.dnetlib.dhp.application; import org.apache.commons.io.IOUtils; import org.junit.Test; +import java.io.ByteArrayOutputStream; +import java.util.Base64; +import java.util.zip.GZIPOutputStream; + import static org.junit.Assert.assertEquals; import static org.junit.Assert.assertNotNull; @@ -24,6 +28,7 @@ public class ArgumentApplicationParserTest { "-ro", "value7", "-rr", "value8", "-w", "value9", + "-cc", ArgumentApplicationParser.compressArgument(jsonConfiguration) }); assertNotNull(parser.get("hdfsPath")); assertNotNull(parser.get("apidescriptor")); @@ -45,7 +50,12 @@ public class ArgumentApplicationParserTest { assertEquals("value7", parser.get("rabbitOngoingQueue")); assertEquals("value8", parser.get("rabbitReportQueue")); assertEquals("value9", parser.get("workflowId")); + assertEquals(jsonConfiguration, parser.get("ccCoco")); } + + + + } diff --git a/dhp-common/src/test/resources/eu/dnetlib/application/parameters.json b/dhp-common/src/test/resources/eu/dnetlib/application/parameters.json index 60c2d391a..13c199166 100644 --- a/dhp-common/src/test/resources/eu/dnetlib/application/parameters.json +++ b/dhp-common/src/test/resources/eu/dnetlib/application/parameters.json @@ -1,12 +1,13 @@ [ - {"paramName":"p", "paramLongName":"hdfsPath", "paramDescription": "the path where storing the sequential file", "paramRequired": true}, - {"paramName":"a", "paramLongName":"apidescriptor", "paramDescription": "the JSON encoding of the API Descriptor", "paramRequired": true}, - {"paramName":"n", "paramLongName":"namenode", "paramDescription": "the Name Node URI", "paramRequired": true}, - {"paramName":"u", "paramLongName":"userHDFS", "paramDescription": "the user wich create the hdfs seq file", "paramRequired": true}, - {"paramName":"ru", "paramLongName":"rabbitUser", "paramDescription": "the user to connect with RabbitMq for messaging", "paramRequired": true}, - {"paramName":"rp", "paramLongName":"rabbitPassWord", "paramDescription": "the password to connect with RabbitMq for messaging", "paramRequired": true}, - {"paramName":"rh", "paramLongName":"rabbitHost", "paramDescription": "the host of the RabbitMq server", "paramRequired": true}, - {"paramName":"ro", "paramLongName":"rabbitOngoingQueue", "paramDescription": "the name of the ongoing queue", "paramRequired": true}, - {"paramName":"rr", "paramLongName":"rabbitReportQueue", "paramDescription": "the name of the report queue", "paramRequired": true}, - {"paramName":"w", "paramLongName":"workflowId", "paramDescription": "the identifier of the dnet Workflow", "paramRequired": true} + {"paramName":"p", "paramLongName":"hdfsPath", "paramDescription": "the path where storing the sequential file", "paramRequired": true}, + {"paramName":"a", "paramLongName":"apidescriptor", "paramDescription": "the JSON encoding of the API Descriptor", "paramRequired": true}, + {"paramName":"n", "paramLongName":"namenode", "paramDescription": "the Name Node URI", "paramRequired": true}, + {"paramName":"u", "paramLongName":"userHDFS", "paramDescription": "the user wich create the hdfs seq file", "paramRequired": true}, + {"paramName":"ru", "paramLongName":"rabbitUser", "paramDescription": "the user to connect with RabbitMq for messaging", "paramRequired": true}, + {"paramName":"rp", "paramLongName":"rabbitPassWord", "paramDescription": "the password to connect with RabbitMq for messaging", "paramRequired": true}, + {"paramName":"rh", "paramLongName":"rabbitHost", "paramDescription": "the host of the RabbitMq server", "paramRequired": true}, + {"paramName":"ro", "paramLongName":"rabbitOngoingQueue", "paramDescription": "the name of the ongoing queue", "paramRequired": true}, + {"paramName":"rr", "paramLongName":"rabbitReportQueue", "paramDescription": "the name of the report queue", "paramRequired": true}, + {"paramName":"w", "paramLongName":"workflowId", "paramDescription": "the identifier of the dnet Workflow", "paramRequired": true}, + {"paramName":"cc", "paramLongName":"ccCoco", "paramDescription": "the identifier of the dnet Workflow", "compressed":true,"paramRequired": true} ] \ No newline at end of file diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Context.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Context.java index 64e23088e..809200463 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Context.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Context.java @@ -23,4 +23,23 @@ public class Context implements Serializable { public void setDataInfo(List dataInfo) { this.dataInfo = dataInfo; } + + @Override + public int hashCode() { + return id ==null? 0 : id.hashCode(); + } + + @Override + public boolean equals(Object obj) { + if (this == obj) + return true; + if (obj == null) + return false; + if (getClass() != obj.getClass()) + return false; + + Context other = (Context) obj; + + return id.equals(other.getId()); + } } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Dataset.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Dataset.java index 44d5226e9..27bee998e 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Dataset.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Dataset.java @@ -19,7 +19,7 @@ public class Dataset extends Result implements Serializable { private List geolocation; - public Field getStoragedate() { + public Field getStoragedate() { return storagedate; } @@ -74,4 +74,26 @@ public class Dataset extends Result implements Serializable { public void setGeolocation(List geolocation) { this.geolocation = geolocation; } + + @Override + public void mergeFrom(OafEntity e) { + super.mergeFrom(e); + final Dataset d = (Dataset) e; + + storagedate = d.getStoragedate() != null && compareTrust(this, e)<0? d.getStoragedate() : storagedate; + + device= d.getDevice() != null && compareTrust(this, e)<0? d.getDevice() : device; + + size= d.getSize() != null && compareTrust(this, e)<0? d.getSize() : size; + + version= d.getVersion() != null && compareTrust(this, e)<0? d.getVersion() : version; + + lastmetadataupdate= d.getLastmetadataupdate() != null && compareTrust(this, e)<0? d.getLastmetadataupdate() :lastmetadataupdate; + + metadataversionnumber= d.getMetadataversionnumber() != null && compareTrust(this, e)<0? d.getMetadataversionnumber() : metadataversionnumber; + + geolocation = mergeLists(geolocation, d.getGeolocation()); + + mergeOAFDataInfo(d); + } } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Datasource.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Datasource.java index 21408a5ec..f52a500fe 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Datasource.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Datasource.java @@ -78,7 +78,7 @@ public class Datasource extends OafEntity implements Serializable { private Field certificates; - private List< KeyValue> policies; + private List policies; private Journal journal; @@ -361,4 +361,67 @@ public class Datasource extends OafEntity implements Serializable { public void setJournal(Journal journal) { this.journal = journal; } + + @Override + public void mergeFrom(OafEntity e) { + super.mergeFrom(e); + + Datasource d = (Datasource)e; + + datasourcetype = d.getDatasourcetype() != null && compareTrust(this, e)<0? d.getDatasourcetype() : datasourcetype; + openairecompatibility = d.getOpenairecompatibility() != null && compareTrust(this, e)<0? d.getOpenairecompatibility() : openairecompatibility; + officialname = d.getOfficialname() != null && compareTrust(this, e)<0? d.getOfficialname() : officialname; + englishname = d.getEnglishname() != null && compareTrust(this, e)<0? d.getEnglishname() : officialname; + websiteurl = d.getWebsiteurl() != null && compareTrust(this, e)<0? d.getWebsiteurl() : websiteurl; + logourl = d.getLogourl() != null && compareTrust(this, e)<0? d.getLogourl() : getLogourl(); + contactemail = d.getContactemail() != null && compareTrust(this, e)<0? d.getContactemail() : contactemail; + namespaceprefix = d.getNamespaceprefix() != null && compareTrust(this, e)<0? d.getNamespaceprefix() : namespaceprefix; + latitude = d.getLatitude() != null && compareTrust(this, e)<0? d.getLatitude() : latitude; + longitude = d.getLongitude() != null && compareTrust(this, e)<0? d.getLongitude() : longitude; + dateofvalidation = d.getDateofvalidation() != null && compareTrust(this, e)<0? d.getDateofvalidation() : dateofvalidation; + description = d.getDescription() != null && compareTrust(this, e)<0? d.getDescription() : description; + subjects = mergeLists(subjects, d.getSubjects()); + + // opendoar specific fields (od*) + odnumberofitems = d.getOdnumberofitems() != null && compareTrust(this, e)<0? d.getOdnumberofitems() : odnumberofitems; + odnumberofitemsdate = d.getOdnumberofitemsdate() != null && compareTrust(this, e)<0? d.getOdnumberofitemsdate() : odnumberofitemsdate; + odpolicies = d.getOdpolicies() != null && compareTrust(this, e)<0? d.getOdpolicies() : odpolicies; + odlanguages = mergeLists(odlanguages, d.getOdlanguages()); + odcontenttypes = mergeLists(odcontenttypes, d.getOdcontenttypes()); + accessinfopackage = mergeLists(accessinfopackage, d.getAccessinfopackage()); + + // re3data fields + releasestartdate = d.getReleasestartdate() != null && compareTrust(this, e)<0? d.getReleasestartdate() : releasestartdate; + releaseenddate = d.getReleaseenddate() != null && compareTrust(this, e)<0? d.getReleaseenddate() : releaseenddate; + missionstatementurl = d.getMissionstatementurl() != null && compareTrust(this, e)<0? d.getMissionstatementurl() : missionstatementurl; + dataprovider = d.getDataprovider() != null && compareTrust(this, e)<0? d.getDataprovider() : dataprovider; + serviceprovider = d.getServiceprovider() != null && compareTrust(this, e)<0? d.getServiceprovider() : serviceprovider; + + // {open, restricted or closed} + databaseaccesstype = d.getDatabaseaccesstype() != null && compareTrust(this, e)<0? d.getDatabaseaccesstype() : databaseaccesstype; + + // {open, restricted or closed} + datauploadtype = d.getDatauploadtype() != null && compareTrust(this, e)<0? d.getDatauploadtype() : datauploadtype; + + // {feeRequired, registration, other} + databaseaccessrestriction = d.getDatabaseaccessrestriction() != null && compareTrust(this, e)<0? d.getDatabaseaccessrestriction() : databaseaccessrestriction; + + // {feeRequired, registration, other} + datauploadrestriction = d.getDatauploadrestriction() != null && compareTrust(this, e)<0? d.getDatauploadrestriction() : datauploadrestriction; + + versioning = d.getVersioning() != null && compareTrust(this, e)<0? d.getVersioning() : versioning; + citationguidelineurl = d.getCitationguidelineurl() != null && compareTrust(this, e)<0? d.getCitationguidelineurl() : citationguidelineurl; + + //{yes, no, unknown} + qualitymanagementkind = d.getQualitymanagementkind() != null && compareTrust(this, e)<0? d.getQualitymanagementkind() : qualitymanagementkind; + pidsystems = d.getPidsystems() != null && compareTrust(this, e)<0? d.getPidsystems() : pidsystems; + + certificates = d.getCertificates() != null && compareTrust(this, e)<0? d.getCertificates() : certificates; + + policies = mergeLists(policies, d.getPolicies()); + + journal = d.getJournal() != null && compareTrust(this, e)<0? d.getJournal() : journal; + + mergeOAFDataInfo(e); + } } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Field.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Field.java index 8834900c9..2ab0b4d3c 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Field.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Field.java @@ -23,4 +23,21 @@ public class Field implements Serializable { public void setDataInfo(DataInfo dataInfo) { this.dataInfo = dataInfo; } + + @Override + public int hashCode() { + return getValue() == null ? 0 : getValue().hashCode(); + } + + @Override + public boolean equals(Object obj) { + if (this == obj) + return true; + if (obj == null) + return false; + if (getClass() != obj.getClass()) + return false; + Field other = (Field) obj; + return getValue().equals(other.getValue()); + } } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/GeoLocation.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/GeoLocation.java index 567254a23..43af60286 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/GeoLocation.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/GeoLocation.java @@ -1,5 +1,7 @@ package eu.dnetlib.dhp.schema.oaf; +import org.apache.commons.lang3.StringUtils; + import java.io.Serializable; public class GeoLocation implements Serializable { @@ -33,4 +35,35 @@ public class GeoLocation implements Serializable { public void setPlace(String place) { this.place = place; } + + + public boolean isBlank() { + return StringUtils.isBlank(point) && + StringUtils.isBlank(box) && + StringUtils.isBlank(place); + } + + public String toComparableString() { + return isBlank()?"":String.format("%s::%s%s", point != null ? point.toLowerCase() : "", box != null ? box.toLowerCase() : "", place != null ? place.toLowerCase() : ""); + } + + @Override + public int hashCode() { + return toComparableString().hashCode(); + } + + @Override + public boolean equals(Object obj) { + if (this == obj) + return true; + if (obj == null) + return false; + if (getClass() != obj.getClass()) + return false; + + GeoLocation other = (GeoLocation) obj; + + return toComparableString() + .equals(other.toComparableString()); + } } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Instance.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Instance.java index 8726b85ce..8f852af65 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Instance.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Instance.java @@ -85,4 +85,34 @@ public class Instance implements Serializable { public void setDateofacceptance(Field dateofacceptance) { this.dateofacceptance = dateofacceptance; } + + + + public String toComparableString(){ + return String.format("%s::%s::%s::%s", + hostedby != null && hostedby.getKey()!= null ? hostedby.getKey().toLowerCase() : "", + accessright!= null && accessright.getClassid()!= null ? accessright.getClassid() : "", + instancetype!= null && instancetype.getClassid()!= null ? instancetype.getClassid() : "", + url != null ? url:""); + } + + @Override + public int hashCode() { + return toComparableString().hashCode(); + } + + @Override + public boolean equals(Object obj) { + if (this == obj) + return true; + if (obj == null) + return false; + if (getClass() != obj.getClass()) + return false; + + Instance other = (Instance) obj; + + return toComparableString() + .equals(other.toComparableString()); + } } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/KeyValue.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/KeyValue.java index 1c4c7e6ef..74d9f77bd 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/KeyValue.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/KeyValue.java @@ -1,5 +1,7 @@ package eu.dnetlib.dhp.schema.oaf; +import org.apache.commons.lang3.StringUtils; + import java.io.Serializable; public class KeyValue implements Serializable { @@ -33,4 +35,31 @@ public class KeyValue implements Serializable { public void setDataInfo(DataInfo dataInfo) { this.dataInfo = dataInfo; } + + public String toComparableString() { + return isBlank()?"":String.format("%s::%s", key != null ? key.toLowerCase() : "", value != null ? value.toLowerCase() : ""); + } + + public boolean isBlank() { + return StringUtils.isBlank(key) && StringUtils.isBlank(value); + } + + @Override + public int hashCode() { + return toComparableString().hashCode(); + } + + @Override + public boolean equals(Object obj) { + if (this == obj) + return true; + if (obj == null) + return false; + if (getClass() != obj.getClass()) + return false; + + KeyValue other = (KeyValue) obj; + + return toComparableString().equals(other.toComparableString()); + } } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java index 010633ec3..cc2ab8428 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java @@ -1,8 +1,5 @@ package eu.dnetlib.dhp.schema.oaf; -import com.fasterxml.jackson.core.JsonProcessingException; -import com.fasterxml.jackson.databind.ObjectMapper; - import java.io.Serializable; public abstract class Oaf implements Serializable { @@ -27,13 +24,23 @@ public abstract class Oaf implements Serializable { this.lastupdatetimestamp = lastupdatetimestamp; } - @Override - public String toString() { - try { - return new ObjectMapper().writeValueAsString(this); - } catch (JsonProcessingException e) { - throw new RuntimeException(e); - } + + public void mergeOAFDataInfo(Oaf e) { + if (e.getDataInfo()!= null && compareTrust(this,e)<0) + dataInfo = e.getDataInfo(); } + protected String extractTrust(Oaf e) { + if (e == null || e.getDataInfo()== null || e.getDataInfo().getTrust()== null) + return "0.0"; + return e.getDataInfo().getTrust(); + + + + } + + protected int compareTrust(Oaf a, Oaf b) { + return extractTrust(a).compareTo(extractTrust(b)); + + } } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OafEntity.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OafEntity.java index 791667b46..8a86f822d 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OafEntity.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OafEntity.java @@ -1,7 +1,8 @@ package eu.dnetlib.dhp.schema.oaf; import java.io.Serializable; -import java.util.List; +import java.util.*; +import java.util.stream.Collectors; public abstract class OafEntity extends Oaf implements Serializable { @@ -84,4 +85,36 @@ public abstract class OafEntity extends Oaf implements Serializable { public void setOaiprovenance(OAIProvenance oaiprovenance) { this.oaiprovenance = oaiprovenance; } + + + public void mergeFrom(OafEntity e) { + + if (e == null) + return; + + originalId = mergeLists(originalId, e.getOriginalId()); + + collectedfrom = mergeLists(collectedfrom, e.getCollectedfrom()); + + pid = mergeLists(pid, e.getPid()); + + if (e.getDateofcollection() != null && compareTrust(this, e) < 0) + dateofcollection = e.getDateofcollection(); + + if (e.getDateoftransformation() != null && compareTrust(this, e) < 0) + dateoftransformation = e.getDateoftransformation(); + + extraInfo = mergeLists(extraInfo, e.getExtraInfo()); + + if (e.getOaiprovenance() != null && compareTrust(this, e) < 0) + oaiprovenance = e.getOaiprovenance(); + + } + + protected List mergeLists(final List... lists) { + + return Arrays.stream(lists).filter(Objects::nonNull).flatMap(List::stream).distinct().collect(Collectors.toList()); + } + + } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Organization.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Organization.java index 6f89eca7e..b0dffb485 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Organization.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Organization.java @@ -164,4 +164,28 @@ public class Organization extends OafEntity implements Serializable { public void setCountry(Qualifier country) { this.country = country; } + + + @Override + public void mergeFrom(OafEntity e) { + super.mergeFrom(e); + final Organization o = (Organization) e; + legalshortname = o.getLegalshortname() != null && compareTrust(this, e)<0? o.getLegalshortname() : legalshortname; + legalname = o.getLegalname() != null && compareTrust(this, e)<0 ? o.getLegalname() : legalname; + alternativeNames = mergeLists(o.getAlternativeNames(), alternativeNames); + websiteurl = o.getWebsiteurl() != null && compareTrust(this, e)<0? o.getWebsiteurl() : websiteurl; + logourl = o.getLogourl() != null && compareTrust(this, e)<0? o.getLogourl() : logourl; + eclegalbody = o.getEclegalbody() != null && compareTrust(this, e)<0? o.getEclegalbody() : eclegalbody; + eclegalperson = o.getEclegalperson() != null && compareTrust(this, e)<0? o.getEclegalperson() : eclegalperson; + ecnonprofit = o.getEcnonprofit() != null && compareTrust(this, e)<0? o.getEcnonprofit() : ecnonprofit; + ecresearchorganization = o.getEcresearchorganization() != null && compareTrust(this, e)<0? o.getEcresearchorganization() : ecresearchorganization; + echighereducation = o.getEchighereducation() != null && compareTrust(this, e)<0? o.getEchighereducation() : echighereducation; + ecinternationalorganizationeurinterests = o.getEcinternationalorganizationeurinterests() != null && compareTrust(this, e)<0? o.getEcinternationalorganizationeurinterests() : ecinternationalorganizationeurinterests; + ecinternationalorganization = o.getEcinternationalorganization() != null && compareTrust(this, e)<0? o.getEcinternationalorganization() : ecinternationalorganization; + ecenterprise = o.getEcenterprise() != null && compareTrust(this, e)<0? o.getEcenterprise() :ecenterprise; + ecsmevalidated = o.getEcsmevalidated() != null && compareTrust(this, e)<0? o.getEcsmevalidated() :ecsmevalidated; + ecnutscode = o.getEcnutscode() != null && compareTrust(this, e)<0? o.getEcnutscode() :ecnutscode; + country = o.getCountry() != null && compareTrust(this, e)<0 ? o.getCountry() :country; + mergeOAFDataInfo(o); + } } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OtherResearchProduct.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OtherResearchProduct.java index 5f32b8895..72bec727e 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OtherResearchProduct.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OtherResearchProduct.java @@ -34,4 +34,16 @@ public class OtherResearchProduct extends Result implements Serializable { public void setTool(List> tool) { this.tool = tool; } + + @Override + public void mergeFrom(OafEntity e) { + super.mergeFrom(e); + + OtherResearchProduct o = (OtherResearchProduct)e; + + contactperson = mergeLists(contactperson, o.getContactperson()); + contactgroup = mergeLists(contactgroup, o.getContactgroup()); + tool = mergeLists(tool, o.getTool()); + mergeOAFDataInfo(e); + } } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Project.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Project.java index 65f22da37..0bc11bb41 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Project.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Project.java @@ -264,4 +264,39 @@ public class Project extends OafEntity implements Serializable { public void setFundedamount(Float fundedamount) { this.fundedamount = fundedamount; } + + + @Override + public void mergeFrom(OafEntity e) { + super.mergeFrom(e); + Project p = (Project)e; + + websiteurl= p.getWebsiteurl()!= null && compareTrust(this,e)<0?p.getWebsiteurl():websiteurl; + code= p.getCode()!=null && compareTrust(this,e)<0?p.getCode():code; + acronym= p.getAcronym()!= null && compareTrust(this,e)<0?p.getAcronym():acronym; + title= p.getTitle()!= null && compareTrust(this,e)<0?p.getTitle():title; + startdate= p.getStartdate()!=null && compareTrust(this,e)<0?p.getStartdate():startdate; + enddate= p.getEnddate()!=null && compareTrust(this,e)<0?p.getEnddate():enddate; + callidentifier= p.getCallidentifier()!=null && compareTrust(this,e)<0?p.getCallidentifier():callidentifier; + keywords= p.getKeywords()!=null && compareTrust(this,e)<0?p.getKeywords():keywords; + duration= p.getDuration()!=null && compareTrust(this,e)<0?p.getDuration():duration; + ecsc39= p.getEcsc39()!=null && compareTrust(this,e)<0?p.getEcsc39():ecsc39; + oamandatepublications= p.getOamandatepublications()!=null && compareTrust(this,e)<0?p.getOamandatepublications():oamandatepublications; + ecarticle29_3= p.getEcarticle29_3()!=null && compareTrust(this,e)<0?p.getEcarticle29_3():ecarticle29_3; + subjects= mergeLists(subjects, p.getSubjects()); + fundingtree= mergeLists(fundingtree, p.getFundingtree()); + contracttype= p.getContracttype()!=null && compareTrust(this,e)<0?p.getContracttype():contracttype; + optional1= p.getOptional1()!=null && compareTrust(this,e)<0?p.getOptional1():optional1; + optional2= p.getOptional2()!=null && compareTrust(this,e)<0?p.getOptional2():optional2; + jsonextrainfo= p.getJsonextrainfo()!=null && compareTrust(this,e)<0?p.getJsonextrainfo():jsonextrainfo; + contactfullname= p.getContactfullname()!=null && compareTrust(this,e)<0?p.getContactfullname():contactfullname; + contactfax= p.getContactfax()!=null && compareTrust(this,e)<0?p.getContactfax():contactfax; + contactphone= p.getContactphone()!=null && compareTrust(this,e)<0?p.getContactphone():contactphone; + contactemail= p.getContactemail()!=null && compareTrust(this,e)<0?p.getContactemail():contactemail; + summary= p.getSummary()!=null && compareTrust(this,e)<0?p.getSummary():summary; + currency= p.getCurrency()!=null && compareTrust(this,e)<0?p.getCurrency():currency; + totalcost= p.getTotalcost()!=null && compareTrust(this,e)<0?p.getTotalcost():totalcost; + fundedamount= p.getFundedamount()!= null && compareTrust(this,e)<0?p.getFundedamount():fundedamount; + mergeOAFDataInfo(e); + } } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Publication.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Publication.java index 9ca9cd3d6..bb6990c1d 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Publication.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Publication.java @@ -14,4 +14,17 @@ public class Publication extends Result implements Serializable { public void setJournal(Journal journal) { this.journal = journal; } + + @Override + public void mergeFrom(OafEntity e) { + super.mergeFrom(e); + + Publication p = (Publication) e; + + if (p.getJournal() != null && compareTrust(this, e)<0) + journal = p.getJournal(); + mergeOAFDataInfo(e); + } + + } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Qualifier.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Qualifier.java index 60889535d..7e4660f4b 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Qualifier.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Qualifier.java @@ -1,5 +1,7 @@ package eu.dnetlib.dhp.schema.oaf; +import org.apache.commons.lang3.StringUtils; + import java.io.Serializable; public class Qualifier implements Serializable { @@ -40,4 +42,37 @@ public class Qualifier implements Serializable { public void setSchemename(String schemename) { this.schemename = schemename; } + + public String toComparableString() { + return isBlank()?"": String.format("%s::%s::%s::%s", + classid != null ? classid : "", + classname != null ? classname : "", + schemeid != null ? schemeid : "", + schemename != null ? schemename : ""); + } + public boolean isBlank() { + return StringUtils.isBlank(classid) && + StringUtils.isBlank(classname) && + StringUtils.isBlank(schemeid) && + StringUtils.isBlank(schemename); + } + @Override + public int hashCode() { + return toComparableString().hashCode(); + } + + @Override + public boolean equals(Object obj) { + if (this == obj) + return true; + if (obj == null) + return false; + if (getClass() != obj.getClass()) + return false; + + Qualifier other = (Qualifier) obj; + + return toComparableString() + .equals(other.toComparableString()); + } } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java index 7b08e71c2..eb5572ce1 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java @@ -1,7 +1,10 @@ package eu.dnetlib.dhp.schema.oaf; +import org.apache.commons.lang3.StringUtils; + import java.io.Serializable; -import java.util.List; +import java.util.*; +import java.util.stream.Collectors; public abstract class Result extends OafEntity implements Serializable { @@ -12,35 +15,35 @@ public abstract class Result extends OafEntity implements Serializable { // common fields private Qualifier language; - + private List country; private List subject; - + private List title; - + private List relevantdate; private List> description; - + private Field dateofacceptance; - + private Field publisher; - + private Field embargoenddate; - + private List> source; - + private List> fulltext; // remove candidate - + private List> format; - + private List> contributor; - + private Qualifier resourcetype; - + private List> coverage; - + private Field refereed; //peer-review status private List context; @@ -240,4 +243,76 @@ public abstract class Result extends OafEntity implements Serializable { this.processingchargecurrency = processingchargecurrency; return this; } + + @Override + public void mergeFrom(OafEntity e) { + super.mergeFrom(e); + + Result r = (Result) e; + + instance = mergeLists(instance, r.getInstance()); + + if (r.getResulttype() != null && compareTrust(this, r) < 0) + resulttype = r.getResulttype(); + + if (r.getLanguage() != null && compareTrust(this, r) < 0) + language = r.getLanguage(); + + country = mergeLists(country, r.getCountry()); + + subject = mergeLists(subject, r.getSubject()); + + title = mergeLists(title, r.getTitle()); + + relevantdate = mergeLists(relevantdate, r.getRelevantdate()); + + description = longestLists(description, r.getDescription()); + + if (r.getPublisher() != null && compareTrust(this, r) < 0) + publisher = r.getPublisher(); + + if (r.getEmbargoenddate() != null && compareTrust(this, r) < 0) + embargoenddate = r.getEmbargoenddate(); + + source = mergeLists(source, r.getSource()); + + fulltext = mergeLists(fulltext, r.getFulltext()); + + format = mergeLists(format, r.getFormat()); + + contributor = mergeLists(contributor, r.getContributor()); + + if (r.getResourcetype() != null) + resourcetype = r.getResourcetype(); + + coverage = mergeLists(coverage, r.getCoverage()); + + if (r.getRefereed() != null && compareTrust(this, r) < 0) + refereed = r.getRefereed(); + + context = mergeLists(context, r.getContext()); + + if (r.getProcessingchargeamount() != null && compareTrust(this, r) < 0) + processingchargeamount = r.getProcessingchargeamount(); + + if (r.getProcessingchargecurrency() != null && compareTrust(this, r) < 0) + processingchargecurrency = r.getProcessingchargecurrency(); + + externalReference = mergeLists(externalReference, r.getExternalReference()); + + } + + + private List> longestLists(List> a, List> b) { + if (a == null || b == null) + return a == null ? b : a; + if (a.size() == b.size()) { + int msa = a.stream().filter(i -> i.getValue() != null).map(i -> i.getValue().length()).max(Comparator.naturalOrder()).orElse(0); + int msb = b.stream().filter(i -> i.getValue() != null).map(i -> i.getValue().length()).max(Comparator.naturalOrder()).orElse(0); + return msa > msb ? a : b; + } + return a.size() > b.size() ? a : b; + } + + } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Software.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Software.java index e696cdb52..7f835fdf8 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Software.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Software.java @@ -44,4 +44,19 @@ public class Software extends Result implements Serializable { public void setProgrammingLanguage(Qualifier programmingLanguage) { this.programmingLanguage = programmingLanguage; } + + @Override + public void mergeFrom(OafEntity e) { + super.mergeFrom(e); + final Software s = (Software) e; + documentationUrl = mergeLists(documentationUrl, s.getDocumentationUrl()); + + license = mergeLists(license, s.getLicense()); + + codeRepositoryUrl = s.getCodeRepositoryUrl()!= null && compareTrust(this, s)<0?s.getCodeRepositoryUrl():codeRepositoryUrl; + + programmingLanguage= s.getProgrammingLanguage()!= null && compareTrust(this, s)<0?s.getProgrammingLanguage():programmingLanguage; + + mergeOAFDataInfo(e); + } } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/StructuredProperty.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/StructuredProperty.java index 79ebdd7f9..f6c6b7335 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/StructuredProperty.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/StructuredProperty.java @@ -33,4 +33,28 @@ public class StructuredProperty implements Serializable { public void setDataInfo(DataInfo dataInfo) { this.dataInfo = dataInfo; } + + public String toComparableString(){ + return value != null ? value.toLowerCase() : ""; + } + + @Override + public int hashCode() { + return toComparableString().hashCode(); + } + + @Override + public boolean equals(Object obj) { + if (this == obj) + return true; + if (obj == null) + return false; + if (getClass() != obj.getClass()) + return false; + + StructuredProperty other = (StructuredProperty) obj; + + return toComparableString() + .equals(other.toComparableString()); + } } diff --git a/dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/oaf/MergeTest.java b/dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/oaf/MergeTest.java new file mode 100644 index 000000000..e487ddcba --- /dev/null +++ b/dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/oaf/MergeTest.java @@ -0,0 +1,89 @@ +package eu.dnetlib.dhp.schema.oaf; + +import org.junit.Assert; +import org.junit.Before; +import org.junit.Test; + +import java.io.IOException; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.List; + +public class MergeTest { + + OafEntity oaf; + + @Before + public void setUp() { + oaf = new Publication(); + } + + @Test + public void mergeListsTest() { + + //string list merge test + List a = Arrays.asList("a", "b", "c", "e"); + List b = Arrays.asList("a", "b", "c", "d"); + List c = null; + + System.out.println("merge result 1 = " + oaf.mergeLists(a, b)); + + System.out.println("merge result 2 = " + oaf.mergeLists(a, c)); + + System.out.println("merge result 3 = " + oaf.mergeLists(c, c)); + } + + @Test + public void mergePublicationCollectedFromTest() { + + Publication a = new Publication(); + Publication b = new Publication(); + + a.setCollectedfrom(Arrays.asList(setKV("a", "open"), setKV("b", "closed"))); + b.setCollectedfrom(Arrays.asList(setKV("A", "open"), setKV("b", "Open"))); + + a.mergeFrom(b); + + Assert.assertNotNull(a.getCollectedfrom()); + Assert.assertEquals(3, a.getCollectedfrom().size()); + + } + + @Test + public void mergePublicationSubjectTest() { + + Publication a = new Publication(); + Publication b = new Publication(); + + a.setSubject(Arrays.asList(setSP("a", "open", "classe"), setSP("b", "open", "classe"))); + b.setSubject(Arrays.asList(setSP("A", "open", "classe"), setSP("c", "open", "classe"))); + + a.mergeFrom(b); + + Assert.assertNotNull(a.getSubject()); + Assert.assertEquals(3, a.getSubject().size()); + + } + + private KeyValue setKV(final String key, final String value) { + + KeyValue k = new KeyValue(); + + k.setKey(key); + k.setValue(value); + + return k; + } + + private StructuredProperty setSP(final String value, final String schema, final String classname) { + StructuredProperty s = new StructuredProperty(); + s.setValue(value); + Qualifier q = new Qualifier(); + q.setClassname(classname); + q.setClassid(classname); + q.setSchemename(schema); + q.setSchemeid(schema); + s.setQualifier(q); + return s; + } +} diff --git a/dhp-workflows/dhp-aggregation/pom.xml b/dhp-workflows/dhp-aggregation/pom.xml index 10d4ff79a..328e783c4 100644 --- a/dhp-workflows/dhp-aggregation/pom.xml +++ b/dhp-workflows/dhp-aggregation/pom.xml @@ -7,6 +7,8 @@ 1.0.5-SNAPSHOT dhp-aggregation + + diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java index d517cca00..5e5e42f1e 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java @@ -89,6 +89,8 @@ public class TransformationJobTest { "-rh", "", "-ro", "", "-rr", ""}); + + } @Test @@ -96,7 +98,7 @@ public class TransformationJobTest { final String path = this.getClass().getResource("/eu/dnetlib/dhp/transform/mdstorenative").getFile(); System.out.println("path = " + path); - Path tempDirWithPrefix = Files.createTempDirectory("mdsotre_output"); + Path tempDirWithPrefix = Files.createTempDirectory("mdstore_output"); System.out.println(tempDirWithPrefix.toFile().getAbsolutePath()); diff --git a/dhp-workflows/dhp-dedup/pom.xml b/dhp-workflows/dhp-dedup/pom.xml new file mode 100644 index 000000000..28ef6a453 --- /dev/null +++ b/dhp-workflows/dhp-dedup/pom.xml @@ -0,0 +1,61 @@ + + + + dhp-workflows + eu.dnetlib.dhp + 1.0.5-SNAPSHOT + + 4.0.0 + + dhp-dedup + + + + + org.apache.spark + spark-core_2.11 + + + org.apache.spark + spark-sql_2.11 + + + + eu.dnetlib.dhp + dhp-common + ${project.version} + + + eu.dnetlib.dhp + dhp-schemas + ${project.version} + + + com.arakelian + java-jq + + + + eu.dnetlib + dnet-pace-core + + + org.apache.spark + spark-graphx_2.11 + + + com.fasterxml.jackson.core + jackson-databind + + + com.fasterxml.jackson.core + jackson-core + + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-dedup/src/main/java/eu/dnetlib/dedup/DatePicker.java b/dhp-workflows/dhp-dedup/src/main/java/eu/dnetlib/dedup/DatePicker.java new file mode 100644 index 000000000..73f178edc --- /dev/null +++ b/dhp-workflows/dhp-dedup/src/main/java/eu/dnetlib/dedup/DatePicker.java @@ -0,0 +1,119 @@ +package eu.dnetlib.dedup; + +import eu.dnetlib.dhp.schema.oaf.Field; +import org.apache.commons.lang.StringUtils; + +import java.time.Year; +import java.util.*; +import java.util.stream.Collectors; + +import static java.util.Collections.reverseOrder; +import static java.util.Map.Entry.comparingByValue; +import static java.util.stream.Collectors.toMap; +import static org.apache.commons.lang.StringUtils.endsWith; +import static org.apache.commons.lang.StringUtils.substringBefore; + +public class DatePicker { + + private static final String DATE_PATTERN = "\\d{4}-\\d{2}-\\d{2}"; + private static final String DATE_DEFAULT_SUFFIX = "01-01"; + private static final int YEAR_LB = 1300; + private static final int YEAR_UB = Year.now().getValue() + 5; + + public static Field pick(final Collection dateofacceptance) { + + final Map frequencies = dateofacceptance + .parallelStream() + .filter(StringUtils::isNotBlank) + .collect( + Collectors.toConcurrentMap( + w -> w, w -> 1, Integer::sum)); + + if (frequencies.isEmpty()) { + return new Field<>(); + } + + final Field date = new Field<>(); + date.setValue(frequencies.keySet().iterator().next()); + + // let's sort this map by values first, filtering out invalid dates + final Map sorted = frequencies + .entrySet() + .stream() + .filter(d -> StringUtils.isNotBlank(d.getKey())) + .filter(d -> d.getKey().matches(DATE_PATTERN)) + .filter(d -> inRange(d.getKey())) + .sorted(reverseOrder(comparingByValue())) + .collect( + toMap( + Map.Entry::getKey, + Map.Entry::getValue, (e1, e2) -> e2, + LinkedHashMap::new)); + + // shortcut + if (sorted.size() == 0) { + return date; + } + + // voting method (1/3 + 1) wins + if (sorted.size() >= 3) { + final int acceptThreshold = (sorted.size() / 3) + 1; + final List accepted = sorted.entrySet().stream() + .filter(e -> e.getValue() >= acceptThreshold) + .map(e -> e.getKey()) + .collect(Collectors.toList()); + + // cannot find strong majority + if (accepted.isEmpty()) { + final int max = sorted.values().iterator().next(); + Optional first = sorted.entrySet().stream() + .filter(e -> e.getValue() == max && !endsWith(e.getKey(), DATE_DEFAULT_SUFFIX)) + .map(Map.Entry::getKey) + .findFirst(); + if (first.isPresent()) { + date.setValue(first.get()); + return date; + } + + date.setValue(sorted.keySet().iterator().next()); + return date; + } + + if (accepted.size() == 1) { + date.setValue(accepted.get(0)); + return date; + } else { + final Optional first = accepted.stream() + .filter(d -> !endsWith(d, DATE_DEFAULT_SUFFIX)) + .findFirst(); + if (first.isPresent()) { + date.setValue(first.get()); + return date; + } + + return date; + } + + //1st non YYYY-01-01 is returned + } else { + if (sorted.size() == 2) { + for (Map.Entry e : sorted.entrySet()) { + if (!endsWith(e.getKey(), DATE_DEFAULT_SUFFIX)) { + date.setValue(e.getKey()); + return date; + } + } + } + + // none of the dates seems good enough, return the 1st one + date.setValue(sorted.keySet().iterator().next()); + return date; + } + } + + private static boolean inRange(final String date) { + final int year = Integer.parseInt(substringBefore(date, "-")); + return year >= YEAR_LB && year <= YEAR_UB; + } + +} \ No newline at end of file diff --git a/dhp-workflows/dhp-dedup/src/main/java/eu/dnetlib/dedup/DedupRecordFactory.java b/dhp-workflows/dhp-dedup/src/main/java/eu/dnetlib/dedup/DedupRecordFactory.java new file mode 100644 index 000000000..5f81669e9 --- /dev/null +++ b/dhp-workflows/dhp-dedup/src/main/java/eu/dnetlib/dedup/DedupRecordFactory.java @@ -0,0 +1,279 @@ +package eu.dnetlib.dedup; + +import com.google.common.collect.Lists; +import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.pace.config.DedupConfig; +import eu.dnetlib.pace.util.MapDocumentUtil; +import org.apache.commons.lang.NotImplementedException; +import org.apache.commons.lang.StringUtils; +import org.apache.spark.api.java.JavaPairRDD; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.PairFunction; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SparkSession; +import org.codehaus.jackson.map.ObjectMapper; +import scala.Tuple2; + +import java.util.Collection; +import java.util.Random; + +import static java.util.stream.Collectors.toMap; + +public class DedupRecordFactory { + + public static JavaRDD createDedupRecord(final JavaSparkContext sc, final SparkSession spark, final String mergeRelsInputPath, final String entitiesInputPath, final OafEntityType entityType, final DedupConfig dedupConf) { + long ts = System.currentTimeMillis(); + // + final JavaPairRDD inputJsonEntities = sc.textFile(entitiesInputPath) + .mapToPair((PairFunction) it -> + new Tuple2(MapDocumentUtil.getJPathString(dedupConf.getWf().getIdPath(), it), it) + ); + + //: source is the dedup_id, target is the id of the mergedIn + JavaPairRDD mergeRels = spark + .read().load(mergeRelsInputPath).as(Encoders.bean(Relation.class)) + .where("relClass=='merges'") + .javaRDD() + .mapToPair( + (PairFunction) r -> + new Tuple2(r.getTarget(), r.getSource()) + ); + + // + final JavaPairRDD joinResult = mergeRels.join(inputJsonEntities).mapToPair((PairFunction>, String, String>) Tuple2::_2); + + JavaPairRDD> sortedJoinResult = joinResult.groupByKey(); + + switch (entityType) { + case publication: + return sortedJoinResult.map(p -> DedupRecordFactory.publicationMerger(p, ts)); + case dataset: + return sortedJoinResult.map(d -> DedupRecordFactory.datasetMerger(d, ts)); + case project: + return sortedJoinResult.map(p -> DedupRecordFactory.projectMerger(p, ts)); + case software: + return sortedJoinResult.map(s -> DedupRecordFactory.softwareMerger(s, ts)); + case datasource: + return sortedJoinResult.map(d -> DedupRecordFactory.datasourceMerger(d, ts)); + case organization: + return sortedJoinResult.map(o -> DedupRecordFactory.organizationMerger(o, ts)); + case otherresearchproduct: + return sortedJoinResult.map(o -> DedupRecordFactory.otherresearchproductMerger(o, ts)); + default: + return null; + } + + } + + private static Publication publicationMerger(Tuple2> e, final long ts) { + + Publication p = new Publication(); //the result of the merge, to be returned at the end + + p.setId(e._1()); + + final ObjectMapper mapper = new ObjectMapper(); + + final Collection dateofacceptance = Lists.newArrayList(); + + if (e._2() != null) + e._2().forEach(pub -> { + try { + Publication publication = mapper.readValue(pub, Publication.class); + + p.mergeFrom(publication); + p.setAuthor(DedupUtility.mergeAuthor(p.getAuthor(), publication.getAuthor())); + //add to the list if they are not null + if (publication.getDateofacceptance() != null) + dateofacceptance.add(publication.getDateofacceptance().getValue()); + } catch (Exception exc) { + throw new RuntimeException(exc); + } + }); + p.setDateofacceptance(DatePicker.pick(dateofacceptance)); + if (p.getDataInfo() == null) + p.setDataInfo(new DataInfo()); + p.getDataInfo().setTrust("0.9"); + p.setLastupdatetimestamp(ts); + return p; + } + + private static Dataset datasetMerger(Tuple2> e, final long ts) { + + Dataset d = new Dataset(); //the result of the merge, to be returned at the end + + d.setId(e._1()); + + final ObjectMapper mapper = new ObjectMapper(); + + final Collection dateofacceptance = Lists.newArrayList(); + + if (e._2() != null) + e._2().forEach(dat -> { + try { + Dataset dataset = mapper.readValue(dat, Dataset.class); + + d.mergeFrom(dataset); + d.setAuthor(DedupUtility.mergeAuthor(d.getAuthor(), dataset.getAuthor())); + //add to the list if they are not null + if (dataset.getDateofacceptance() != null) + dateofacceptance.add(dataset.getDateofacceptance().getValue()); + } catch (Exception exc) { + throw new RuntimeException(exc); + } + }); + d.setDateofacceptance(DatePicker.pick(dateofacceptance)); + if (d.getDataInfo() == null) + d.setDataInfo(new DataInfo()); + d.getDataInfo().setTrust("0.9"); + d.setLastupdatetimestamp(ts); + return d; + } + + private static Project projectMerger(Tuple2> e, final long ts) { + + Project p = new Project(); //the result of the merge, to be returned at the end + + p.setId(e._1()); + + final ObjectMapper mapper = new ObjectMapper(); + if (e._2() != null) + e._2().forEach(proj -> { + try { + Project project = mapper.readValue(proj, Project.class); + + p.mergeFrom(project); + } catch (Exception exc) { + throw new RuntimeException(exc); + } + }); + if (p.getDataInfo() == null) + p.setDataInfo(new DataInfo()); + p.getDataInfo().setTrust("0.9"); + p.setLastupdatetimestamp(ts); + return p; + } + + private static Software softwareMerger(Tuple2> e, final long ts) { + + Software s = new Software(); //the result of the merge, to be returned at the end + + s.setId(e._1()); + final ObjectMapper mapper = new ObjectMapper(); + final Collection dateofacceptance = Lists.newArrayList(); + if (e._2() != null) + e._2().forEach(soft -> { + try { + Software software = mapper.readValue(soft, Software.class); + + s.mergeFrom(software); + s.setAuthor(DedupUtility.mergeAuthor(s.getAuthor(), software.getAuthor())); + //add to the list if they are not null + if (software.getDateofacceptance() != null) + dateofacceptance.add(software.getDateofacceptance().getValue()); + } catch (Exception exc) { + throw new RuntimeException(exc); + } + }); + s.setDateofacceptance(DatePicker.pick(dateofacceptance)); + if (s.getDataInfo() == null) + s.setDataInfo(new DataInfo()); + s.getDataInfo().setTrust("0.9"); + s.setLastupdatetimestamp(ts); + return s; + } + + private static Datasource datasourceMerger(Tuple2> e, final long ts) { + Datasource d = new Datasource(); //the result of the merge, to be returned at the end + d.setId(e._1()); + final ObjectMapper mapper = new ObjectMapper(); + if (e._2() != null) + e._2().forEach(dat -> { + try { + Datasource datasource = mapper.readValue(dat, Datasource.class); + + d.mergeFrom(datasource); + } catch (Exception exc) { + throw new RuntimeException(exc); + } + }); + if (d.getDataInfo() == null) + d.setDataInfo(new DataInfo()); + d.getDataInfo().setTrust("0.9"); + d.setLastupdatetimestamp(ts); + return d; + } + + private static Organization organizationMerger(Tuple2> e, final long ts) { + + Organization o = new Organization(); //the result of the merge, to be returned at the end + + o.setId(e._1()); + + final ObjectMapper mapper = new ObjectMapper(); + + + StringBuilder trust = new StringBuilder("0.0"); + + if (e._2() != null) + e._2().forEach(pub -> { + try { + Organization organization = mapper.readValue(pub, Organization.class); + + final String currentTrust = organization.getDataInfo().getTrust(); + if (!"1.0".equals(currentTrust)) { + trust.setLength(0); + trust.append(currentTrust); + } + o.mergeFrom(organization); + + } catch (Exception exc) { + throw new RuntimeException(exc); + } + }); + + if (o.getDataInfo() == null) + { + o.setDataInfo(new DataInfo()); + } + if (o.getDataInfo() == null) + o.setDataInfo(new DataInfo()); + o.getDataInfo().setTrust("0.9"); + o.setLastupdatetimestamp(ts); + + return o; + } + + private static OtherResearchProduct otherresearchproductMerger(Tuple2> e, final long ts) { + + OtherResearchProduct o = new OtherResearchProduct(); //the result of the merge, to be returned at the end + + o.setId(e._1()); + + final ObjectMapper mapper = new ObjectMapper(); + + final Collection dateofacceptance = Lists.newArrayList(); + + if (e._2() != null) + e._2().forEach(orp -> { + try { + OtherResearchProduct otherResearchProduct = mapper.readValue(orp, OtherResearchProduct.class); + + o.mergeFrom(otherResearchProduct); + o.setAuthor(DedupUtility.mergeAuthor(o.getAuthor(), otherResearchProduct.getAuthor())); + //add to the list if they are not null + if (otherResearchProduct.getDateofacceptance() != null) + dateofacceptance.add(otherResearchProduct.getDateofacceptance().getValue()); + } catch (Exception exc) { + throw new RuntimeException(exc); + } + }); + if (o.getDataInfo() == null) + o.setDataInfo(new DataInfo()); + o.setDateofacceptance(DatePicker.pick(dateofacceptance)); + o.getDataInfo().setTrust("0.9"); + o.setLastupdatetimestamp(ts); + return o; + } + +} diff --git a/dhp-workflows/dhp-dedup/src/main/java/eu/dnetlib/dedup/DedupUtility.java b/dhp-workflows/dhp-dedup/src/main/java/eu/dnetlib/dedup/DedupUtility.java new file mode 100644 index 000000000..3bed74f86 --- /dev/null +++ b/dhp-workflows/dhp-dedup/src/main/java/eu/dnetlib/dedup/DedupUtility.java @@ -0,0 +1,219 @@ +package eu.dnetlib.dedup; + +import com.google.common.collect.Sets; +import com.wcohen.ss.JaroWinkler; +import eu.dnetlib.dhp.schema.oaf.Author; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import eu.dnetlib.pace.clustering.BlacklistAwareClusteringCombiner; +import eu.dnetlib.pace.config.DedupConfig; + +import eu.dnetlib.pace.model.MapDocument; +import eu.dnetlib.pace.model.Person; +import org.apache.commons.codec.binary.Hex; +import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FSDataInputStream; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.apache.spark.SparkContext; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.util.LongAccumulator; +import scala.Tuple2; + +import java.io.IOException; +import java.io.StringWriter; +import java.nio.charset.StandardCharsets; +import java.security.MessageDigest; +import java.text.Normalizer; +import java.util.*; +import java.util.stream.Collectors; +import java.util.stream.Stream; + +public class DedupUtility { + private static final Double THRESHOLD = 0.95; + + public static Map constructAccumulator(final DedupConfig dedupConf, final SparkContext context) { + + Map accumulators = new HashMap<>(); + + String acc1 = String.format("%s::%s", dedupConf.getWf().getEntityType(), "records per hash key = 1"); + accumulators.put(acc1, context.longAccumulator(acc1)); + String acc2 = String.format("%s::%s", dedupConf.getWf().getEntityType(), "missing " + dedupConf.getWf().getOrderField()); + accumulators.put(acc2, context.longAccumulator(acc2)); + String acc3 = String.format("%s::%s", dedupConf.getWf().getEntityType(), String.format("Skipped records for count(%s) >= %s", dedupConf.getWf().getOrderField(), dedupConf.getWf().getGroupMaxSize())); + accumulators.put(acc3, context.longAccumulator(acc3)); + String acc4 = String.format("%s::%s", dedupConf.getWf().getEntityType(), "skip list"); + accumulators.put(acc4, context.longAccumulator(acc4)); + String acc5 = String.format("%s::%s", dedupConf.getWf().getEntityType(), "dedupSimilarity (x2)"); + accumulators.put(acc5, context.longAccumulator(acc5)); + String acc6 = String.format("%s::%s", dedupConf.getWf().getEntityType(), "d < " + dedupConf.getWf().getThreshold()); + accumulators.put(acc6, context.longAccumulator(acc6)); + + return accumulators; + } + + public static JavaRDD loadDataFromHDFS(String path, JavaSparkContext context) { + return context.textFile(path); + } + + public static void deleteIfExists(String path) throws IOException { + Configuration conf = new Configuration(); + FileSystem fileSystem = FileSystem.get(conf); + if (fileSystem.exists(new Path(path))) { + fileSystem.delete(new Path(path), true); + } + } + + public static DedupConfig loadConfigFromHDFS(String path) throws IOException { + + Configuration conf = new Configuration(); + FileSystem fileSystem = FileSystem.get(conf); + FSDataInputStream inputStream = new FSDataInputStream(fileSystem.open(new Path(path))); + + return DedupConfig.load(IOUtils.toString(inputStream, StandardCharsets.UTF_8.name())); + + } + + static String readFromClasspath(final String filename, final Class clazz) { + final StringWriter sw = new StringWriter(); + try { + IOUtils.copy(clazz.getResourceAsStream(filename), sw); + return sw.toString(); + } catch (final IOException e) { + throw new RuntimeException("cannot load resource from classpath: " + filename); + } + } + + static Set getGroupingKeys(DedupConfig conf, MapDocument doc) { + return Sets.newHashSet(BlacklistAwareClusteringCombiner.filterAndCombine(doc, conf)); + } + + public static String md5(final String s) { + try { + final MessageDigest md = MessageDigest.getInstance("MD5"); + md.update(s.getBytes("UTF-8")); + return new String(Hex.encodeHex(md.digest())); + } catch (final Exception e) { + System.err.println("Error creating id"); + return null; + } + } + + + public static List mergeAuthor(final List a, final List b) { + int pa = countAuthorsPids(a); + int pb = countAuthorsPids(b); + List base, enrich; + int sa = authorsSize(a); + int sb = authorsSize(b); + + if (pa == pb) { + base = sa > sb ? a : b; + enrich = sa > sb ? b : a; + } else { + base = pa > pb ? a : b; + enrich = pa > pb ? b : a; + } + enrichPidFromList(base, enrich); + return base; + } + + private static void enrichPidFromList(List base, List enrich) { + if (base == null || enrich == null) + return; + final Map basePidAuthorMap = base.stream() + .filter(a -> a.getPid() != null && a.getPid().size() > 0) + .flatMap(a -> a.getPid() + .stream() + .map(p -> new Tuple2<>(p.toComparableString(), a)) + ).collect(Collectors.toMap(Tuple2::_1, Tuple2::_2, (x1, x2) -> x1)); + + final List> pidToEnrich = enrich + .stream() + .filter(a -> a.getPid() != null && a.getPid().size() > 0) + .flatMap(a -> a.getPid().stream().filter(p -> !basePidAuthorMap.containsKey(p.toComparableString())).map(p -> new Tuple2<>(p, a))) + .collect(Collectors.toList()); + + + pidToEnrich.forEach(a -> { + Optional> simAuhtor = base.stream().map(ba -> new Tuple2<>(sim(ba, a._2()), ba)).max(Comparator.comparing(Tuple2::_1)); + if (simAuhtor.isPresent() && simAuhtor.get()._1() > THRESHOLD) { + Author r = simAuhtor.get()._2(); + r.getPid().add(a._1()); + } + }); + } + + public static String createEntityPath(final String basePath, final String entityType) { + return String.format("%s/%s", basePath, entityType); + } + + public static String createSimRelPath(final String basePath, final String entityType) { + return String.format("%s/%s_simRel", basePath, entityType); + } + + public static String createMergeRelPath(final String basePath, final String entityType) { + return String.format("%s/%s_mergeRel", basePath, entityType); + } + + private static Double sim(Author a, Author b) { + + final Person pa = parse(a); + final Person pb = parse(b); + + if (pa.isAccurate() & pb.isAccurate()) { + return new JaroWinkler().score( + normalize(pa.getSurnameString()), + normalize(pb.getSurnameString())); + } else { + return new JaroWinkler().score( + normalize(pa.getNormalisedFullname()), + normalize(pb.getNormalisedFullname())); + } + } + + private static String normalize(final String s) { + return nfd(s).toLowerCase() + // do not compact the regexes in a single expression, would cause StackOverflowError in case of large input strings + .replaceAll("(\\W)+", " ") + .replaceAll("(\\p{InCombiningDiacriticalMarks})+", " ") + .replaceAll("(\\p{Punct})+", " ") + .replaceAll("(\\d)+", " ") + .replaceAll("(\\n)+", " ") + .trim(); + } + + private static String nfd(final String s) { + return Normalizer.normalize(s, Normalizer.Form.NFD); + } + + private static Person parse(Author author) { + if (StringUtils.isNotBlank(author.getSurname())) { + return new Person(author.getSurname() + ", " + author.getName(), false); + } else { + return new Person(author.getFullname(), false); + } + } + + + private static int countAuthorsPids(List authors) { + if (authors == null) + return 0; + + return (int) authors.stream().filter(DedupUtility::hasPid).count(); + } + + private static int authorsSize(List authors) { + if (authors == null) + return 0; + return authors.size(); + } + + private static boolean hasPid(Author a) { + if (a == null || a.getPid() == null || a.getPid().size() == 0) + return false; + return a.getPid().stream().anyMatch(p -> p != null && StringUtils.isNotBlank(p.getValue())); + } +} diff --git a/dhp-workflows/dhp-dedup/src/main/java/eu/dnetlib/dedup/Deduper.java b/dhp-workflows/dhp-dedup/src/main/java/eu/dnetlib/dedup/Deduper.java new file mode 100644 index 000000000..7206f892f --- /dev/null +++ b/dhp-workflows/dhp-dedup/src/main/java/eu/dnetlib/dedup/Deduper.java @@ -0,0 +1,162 @@ +package eu.dnetlib.dedup; + +import eu.dnetlib.pace.config.DedupConfig; +import eu.dnetlib.pace.model.Field; +import eu.dnetlib.pace.model.MapDocument; +import eu.dnetlib.pace.util.BlockProcessor; +import eu.dnetlib.pace.util.MapDocumentUtil; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.apache.spark.api.java.JavaPairRDD; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.Function2; +import org.apache.spark.api.java.function.PairFlatMapFunction; +import org.apache.spark.api.java.function.PairFunction; +import org.apache.spark.util.LongAccumulator; +import scala.Serializable; +import scala.Tuple2; + +import java.util.*; +import java.util.stream.Collectors; + +public class Deduper implements Serializable { + + private static final Log log = LogFactory.getLog(Deduper.class); + + /** + * @return the list of relations generated by the deduplication + * @param: the spark context + * @param: list of JSON entities to be deduped + * @param: the dedup configuration + */ + public static JavaPairRDD dedup(JavaSparkContext context, JavaRDD entities, DedupConfig config) { + + Map accumulators = DedupUtility.constructAccumulator(config, context.sc()); + + //create vertexes of the graph: + JavaPairRDD mapDocs = mapToVertexes(context, entities, config); + + + //create blocks for deduplication + JavaPairRDD> blocks = createBlocks(context, mapDocs, config); + + //create relations by comparing only elements in the same group + return computeRelations(context, blocks, config); + +// final RDD> edgeRdd = relationRDD.map(it -> new Edge<>(it._1().hashCode(), it._2().hashCode(), "equalTo")).rdd(); +// +// RDD> vertexes = mapDocs.mapToPair((PairFunction, Object, MapDocument>) t -> new Tuple2((long) t._1().hashCode(), t._2())).rdd(); +// accumulators.forEach((name, acc) -> log.info(name + " -> " + acc.value())); +// +// return GraphProcessor.findCCs(vertexes, edgeRdd, 20).toJavaRDD(); + } + + /** + * @return the list of relations generated by the deduplication + * @param: the spark context + * @param: list of blocks + * @param: the dedup configuration + */ + public static JavaPairRDD computeRelations(JavaSparkContext context, JavaPairRDD> blocks, DedupConfig config) { + + Map accumulators = DedupUtility.constructAccumulator(config, context.sc()); + + return blocks.flatMapToPair((PairFlatMapFunction>, String, String>) it -> { + final SparkReporter reporter = new SparkReporter(accumulators); + new BlockProcessor(config).process(it._1(), it._2(), reporter); + return reporter.getRelations().iterator(); + + }).mapToPair( + (PairFunction, String, Tuple2>) item -> + new Tuple2>(item._1() + item._2(), item)) + .reduceByKey((a, b) -> a) + .mapToPair((PairFunction>, String, String>) Tuple2::_2); + } + + + /** + * @return the list of blocks based on clustering of dedup configuration + * @param: the spark context + * @param: list of entities: + * @param: the dedup configuration + */ + public static JavaPairRDD> createBlocks(JavaSparkContext context, JavaPairRDD mapDocs, DedupConfig config) { + return mapDocs + //the reduce is just to be sure that we haven't document with same id + .reduceByKey((a, b) -> a) + .map(Tuple2::_2) + //Clustering: from to List + .flatMapToPair((PairFlatMapFunction) a -> + DedupUtility.getGroupingKeys(config, a) + .stream() + .map(it -> new Tuple2<>(it, a)) + .collect(Collectors.toList()) + .iterator()) + .groupByKey(); + } + + + public static JavaPairRDD> createsortedBlocks(JavaSparkContext context, JavaPairRDD mapDocs, DedupConfig config) { + final String of = config.getWf().getOrderField(); + final int maxQueueSize = config.getWf().getGroupMaxSize(); + return mapDocs + //the reduce is just to be sure that we haven't document with same id + .reduceByKey((a, b) -> a) + .map(Tuple2::_2) + //Clustering: from to List + .flatMapToPair((PairFlatMapFunction>) a -> + DedupUtility.getGroupingKeys(config, a) + .stream() + .map(it -> { + List tmp = new ArrayList<>(); + tmp.add(a); + return new Tuple2<>(it, tmp); + } + ) + .collect(Collectors.toList()) + .iterator()) + .reduceByKey((Function2, List, List>) (v1, v2) -> { + v1.addAll(v2); + v1.sort(Comparator.comparing(a -> a.getFieldMap().get(of).stringValue())); + if (v1.size() > maxQueueSize) + return new ArrayList<>(v1.subList(0, maxQueueSize)); + return v1; + }); + } + + /** + * @return the list of vertexes: + * @param: the spark context + * @param: list of JSON entities + * @param: the dedup configuration + */ + public static JavaPairRDD mapToVertexes(JavaSparkContext context, JavaRDD entities, DedupConfig config) { + + return entities.mapToPair((PairFunction) s -> { + + MapDocument mapDocument = MapDocumentUtil.asMapDocumentWithJPath(config, s); + return new Tuple2(mapDocument.getIdentifier(), mapDocument); + + + }); + } + + public static JavaPairRDD computeRelations2(JavaSparkContext context, JavaPairRDD> blocks, DedupConfig config) { + Map accumulators = DedupUtility.constructAccumulator(config, context.sc()); + + return blocks.flatMapToPair((PairFlatMapFunction>, String, String>) it -> { + try { + final SparkReporter reporter = new SparkReporter(accumulators); + new BlockProcessor(config).processSortedBlock(it._1(), it._2(), reporter); + return reporter.getRelations().iterator(); + } catch (Exception e) { + throw new RuntimeException(it._2().get(0).getIdentifier(), e); + } + }).mapToPair( + (PairFunction, String, Tuple2>) item -> + new Tuple2>(item._1() + item._2(), item)) + .reduceByKey((a, b) -> a) + .mapToPair((PairFunction>, String, String>) Tuple2::_2); + } +} \ No newline at end of file diff --git a/dhp-workflows/dhp-dedup/src/main/java/eu/dnetlib/dedup/OafEntityType.java b/dhp-workflows/dhp-dedup/src/main/java/eu/dnetlib/dedup/OafEntityType.java new file mode 100644 index 000000000..fb347ed51 --- /dev/null +++ b/dhp-workflows/dhp-dedup/src/main/java/eu/dnetlib/dedup/OafEntityType.java @@ -0,0 +1,15 @@ +package eu.dnetlib.dedup; + +public enum OafEntityType { + + datasource, + organization, + project, + dataset, + otherresearchproduct, + software, + publication + + + +} diff --git a/dhp-workflows/dhp-dedup/src/main/java/eu/dnetlib/dedup/SparkCreateConnectedComponent.java b/dhp-workflows/dhp-dedup/src/main/java/eu/dnetlib/dedup/SparkCreateConnectedComponent.java new file mode 100644 index 000000000..16e112c25 --- /dev/null +++ b/dhp-workflows/dhp-dedup/src/main/java/eu/dnetlib/dedup/SparkCreateConnectedComponent.java @@ -0,0 +1,79 @@ +package eu.dnetlib.dedup; + +import com.google.common.collect.Iterables; +import com.google.common.collect.Lists; +import com.google.common.hash.HashFunction; +import com.google.common.hash.Hashing; +import eu.dnetlib.dedup.graph.ConnectedComponent; +import eu.dnetlib.dedup.graph.GraphProcessor; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.schema.oaf.Relation; +import eu.dnetlib.pace.config.DedupConfig; +import eu.dnetlib.pace.util.MapDocumentUtil; +import org.apache.commons.io.IOUtils; +import org.apache.spark.api.java.JavaPairRDD; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.FlatMapFunction; +import org.apache.spark.api.java.function.PairFunction; +import org.apache.spark.graphx.Edge; +import org.apache.spark.rdd.RDD; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SparkSession; +import scala.Tuple2; + +import java.util.ArrayList; +import java.util.List; + +public class SparkCreateConnectedComponent { + + public static void main(String[] args) throws Exception { + final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkCreateConnectedComponent.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/dedup_parameters.json"))); + parser.parseArgument(args); + final SparkSession spark = SparkSession + .builder() + .appName(SparkCreateConnectedComponent.class.getSimpleName()) + .master(parser.get("master")) + .getOrCreate(); + + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + final String inputPath = parser.get("sourcePath"); + final String entity = parser.get("entity"); + final String targetPath = parser.get("targetPath"); +// final DedupConfig dedupConf = DedupConfig.load(IOUtils.toString(SparkCreateConnectedComponent.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/org.curr.conf2.json"))); + final DedupConfig dedupConf = DedupConfig.load(parser.get("dedupConf")); + + final JavaPairRDD vertexes = sc.textFile(inputPath + "/" + entity) + .map(s -> MapDocumentUtil.getJPathString(dedupConf.getWf().getIdPath(), s)) + .mapToPair((PairFunction) + s -> new Tuple2(getHashcode(s), s) + ); + + final Dataset similarityRelations = spark.read().load(DedupUtility.createSimRelPath(targetPath,entity)).as(Encoders.bean(Relation.class)); + final RDD> edgeRdd = similarityRelations.javaRDD().map(it -> new Edge<>(getHashcode(it.getSource()), getHashcode(it.getTarget()), it.getRelClass())).rdd(); + final JavaRDD cc = GraphProcessor.findCCs(vertexes.rdd(), edgeRdd, dedupConf.getWf().getMaxIterations()).toJavaRDD(); + final Dataset mergeRelation = spark.createDataset(cc.filter(k->k.getDocIds().size()>1).flatMap((FlatMapFunction) c -> + c.getDocIds() + .stream() + .flatMap(id -> { + List tmp = new ArrayList<>(); + Relation r = new Relation(); + r.setSource(c.getCcId()); + r.setTarget(id); + r.setRelClass("merges"); + tmp.add(r); + r = new Relation(); + r.setTarget(c.getCcId()); + r.setSource(id); + r.setRelClass("isMergedIn"); + tmp.add(r); + return tmp.stream(); + }).iterator()).rdd(), Encoders.bean(Relation.class)); + mergeRelation.write().mode("overwrite").save(DedupUtility.createMergeRelPath(targetPath,entity)); + } + + public static long getHashcode(final String id) { + return Hashing.murmur3_128().hashUnencodedChars(id).asLong(); + } +} diff --git a/dhp-workflows/dhp-dedup/src/main/java/eu/dnetlib/dedup/SparkCreateDedupRecord.java b/dhp-workflows/dhp-dedup/src/main/java/eu/dnetlib/dedup/SparkCreateDedupRecord.java new file mode 100644 index 000000000..db2306526 --- /dev/null +++ b/dhp-workflows/dhp-dedup/src/main/java/eu/dnetlib/dedup/SparkCreateDedupRecord.java @@ -0,0 +1,39 @@ +package eu.dnetlib.dedup; + +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.schema.oaf.OafEntity; +import eu.dnetlib.pace.config.DedupConfig; +import org.apache.commons.io.IOUtils; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.sql.SparkSession; + +public class SparkCreateDedupRecord { + + public static void main(String[] args) throws Exception { + final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkCreateDedupRecord.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/dedupRecord_parameters.json"))); + parser.parseArgument(args); + final SparkSession spark = SparkSession + .builder() + .appName(SparkCreateDedupRecord.class.getSimpleName()) + .master(parser.get("master")) + .getOrCreate(); + + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + final String sourcePath = parser.get("sourcePath"); + final String entity = parser.get("entity"); + final String dedupPath = parser.get("dedupPath"); +// final DedupConfig dedupConf = DedupConfig.load(IOUtils.toString(SparkCreateDedupRecord.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/org.curr.conf2.json"))); + final DedupConfig dedupConf = DedupConfig.load(parser.get("dedupConf")); + + final JavaRDD dedupRecord = DedupRecordFactory.createDedupRecord(sc, spark, DedupUtility.createMergeRelPath(dedupPath,entity), DedupUtility.createEntityPath(sourcePath,entity), OafEntityType.valueOf(entity), dedupConf); + dedupRecord.map(r-> { + ObjectMapper mapper = new ObjectMapper(); + return mapper.writeValueAsString(r); + }).saveAsTextFile(dedupPath+"/"+entity+"_dedup_record_json"); + + + } + +} diff --git a/dhp-workflows/dhp-dedup/src/main/java/eu/dnetlib/dedup/SparkCreateSimRels.java b/dhp-workflows/dhp-dedup/src/main/java/eu/dnetlib/dedup/SparkCreateSimRels.java new file mode 100644 index 000000000..831e45daf --- /dev/null +++ b/dhp-workflows/dhp-dedup/src/main/java/eu/dnetlib/dedup/SparkCreateSimRels.java @@ -0,0 +1,73 @@ +package eu.dnetlib.dedup; + +import com.google.common.hash.Hashing; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.schema.oaf.Relation; +import eu.dnetlib.pace.config.DedupConfig; +import eu.dnetlib.pace.model.MapDocument; +import eu.dnetlib.pace.util.MapDocumentUtil; +import org.apache.commons.io.IOUtils; +import org.apache.spark.api.java.JavaPairRDD; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.PairFunction; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SparkSession; +import scala.Tuple2; + +import java.util.List; + + +/** + * This Spark class creates similarity relations between entities, saving result + * + * param request: + * sourcePath + * entityType + * target Path + */ +public class SparkCreateSimRels { + + public static void main(String[] args) throws Exception { + final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkCreateSimRels.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/dedup_parameters.json"))); + parser.parseArgument(args); + final SparkSession spark = SparkSession + .builder() + .appName(SparkCreateSimRels.class.getSimpleName()) + .master(parser.get("master")) + .getOrCreate(); + + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + final String inputPath = parser.get("sourcePath"); + final String entity = parser.get("entity"); + final String targetPath = parser.get("targetPath"); +// final DedupConfig dedupConf = DedupConfig.load(IOUtils.toString(SparkCreateSimRels.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json"))); + final DedupConfig dedupConf = DedupConfig.load(parser.get("dedupConf")); + + final long total = sc.textFile(inputPath + "/" + entity).count(); + + JavaPairRDD mapDocument = sc.textFile(inputPath + "/" + entity) + .mapToPair(s->{ + MapDocument d = MapDocumentUtil.asMapDocumentWithJPath(dedupConf,s); + return new Tuple2<>(d.getIdentifier(), d);}); + + //create blocks for deduplication + JavaPairRDD> blocks = Deduper.createsortedBlocks(sc, mapDocument, dedupConf); +// JavaPairRDD> blocks = Deduper.createBlocks(sc, mapDocument, dedupConf); + + //create relations by comparing only elements in the same group + final JavaPairRDD dedupRels = Deduper.computeRelations2(sc, blocks, dedupConf); +// final JavaPairRDD dedupRels = Deduper.computeRelations(sc, blocks, dedupConf); + + final JavaRDD isSimilarToRDD = dedupRels.map(simRel -> { + final Relation r = new Relation(); + r.setSource(simRel._1()); + r.setTarget(simRel._2()); + r.setRelClass("isSimilarTo"); + return r; + }); + + spark.createDataset(isSimilarToRDD.rdd(), Encoders.bean(Relation.class)).write().mode("overwrite").save( DedupUtility.createSimRelPath(targetPath,entity)); + + } +} \ No newline at end of file diff --git a/dhp-workflows/dhp-dedup/src/main/java/eu/dnetlib/dedup/SparkReporter.java b/dhp-workflows/dhp-dedup/src/main/java/eu/dnetlib/dedup/SparkReporter.java new file mode 100644 index 000000000..165a10b25 --- /dev/null +++ b/dhp-workflows/dhp-dedup/src/main/java/eu/dnetlib/dedup/SparkReporter.java @@ -0,0 +1,47 @@ +package eu.dnetlib.dedup; + +import eu.dnetlib.pace.util.Reporter; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.apache.spark.util.LongAccumulator; +import scala.Serializable; +import scala.Tuple2; + +import java.util.ArrayList; +import java.util.List; +import java.util.Map; + +public class SparkReporter implements Serializable, Reporter { + + final List> relations = new ArrayList<>(); + private static final Log log = LogFactory.getLog(SparkReporter.class); + Map accumulators; + + public SparkReporter(Map accumulators){ + this.accumulators = accumulators; + } + + public void incrementCounter(String counterGroup, String counterName, long delta, Map accumulators) { + + final String accumulatorName = String.format("%s::%s", counterGroup, counterName); + if (accumulators.containsKey(accumulatorName)){ + accumulators.get(accumulatorName).add(delta); + } + + } + + @Override + public void incrementCounter(String counterGroup, String counterName, long delta) { + + incrementCounter(counterGroup, counterName, delta, accumulators); + } + + @Override + public void emit(String type, String from, String to) { + relations.add(new Tuple2<>(from, to)); + } + + public List> getRelations() { + return relations; + } +} diff --git a/dhp-workflows/dhp-dedup/src/main/java/eu/dnetlib/dedup/graph/ConnectedComponent.java b/dhp-workflows/dhp-dedup/src/main/java/eu/dnetlib/dedup/graph/ConnectedComponent.java new file mode 100644 index 000000000..27a61c02d --- /dev/null +++ b/dhp-workflows/dhp-dedup/src/main/java/eu/dnetlib/dedup/graph/ConnectedComponent.java @@ -0,0 +1,80 @@ +package eu.dnetlib.dedup.graph; + +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dedup.DedupUtility; +import eu.dnetlib.pace.util.PaceException; +import org.apache.commons.lang.StringUtils; +import org.codehaus.jackson.annotate.JsonIgnore; + +import java.io.IOException; +import java.io.Serializable; +import java.util.Set; + +public class ConnectedComponent implements Serializable { + + private Set docIds; + private String ccId; + + + public ConnectedComponent() { + } + + public ConnectedComponent(Set docIds) { + this.docIds = docIds; + createID(); + } + + public String createID() { + if (docIds.size() > 1) { + final String s = getMin(); + String prefix = s.split("\\|")[0]; + ccId =prefix + "|dedup_______::" + DedupUtility.md5(s); + return ccId; + } else { + return docIds.iterator().next(); + } + } + + @JsonIgnore + public String getMin(){ + + final StringBuilder min = new StringBuilder(); + docIds.forEach(i -> { + if (StringUtils.isBlank(min.toString())) { + min.append(i); + } else { + if (min.toString().compareTo(i) > 0) { + min.setLength(0); + min.append(i); + } + } + }); + return min.toString(); + } + + @Override + public String toString(){ + ObjectMapper mapper = new ObjectMapper(); + try { + return mapper.writeValueAsString(this); + } catch (IOException e) { + throw new PaceException("Failed to create Json: ", e); + } + } + + public Set getDocIds() { + return docIds; + } + + public void setDocIds(Set docIds) { + this.docIds = docIds; + } + + public String getCcId() { + return ccId; + } + + public void setCcId(String ccId) { + this.ccId = ccId; + } +} diff --git a/dhp-workflows/dhp-dedup/src/main/java/eu/dnetlib/dedup/graph/GraphProcessor.scala b/dhp-workflows/dhp-dedup/src/main/java/eu/dnetlib/dedup/graph/GraphProcessor.scala new file mode 100644 index 000000000..38c695152 --- /dev/null +++ b/dhp-workflows/dhp-dedup/src/main/java/eu/dnetlib/dedup/graph/GraphProcessor.scala @@ -0,0 +1,37 @@ +package eu.dnetlib.dedup.graph + +import org.apache.spark.graphx._ +import org.apache.spark.rdd.RDD + +import scala.collection.JavaConversions; + +object GraphProcessor { + + def findCCs(vertexes: RDD[(VertexId, String)], edges: RDD[Edge[String]], maxIterations: Int): RDD[ConnectedComponent] = { + val graph: Graph[String, String] = Graph(vertexes, edges).partitionBy(PartitionStrategy.RandomVertexCut) //TODO remember to remove partitionby + val cc = graph.connectedComponents(maxIterations).vertices + + val joinResult = vertexes.leftOuterJoin(cc).map { + case (id, (openaireId, cc)) => { + if (cc.isEmpty) { + (id, openaireId) + } + else { + (cc.get, openaireId) + } + } + } + val connectedComponents = joinResult.groupByKey() + .map[ConnectedComponent](cc => asConnectedComponent(cc)) + connectedComponents + } + + + + def asConnectedComponent(group: (VertexId, Iterable[String])): ConnectedComponent = { + val docs = group._2.toSet[String] + val connectedComponent = new ConnectedComponent(JavaConversions.setAsJavaSet[String](docs)); + connectedComponent + } + +} \ No newline at end of file diff --git a/dhp-workflows/dhp-dedup/src/main/resources/eu/dnetlib/dhp/dedup/dedupRecord_parameters.json b/dhp-workflows/dhp-dedup/src/main/resources/eu/dnetlib/dhp/dedup/dedupRecord_parameters.json new file mode 100644 index 000000000..de744dfb6 --- /dev/null +++ b/dhp-workflows/dhp-dedup/src/main/resources/eu/dnetlib/dhp/dedup/dedupRecord_parameters.json @@ -0,0 +1,33 @@ +[ + { + "paramName": "mt", + "paramLongName": "master", + "paramDescription": "should be local or yarn", + "paramRequired": true + }, + { + "paramName": "s", + "paramLongName": "sourcePath", + "paramDescription": "the path of the sequential file to read", + "paramRequired": true + }, + { + "paramName": "e", + "paramLongName": "entity", + "paramDescription": "the type of entity to be deduped", + "paramRequired": true + }, + { + "paramName": "c", + "paramLongName": "dedupConf", + "paramDescription": "dedup configuration to be used", + "compressed": true, + "paramRequired": true + }, + { + "paramName": "d", + "paramLongName": "dedupPath", + "paramDescription": "dedup path to load mergeRelation", + "paramRequired": true + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-dedup/src/main/resources/eu/dnetlib/dhp/dedup/dedup_parameters.json b/dhp-workflows/dhp-dedup/src/main/resources/eu/dnetlib/dhp/dedup/dedup_parameters.json new file mode 100644 index 000000000..8ba8515d0 --- /dev/null +++ b/dhp-workflows/dhp-dedup/src/main/resources/eu/dnetlib/dhp/dedup/dedup_parameters.json @@ -0,0 +1,33 @@ +[ + { + "paramName": "mt", + "paramLongName": "master", + "paramDescription": "should be local or yarn", + "paramRequired": true + }, + { + "paramName": "s", + "paramLongName": "sourcePath", + "paramDescription": "the path of the sequential file to read", + "paramRequired": true + }, + { + "paramName": "e", + "paramLongName": "entity", + "paramDescription": "the type of entity to be deduped", + "paramRequired": true + }, + { + "paramName": "c", + "paramLongName": "dedupConf", + "paramDescription": "dedup configuration to be used", + "compressed": true, + "paramRequired": true + }, + { + "paramName": "t", + "paramLongName": "targetPath", + "paramDescription": "target path to save dedup result", + "paramRequired": true + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-dedup/src/main/resources/eu/dnetlib/dhp/dedup/oozie_app/config-default.xml b/dhp-workflows/dhp-dedup/src/main/resources/eu/dnetlib/dhp/dedup/oozie_app/config-default.xml new file mode 100644 index 000000000..fcab9dd00 --- /dev/null +++ b/dhp-workflows/dhp-dedup/src/main/resources/eu/dnetlib/dhp/dedup/oozie_app/config-default.xml @@ -0,0 +1,26 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + + hive_metastore_uris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + hive_db_name + openaire + + \ No newline at end of file diff --git a/dhp-workflows/dhp-dedup/src/main/resources/eu/dnetlib/dhp/dedup/oozie_app/workflow.xml b/dhp-workflows/dhp-dedup/src/main/resources/eu/dnetlib/dhp/dedup/oozie_app/workflow.xml new file mode 100644 index 000000000..5a00a5967 --- /dev/null +++ b/dhp-workflows/dhp-dedup/src/main/resources/eu/dnetlib/dhp/dedup/oozie_app/workflow.xml @@ -0,0 +1,126 @@ + + + + sourcePath + the source path + + + entity + the entity that should be processed + + + dedupConf + the dedup Configuration + + + targetPath + the target path + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + + + + + + + + + ${jobTracker} + ${nameNode} + yarn-cluster + cluster + Create Similarity Relations + eu.dnetlib.dedup.SparkCreateSimRels + dhp-dedup-${projectVersion}.jar + --executor-memory ${sparkExecutorMemory} --executor-cores ${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} --conf + spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener" --conf + spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener" --conf + spark.sql.warehouse.dir="/user/hive/warehouse" + + -mtyarn-cluster + --sourcePath${sourcePath} + --targetPath${targetPath} + --entity${entity} + --dedupConf${dedupConf} + + + + + + + + + ${jobTracker} + ${nameNode} + yarn-cluster + cluster + Create Connected Components + eu.dnetlib.dedup.SparkCreateConnectedComponent + dhp-dedup-${projectVersion}.jar + --executor-memory ${sparkExecutorMemory} --executor-cores ${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} --conf + spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener" --conf + spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener" --conf + spark.sql.warehouse.dir="/user/hive/warehouse" + + -mtyarn-cluster + --sourcePath${sourcePath} + --targetPath${targetPath} + --entity${entity} + --dedupConf${dedupConf} + + + + + + + + ${jobTracker} + ${nameNode} + yarn-cluster + cluster + Create Dedup Record + eu.dnetlib.dedup.SparkCreateDedupRecord + dhp-dedup-${projectVersion}.jar + --executor-memory ${sparkExecutorMemory} --executor-cores ${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} --conf + spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener" --conf + spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener" --conf + spark.sql.warehouse.dir="/user/hive/warehouse" + + -mtyarn-cluster + --sourcePath${sourcePath} + --dedupPath${dedupPath} + --entity${entity} + --dedupConf${dedupConf} + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-dedup/src/test/java/eu/dnetlib/dedup/MergeAuthorTest.java b/dhp-workflows/dhp-dedup/src/test/java/eu/dnetlib/dedup/MergeAuthorTest.java new file mode 100644 index 000000000..817f2075c --- /dev/null +++ b/dhp-workflows/dhp-dedup/src/test/java/eu/dnetlib/dedup/MergeAuthorTest.java @@ -0,0 +1,61 @@ +package eu.dnetlib.dedup; + +import eu.dnetlib.dhp.schema.oaf.Publication; +import org.apache.commons.io.IOUtils; +import org.codehaus.jackson.map.ObjectMapper; +import org.junit.Before; +import org.junit.Test; + +import java.io.IOException; +import java.util.Arrays; +import java.util.List; +import java.util.stream.Collectors; + +public class MergeAuthorTest { + + List publicationsToMerge; + final ObjectMapper mapper = new ObjectMapper(); + + @Before + public void setUp() throws Exception { + final String json = IOUtils.toString(this.getClass().getResourceAsStream("/eu/dnetlib/dedup/json/authors_merge.json")); + + + publicationsToMerge = Arrays.asList(json.split("\n")).stream().map(s-> { + try { + return mapper.readValue(s, Publication.class); + } catch (IOException e) { + throw new RuntimeException(e); + } + }).collect(Collectors.toList()); + + + + } + + + @Test + public void test() throws Exception { + Publication dedup = new Publication(); + + + publicationsToMerge.forEach(p-> { + dedup.mergeFrom(p); + dedup.setAuthor(DedupUtility.mergeAuthor(dedup.getAuthor(),p.getAuthor())); + }); + + + + + + + + + System.out.println(mapper.writeValueAsString(dedup)); + + + } + + + +} diff --git a/dhp-workflows/dhp-dedup/src/test/java/eu/dnetlib/dedup/SparkCreateDedupTest.java b/dhp-workflows/dhp-dedup/src/test/java/eu/dnetlib/dedup/SparkCreateDedupTest.java new file mode 100644 index 000000000..f93703e37 --- /dev/null +++ b/dhp-workflows/dhp-dedup/src/test/java/eu/dnetlib/dedup/SparkCreateDedupTest.java @@ -0,0 +1,86 @@ +package eu.dnetlib.dedup; + +import com.fasterxml.jackson.databind.ObjectMapper; +import com.google.common.hash.HashFunction; +import com.google.common.hash.Hashing; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.schema.oaf.Publication; +import org.apache.commons.io.FileUtils; +import org.apache.commons.io.IOUtils; +import org.junit.Before; +import org.junit.Ignore; +import org.junit.Test; + +import java.io.File; +import java.io.IOException; +import java.util.List; + +public class SparkCreateDedupTest { + + String configuration; + String entity = "organization"; + + @Before + public void setUp() throws IOException { + configuration = IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dedup/conf/org.curr.conf.json")); + + } + + @Test + @Ignore + public void createSimRelsTest() throws Exception { + SparkCreateSimRels.main(new String[] { + "-mt", "local[*]", + "-s", "/Users/miconis/dumps", + "-e", entity, + "-c", ArgumentApplicationParser.compressArgument(configuration), + "-t", "/tmp/dedup", + }); + } + + @Test + @Ignore + public void createCCTest() throws Exception { + + SparkCreateConnectedComponent.main(new String[] { + "-mt", "local[*]", + "-s", "/Users/miconis/dumps", + "-e", entity, + "-c", ArgumentApplicationParser.compressArgument(configuration), + "-t", "/tmp/dedup", + }); + } + + @Test + @Ignore + public void dedupRecordTest() throws Exception { + SparkCreateDedupRecord.main(new String[] { + "-mt", "local[*]", + "-s", "/Users/miconis/dumps", + "-e", entity, + "-c", ArgumentApplicationParser.compressArgument(configuration), + "-d", "/tmp/dedup", + }); + } + + @Test + public void printConfiguration() throws Exception { + System.out.println(ArgumentApplicationParser.compressArgument(configuration)); + } + + @Test + public void testHashCode() { + final String s1 = "20|grid________::6031f94bef015a37783268ec1e75f17f"; + final String s2 = "20|nsf_________::b12be9edf414df8ee66b4c52a2d8da46"; + + final HashFunction hashFunction = Hashing.murmur3_128(); + + System.out.println( s1.hashCode()); + System.out.println(hashFunction.hashUnencodedChars(s1).asLong()); + System.out.println( s2.hashCode()); + System.out.println(hashFunction.hashUnencodedChars(s2).asLong()); + + } + + +} diff --git a/dhp-workflows/dhp-dedup/src/test/java/eu/dnetlib/dedup/jpath/JsonPathTest.java b/dhp-workflows/dhp-dedup/src/test/java/eu/dnetlib/dedup/jpath/JsonPathTest.java new file mode 100644 index 000000000..7a63cfe24 --- /dev/null +++ b/dhp-workflows/dhp-dedup/src/test/java/eu/dnetlib/dedup/jpath/JsonPathTest.java @@ -0,0 +1,31 @@ +package eu.dnetlib.dedup.jpath; + +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.ObjectMapper; +import com.jayway.jsonpath.JsonPath; +import org.apache.commons.io.IOUtils; +import org.junit.Test; +import java.util.List; +import java.util.Map; + +public class JsonPathTest { + + @Test + public void testJPath () throws Exception { + final String json = IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dedup/conf/sample.json")); + List> pid = JsonPath.read(json, "$.pid[*]"); +// System.out.println(json); + + pid.forEach(it -> { + try { + System.out.println(new ObjectMapper().writeValueAsString(it)); + } catch (JsonProcessingException e) { + e.printStackTrace(); + } + }); + + + + + } +} diff --git a/dhp-workflows/dhp-dedup/src/test/resources/eu/dnetlib/dedup/conf/org.curr.conf.json b/dhp-workflows/dhp-dedup/src/test/resources/eu/dnetlib/dedup/conf/org.curr.conf.json new file mode 100644 index 000000000..2d0905562 --- /dev/null +++ b/dhp-workflows/dhp-dedup/src/test/resources/eu/dnetlib/dedup/conf/org.curr.conf.json @@ -0,0 +1,266 @@ +{ + "wf" : { + "threshold" : "0.99", + "dedupRun" : "001", + "entityType" : "organization", + "orderField" : "legalname", + "queueMaxSize" : "2000", + "groupMaxSize" : "50", + "slidingWindowSize" : "200", + "idPath":"$.id", + "rootBuilder" : [ "organization", "projectOrganization_participation_isParticipant", "datasourceOrganization_provision_isProvidedBy" ], + "includeChildren" : "true", + "maxIterations": "20" + }, + "pace" : { + "clustering" : [ + { "name" : "sortedngrampairs", "fields" : [ "legalname" ], "params" : { "max" : 2, "ngramLen" : "3"} }, + { "name" : "suffixprefix", "fields" : [ "legalname" ], "params" : { "max" : 1, "len" : "3" } }, + { "name" : "urlclustering", "fields" : [ "websiteurl" ], "params" : { } }, + { "name" : "keywordsclustering", "fields" : [ "legalname" ], "params" : { "max": 2, "windowSize": 4} } + ], + "decisionTree" : { + "start": { + "fields": [ + { + "field": "gridid", + "comparator": "exactMatch", + "weight": 1, + "countIfUndefined": "false", + "params": {} + } + ], + "threshold": 1, + "aggregation": "AVG", + "positive": "MATCH", + "negative": "NO_MATCH", + "undefined": "layer2", + "ignoreUndefined": "false" + }, + "layer2": { + "fields": [ + { + "field": "websiteurl", + "comparator": "domainExactMatch", + "weight": 1, + "countIfUndefined": "false", + "params": {} + }, + { + "field": "country", + "comparator": "exactMatch", + "weight": 1, + "countIfUndefined": "true", + "params": {} + }, + { + "field": "legalname", + "comparator": "numbersMatch", + "weight": 1, + "countIfUndefined": "true", + "params": {} + }, + { + "field": "legalname", + "comparator": "romansMatch", + "weight": 1, + "countIfUndefined": "true", + "params": {} + } + ], + "threshold": 1, + "aggregation": "AND", + "positive": "layer3", + "negative": "NO_MATCH", + "undefined": "layer3", + "ignoreUndefined": "true" + }, + "layer3": { + "fields": [ + { + "field": "legalname", + "comparator": "cityMatch", + "weight": 1.0, + "countIfUndefined": "true", + "params": { + "windowSize": "4" + } + } + ], + "threshold": 0.7, + "aggregation": "W_MEAN", + "positive": "layer4", + "negative": "NO_MATCH", + "undefined": "NO_MATCH", + "ignoreUndefined": "true" + }, + "layer4": { + "fields": [ + { + "field": "legalname", + "comparator": "keywordMatch", + "weight": 1.0, + "countIfUndefined": "true", + "params": { + "windowSize": "4" + } + } + ], + "threshold": 0.9, + "aggregation": "AVG", + "positive": "layer5", + "negative": "NO_MATCH", + "undefined": "layer5", + "ignoreUndefined": "true" + }, + "layer5": { + "fields": [ + { + "field": "legalname", + "comparator": "jaroWinklerNormalizedName", + "weight": 0.9, + "countIfUndefined": "true", + "params": { + "windowSize": "4" + } + }, + { + "field": "legalshortname", + "comparator": "jaroWinklerNormalizedName", + "weight": 0.1, + "countIfUndefined": "false", + "params": {} + } + ], + "threshold": 0.9, + "aggregation": "W_MEAN", + "positive": "MATCH", + "negative": "NO_MATCH", + "undefined": "NO_MATCH", + "ignoreUndefined": "true" + } + }, + "model" : [ + { "name" : "country", "type" : "String", "path" : "$.country.classid"}, + { "name" : "legalshortname", "type" : "String", "path" : "$.legalshortname.value"}, + { "name" : "legalname", "type" : "String", "path" : "$.legalname.value" }, + { "name" : "websiteurl", "type" : "URL", "path" : "$.websiteurl.value" }, + { "name" : "gridid", "type" : "String", "path" : "$.pid[?(@.qualifier.classid =='grid.ac')].value"}, + { "name" : "originalId", "type" : "String", "path" : "$.id" } + ], + "blacklists" : { + "legalname" : [] + }, + "synonyms": { + "key::1": ["university","università","università studi","universitario","universitaria","université", "universite", "universitaire","universitaires","universidad","universitade","Universität","universitaet","Uniwersytet","университет","universiteit","πανεπιστήμιο","universitesi","universiteti", "universiti"], + "key::2": ["studies","studi","études","estudios","estudos","Studien","studia","исследования","studies","σπουδές"], + "key::3": ["advanced","superiore","supérieur","supérieure","supérieurs","supérieures","avancado","avancados","fortgeschrittene","fortgeschritten","zaawansowany","передовой","gevorderd","gevorderde","προχωρημένος","προχωρημένη","προχωρημένο","προχωρημένες","προχωρημένα","wyzsza"], + "key::4": ["institute","istituto","institut","instituto","instituto","Institut","instytut","институт","instituut","ινστιτούτο"], + "key::5": ["hospital","ospedale","hôpital","hospital","hospital","Krankenhaus","szpital","больница","ziekenhuis","νοσοκομείο"], + "key::6": ["research","ricerca","recherche","investigacion","pesquisa","Forschung","badania","исследования","onderzoek","έρευνα","erevna","erevnas"], + "key::7": ["college","collegio","colegio","faculdade","Hochschule","Szkoła Wyższa","Высшая школа","κολλέγιο"], + "key::8": ["foundation","fondazione","fondation","fundación","fundação","Stiftung","Fundacja","фонд","stichting","ίδρυμα","idryma"], + "key::9": ["center","centro","centre","centro","centro","zentrum","centrum","центр","centrum","κέντρο"], + "key::10": ["national","nazionale","national","nationale","nationaux","nationales","nacional","nacional","national","krajowy","национальный","nationaal","nationale","εθνικό"], + "key::11": ["association","associazione","association","asociación","associação","Verein","verband","stowarzyszenie","ассоциация","associatie"], + "key::12": ["society","societa","société","sociedad","sociedade","gesellschaft","społeczeństwo","общество","maatschappij","κοινωνία"], + "key::13": ["international","internazionale","international","internacional","internacional","international","międzynarodowy","Международный","internationaal","internationale","διεθνής","διεθνή","διεθνές"], + "key::14": ["community","comunita","communauté","comunidad","comunidade","Gemeinschaft","społeczność","сообщество","gemeenschap","κοινότητα"], + "key::15": ["school","scuola","école","escuela","escola","schule","Szkoła","школа","school","σχολείο"], + "key::16": ["education","educazione","éducation","educacion","Educação","Bildung","Edukacja","образование","opleiding","εκπαίδευση"], + "key::17": ["academy","accademia","académie","academia","academia","Akademie","akademie","академия","academie","ακαδημία"], + "key::18": ["public","pubblico","public","publique","publics","publiques","publico","publico","Öffentlichkeit","publiczny","публичный","publiek","publieke","δημόσιος","δημόσια","δημόσιο"], + "key::19": ["museum","museo","musée","mueso","museu","museum","muzeum","музей","museum","μουσείο"], + "key::20": ["group","gruppo","groupe","grupo","grupo","gruppe","grupa","группа","groep","ομάδα","όμιλος"], + "key::21": ["department","dipartimento","département","departamento","departamento","abteilung","departament","отдел","afdeling","τμήμα"], + "key::22": ["council","consiglio","conseil","Consejo","conselho","gesellschaft","rada","совет","raad","συμβούλιο"], + "key::23": ["library","biblioteca","bibliothèque","biblioteca","biblioteca","Bibliothek","biblioteka","библиотека","bibliotheek","βιβλιοθήκη"], + "key::24": ["ministry","ministero","ministère","ministerio","ministério","Ministerium","ministerstwo","министерство","ministerie","υπουργείο"], + "key::25": ["services","servizi","services","servicios","Serviços","Dienstleistungen","usługi","услуги","diensten","υπηρεσίες"], + "key::26": ["central","centrale","central","centrale","centrales","central","central","zentral","centralny","цетральный","centraal","κεντρικός","κεντρική","κεντρικό","κεντρικά"], + "key::27": ["general","generale","général","générale","généraux","générales","general","geral","general","Allgemeines","general","общий","algemeen","algemene","γενικός","γενική","γενικό","γενικά"], + "key::28": ["applied","applicati","appliqué","appliquée","appliqués","appliquées","aplicado","aplicada","angewendet","stosowany","прикладной","toegepast","toegepaste","εφαρμοσμένος","εφαρμοσμένη","εφαρμοσμένο","εφαρμοσμένα"], + "key::29": ["european","europee","europea","européen","européenne","européens","européennes","europeo","europeu","europäisch","europejski","европейский","Europees","Europese","ευρωπαϊκός","ευρωπαϊκή","ευρωπαϊκό","ευρωπαϊκά"], + "key::30": ["agency","agenzia","agence","agencia","agencia","agentur","agencja","агенция","agentschap","πρακτορείο"], + "key::31": ["laboratory","laboratorio","laboratoire","laboratorio","laboratorio","labor","laboratorium","лаборатория","laboratorium","εργαστήριο"], + "key::32": ["industry","industria","industrie","индустрия","industrie","βιομηχανία"], + "key::33": ["industrial","industriale","industriel","industrielle","industriels","industrielles","индустриальный","industrieel","βιομηχανικός","βιομηχανική","βιομηχανικό","βιομηχανικά","βιομηχανικές"], + "key::34": ["consortium","consorzio","consortium","консорциум","consortium","κοινοπραξία"], + "key::35": ["organization","organizzazione","organisation","organización","organização","organizacja","организация","organisatie","οργανισμός"], + "key::36": ["authority","autorità","autorité","авторитет","autoriteit"], + "key::37": ["federation","federazione","fédération","федерация","federatie","ομοσπονδία"], + "key::38": ["observatory","osservatorio","observatoire","обсерватория","observatorium","αστεροσκοπείο"], + "key::39": ["bureau","ufficio","bureau","офис","bureau","γραφείο"], + "key::40": ["company","impresa","compagnie","société","компания","bedrijf","εταιρία"], + "key::41": ["polytechnic","politecnico","polytechnique","политехника","polytechnisch","πολυτεχνείο","universita politecnica","polytechnic university","universidad politecnica","universitat politecnica","politechnika","politechniki","university technology","university science technology"], + "key::42": ["coalition","coalizione","coalition","коалиция","coalitie","συνασπισμός"], + "key::43": ["initiative","iniziativa","initiative","инициатива","initiatief","πρωτοβουλία"], + "key::44": ["academic","accademico","académique","universitaire","акадеческий academisch","ακαδημαϊκός","ακαδημαϊκή","ακαδημαϊκό","ακαδημαϊκές","ακαδημαϊκοί"], + "key::45": ["institution","istituzione","institution","институциональный","instelling","ινστιτούτο"], + "key::46": ["division","divisione","division","отделение","divisie","τμήμα"], + "key::47": ["committee","comitato","comité","комитет","commissie","επιτροπή"], + "key::48": ["promotion","promozione","продвижение","proothisis","forderung"], + "key::49": ["medical","medicine","clinical","medicina","clinici","médico","medicina","clínica","médico","medicina","clínica","medizinisch","Medizin","klinisch","medisch","geneeskunde","klinisch","ιατρικός","ιατρική","ιατρικό","ιατρικά","κλινικός","κλινική","κλινικό","κλινικά","tıbbi","tıp","klinik","orvosi","orvostudomány","klinikai","zdravniški","medicinski","klinični","meditsiini","kliinik","kliiniline"], + "key::50": ["technology","technological","tecnologia","tecnologie","tecnología","tecnológico","tecnologia","tecnológico","Technologie","technologisch","technologie","technologisch","τεχνολογία","τεχνολογικός","τεχνολογική","τεχνολογικό","teknoloji","teknolojik","technológia","technológiai","tehnologija","tehnološki","tehnoloogia","tehnoloogiline","technologii","technical","texniki","teknik"], + "key::51": ["science","scientific","scienza","scientifiche","scienze","ciencia","científico","ciência","científico","Wissenschaft","wissenschaftlich","wetenschap","wetenschappelijk","επιστήμη","επιστημονικός","επιστημονική","επιστημονικό","επιστημονικά","bilim","bilimsel","tudomány","tudományos","znanost","znanstveni","teadus","teaduslik",""], + "key::52": ["engineering","ingegneria","ingeniería","engenharia","Ingenieurwissenschaft","ingenieurswetenschappen","bouwkunde","μηχανικός","μηχανική","μηχανικό","mühendislik","mérnöki","Inženirstvo","inseneeria","inseneri",""], + "key::53": ["management","gestione","gestionale","gestionali","gestión","administración","gestão","administração","Verwaltung","management","διαχείριση","yönetim","menedzsment","vodstvo","upravljanje","management","juhtkond","juhtimine","haldus",""], + "key::54": ["energy","energia","energía","energia","Energie","energie","ενέργεια","enerji","energia","energija","energia",""], + "key::55": ["agricultural","agriculture","agricoltura","agricole","agrícola","agricultura","agrícola","agricultura","landwirtschaftlich","Landwirtschaft","landbouwkundig","landbouw","αγροτικός","αγροτική","αγροτικό","γεωργικός","γεωργική","γεωργικό","γεωργία","tarımsal","tarım","mezőgazdasági","mezőgazdaság","poljedelski","poljedelstvo","põllumajandus","põllumajanduslik",""], + "key::56": ["information","informazione","información","informação","Information","informatie","πληροφορία","bilgi","információ","informacija","informatsioon","informatycznych",""], + "key::57": ["social","sociali","social","social","Sozial","sociaal","maatschappelijk","κοινωνικός","κοινωνική","κοινωνικό","κοινωνικά","sosyal","szociális","družbeni","sotsiaal","sotsiaalne",""], + "key::58": ["environmental","ambiente","medioambiental","ambiente","medioambiente","meioambiente","Umwelt","milieu","milieuwetenschap","milieukunde","περιβαλλοντικός","περιβαλλοντική","περιβαλλοντικό","περιβαλλοντικά","çevre","környezeti","okoliški","keskonna",""], + "key::59": ["business","economia","economiche","economica","negocio","empresa","negócio","Unternehmen","bedrijf","bedrijfskunde","επιχείρηση","iş","üzleti","posel","ettevõte/äri",""], + "key::60": ["pharmaceuticals","pharmacy","farmacia","farmaceutica","farmacéutica","farmacia","farmacêutica","farmácia","Pharmazeutika","Arzneimittelkunde","farmaceutica","geneesmiddelen","apotheek","φαρμακευτικός","φαρμακευτική","φαρμακευτικό","φαρμακευτικά","φαρμακείο","ilaç","eczane","gyógyszerészeti","gyógyszertár","farmacevtika","lekarništvo","farmaatsia","farmatseutiline",""], + "key::61": ["healthcare","health services","salute","atenciónmédica","cuidadodelasalud","cuidadoscomasaúde","Gesundheitswesen","gezondheidszorg","ιατροφαρμακευτικήπερίθαλψη","sağlıkhizmeti","egészségügy","zdravstvo","tervishoid","tervishoiu",""], + "key::62": ["history","storia","historia","história","Geschichte","geschiedenis","geschiedkunde","ιστορία","tarih","történelem","zgodovina","ajalugu",""], + "key::63": ["materials","materiali","materia","materiales","materiais","materialen","υλικά","τεκμήρια","malzemeler","anyagok","materiali","materjalid","vahendid",""], + "key::64": ["economics","economia","economiche","economica","economía","economia","Wirtschaft","economie","οικονομικά","οικονομικέςεπιστήμες","ekonomi","közgazdaságtan","gospodarstvo","ekonomija","majanduslik","majandus",""], + "key::65": ["therapeutics","terapeutica","terapéutica","terapêutica","therapie","θεραπευτική","tedavibilimi","gyógykezelés","terapevtika","terapeutiline","ravi",""], + "key::66": 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Hospitals$", + "(?i)^news and events$", + "(?i)^NOVOSTI I DOGAĐAJI$", + "^Sansū no gakushū$", + "^Posouzení informačního systému firmy a návrh změn$", + "^Information System Assessment and Proposal for ICT Modification$", + "^Stresové zatížení pracovníků ve vybrané profesi$", + "^Stress load in a specific job$", + + "^Sunday: Poster Sessions, Pt.*$", + "^Monday: Poster Sessions, Pt.*$", + "^Wednesday: Poster Sessions, Pt.*", + "^Tuesday: Poster Sessions, Pt.*$", + + "^Analýza reklamy$", + "^Analysis of advertising$", + + "^Shōgaku shūshinsho$", + "^Shōgaku sansū$", + "^Shintei joshi kokubun$", + "^Taishō joshi kokubun dokuhon$", + "^Joshi kokubun$", + + "^Účetní uzávěrka a účetní závěrka v ČR$", + "(?i)^The \"?Causes\"? of Cancer$", + "^Normas para la publicación de artículos$", + "^Editor('|s)(s|') [Rr]eply$", + "^Editor(’|s)(s|’) letter$", + "^Redaktoriaus žodis$", + "^DISCUSSION ON THE PRECEDING PAPER$", + "^Kōtō shōgaku shūshinsho jidōyō$", + "^Shōgaku nihon rekishi$", + "^(Theory of the flow of action currents in isolated myelinated nerve fibers).*$", + "^Préface$", + "^Occupational [Hh]ealth [Ss]ervices.$", + "^In Memoriam Professor Toshiyuki TAKESHIMA$", + "^Účetní závěrka ve vybraném podniku.*$", + "^Financial statements in selected company$", + "^Abdominal [Aa]ortic [Aa]neurysms.*$", + "^Pseudomyxoma peritonei$", + "^Kazalo autora$", + + "(?i)^uvodna riječ$", + "^Motivace jako způsob vedení lidí$", + "^Motivation as a leadership$", + "^Polyfunkční dům$", + "^Multi\\-funkcional building$", + "^Podnikatelský plán$", + "(?i)^Podnikatelský záměr$", + "(?i)^Business Plan$", + "^Oceňování nemovitostí$", + "^Marketingová komunikace$", + "^Marketing communication$", + "^Sumario Analítico$", + "^Riječ uredništva$", + "^Savjetovanja i priredbe$", + "^Índice$", + "^(Starobosanski nadpisi).*$", + "^Vzdělávání pracovníků v organizaci$", + "^Staff training in organization$", + "^(Life Histories of North American Geometridae).*$", + "^Strategická analýza podniku$", + "^Strategic Analysis of an Enterprise$", + "^Sadržaj$", + "^Upute suradnicima$", + "^Rodinný dům$", + "(?i)^Fami(l)?ly house$", + "^Upute autorima$", + "^Strategic Analysis$", + "^Finanční analýza vybraného podniku$", + "^Finanční analýza$", + "^Riječ urednika$", + "(?i)^Content(s?)$", + "(?i)^Inhalt$", + "^Jinjō shōgaku shūshinsho jidōyō$", + "(?i)^Index$", + "^Chūgaku kokubun kyōkasho$", + "^Retrato de una mujer$", + "^Retrato de un hombre$", + "^Kōtō shōgaku dokuhon$", + "^Shotōka kokugo$", + "^Shōgaku dokuhon$", + "^Jinjō shōgaku kokugo dokuhon$", + "^Shinsei kokugo dokuhon$", + "^Teikoku dokuhon$", + "^Instructions to Authors$", + "^KİTAP TAHLİLİ$", + "^PRZEGLĄD PIŚMIENNICTWA$", + "(?i)^Presentación$", + "^İçindekiler$", + "(?i)^Tabl?e of contents$", + "^(CODICE DEL BEATO DE LOS REYES FERNANDO I Y SANCHA).*$", + "^(\\[MADRID\\. BIBL\\. NAC\\. N.*KING FERDINAND I.*FROM SAN ISIDORO DE LEON\\. FACUNDUS SCRIPSIT DATED.*\\]).*", + "^Editorial( Board)?$", + "(?i)^Editorial \\(English\\)$", + "^Editörden$", + "^(Corpus Oral Dialectal \\(COD\\)\\.).*$", + "^(Kiri Karl Morgensternile).*$", + "^(\\[Eksliibris Aleksandr).*\\]$", + "^(\\[Eksliibris Aleksandr).*$", + "^(Eksliibris Aleksandr).*$", + "^(Kiri A\\. de Vignolles).*$", + "^(2 kirja Karl Morgensternile).*$", + "^(Pirita kloostri idaosa arheoloogilised).*$", + "^(Kiri tundmatule).*$", + "^(Kiri Jenaer Allgemeine Literaturzeitung toimetusele).*$", + "^(Eksliibris Nikolai Birukovile).*$", + "^(Eksliibris Nikolai Issakovile).*$", + "^(WHP Cruise Summary Information of section).*$", + "^(Measurement of the top quark\\-pair production cross section with ATLAS in pp collisions at).*$", + "^(Measurement of the spin\\-dependent structure function).*", + "(?i)^.*authors['’′]? reply\\.?$", + "(?i)^.*authors['’′]? response\\.?$" + ] + } + } +} \ No newline at end of file diff --git a/dhp-workflows/dhp-dedup/src/test/resources/eu/dnetlib/dedup/conf/pub_dt.curr.conf.json b/dhp-workflows/dhp-dedup/src/test/resources/eu/dnetlib/dedup/conf/pub_dt.curr.conf.json new file mode 100644 index 000000000..6ca0ecd53 --- /dev/null +++ b/dhp-workflows/dhp-dedup/src/test/resources/eu/dnetlib/dedup/conf/pub_dt.curr.conf.json @@ -0,0 +1,386 @@ +{ + "wf": { + "threshold": "0.99", + "dedupRun": "001", + "entityType": "result", + "subEntityType": "resulttype", + "subEntityValue": "publication", + "orderField": "title", + "queueMaxSize": "2000", + "groupMaxSize": "100", + "maxChildren": "100", + "slidingWindowSize": "200", + "rootBuilder": [ + "result", + "resultProject_outcome_isProducedBy", + "resultResult_publicationDataset_isRelatedTo", + "resultResult_similarity_isAmongTopNSimilarDocuments", + "resultResult_similarity_hasAmongTopNSimilarDocuments", + "resultOrganization_affiliation_isAffiliatedWith", + "resultResult_part_hasPart", + "resultResult_part_isPartOf", + "resultResult_supplement_isSupplementTo", + "resultResult_supplement_isSupplementedBy", + "resultResult_version_isVersionOf" + ], + "includeChildren": "true", + "maxIterations": 20, + "idPath": "$.id" + }, + "pace": { + "clustering": [ + { + "name": "ngrampairs", + "fields": [ + "title" + ], + "params": { + "max": "1", + "ngramLen": "3" + } + }, + { + "name": "suffixprefix", + "fields": [ + "title" + ], + "params": { + "max": "1", + "len": "3" + } + }, + { + "name": "lowercase", + "fields": [ + "doi" + ], + "params": {} + } + ], + "decisionTree": { + "start": { + "fields": [ + { + "field": "pid", + "comparator": "jsonListMatch", + "weight": 1.0, + "countIfUndefined": "false", + "params": { + "jpath_value": "$.value", + "jpath_classid": "$.qualifier.classid" + } + } + ], + "threshold": 0.5, + "aggregation": "AVG", + "positive": "MATCH", + "negative": "layer2", + "undefined": "layer2", + "ignoreUndefined": "true" + }, + "layer2": { + "fields": [ + { + "field": "title", + "comparator": "titleVersionMatch", + "weight": 1.0, + "countIfUndefined": "false", + "params": {} + }, + { + "field": "authors", + "comparator": "sizeMatch", + "weight": 1.0, + "countIfUndefined": "false", + "params": {} + } + ], + "threshold": 1.0, + "aggregation": "AND", + "positive": "layer3", + "negative": "NO_MATCH", + "undefined": "layer3", + "ignoreUndefined": "false" + }, + "layer3": { + "fields": [ + { + "field": "title", + "comparator": "levensteinTitle", + "weight": 1.0, + "countIfUndefined": "true", + "params": {} + } + ], + "threshold": 0.99, + "aggregation": "AVG", + "positive": "MATCH", + "negative": "NO_MATCH", + "undefined": "NO_MATCH", + "ignoreUndefined": "true" + } + }, + "model": [ + { + "name": "doi", + "type": "String", + "path": "$.pid[?(@.qualifier.classid == 'doi')].value" + }, + { + "name": "pid", + "type": "JSON", + "path": "$.pid", + "overrideMatch": "true" + }, + { + "name": "title", + "type": "String", + "path": "$.title[?(@.qualifier.classid == 'main title')].value", + "length": 250, + "size": 5 + }, + { + "name": "authors", + "type": "List", + "path": "$.author[*].fullname", + "size": 200 + }, + { + "name": "resulttype", + "type": "String", + "path": "$.resulttype.classid" + } + ], + "blacklists": { + "title": [ + "^Inside Front Cover$", + "(?i)^Poster presentations$", + "^THE ASSOCIATION AND THE GENERAL MEDICAL COUNCIL$", + "^Problems with perinatal pathology\\.?$", + "(?i)^Cases? of Puerperal Convulsions$", + "(?i)^Operative Gyna?ecology$", + "(?i)^Mind the gap\\!?\\:?$", + "^Chronic fatigue syndrome\\.?$", + "^Cartas? ao editor Letters? to the Editor$", + "^Note from the Editor$", + "^Anesthesia Abstract$", + "^Annual report$", + "(?i)^“?THE RADICAL PREVENTION OF VENEREAL DISEASE\\.?”?$", + "(?i)^Graph and Table of Infectious Diseases?$", + "^Presentation$", + "(?i)^Reviews and Information on Publications$", + "(?i)^PUBLIC HEALTH SERVICES?$", + "(?i)^COMBINED TEXT-?BOOK OF OBSTETRICS AND GYN(Æ|ae)COLOGY$", + "(?i)^Adrese autora$", + "(?i)^Systematic Part .*\\. 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Patrick's Cathedral, Dublin, County Dublin - Head(s)? and Capital(s)?$", + "(?i)^St\\. Patrick's Cathedral, Dublin, County Dublin - Bases?$", + "(?i)^PUBLIC HEALTH VERSUS THE STATE$", + "^Viñetas de Cortázar$", + "(?i)^Search for heavy neutrinos and W(\\[|_|\\(|_\\{|-)?R(\\]|\\)|\\})? bosons with right-handed couplings in a left-right symmetric model in pp collisions at.*TeV(\\.)?$", + "(?i)^Measurement of the pseudorapidity and centrality dependence of the transverse energy density in Pb(-?)Pb collisions at.*tev(\\.?)$", + "(?i)^Search for resonances decaying into top-quark pairs using fully hadronic decays in pp collisions with ATLAS at.*TeV$", + "(?i)^Search for neutral minimal supersymmetric standard model Higgs bosons decaying to tau pairs in pp collisions at.*tev$", + "(?i)^Relatório de Estágio (de|em) Angiologia e Cirurgia Vascular$", + "^Aus der AGMB$", + "^Znanstveno-stručni prilozi$", + "(?i)^Zhodnocení finanční situace podniku a návrhy na zlepšení$", + "(?i)^Evaluation of the Financial Situation in the Firm and Proposals to its Improvement$", + "(?i)^Hodnocení finanční situace podniku a návrhy na její zlepšení$", + "^Finanční analýza podniku$", + "^Financial analysis( of business)?$", + "(?i)^Textbook of Gyn(a)?(Æ)?(e)?cology$", + "^Jikken nihon shūshinsho$", + "(?i)^CORONER('|s)(s|') INQUESTS$", + "(?i)^(Μελέτη παραγόντων )?risk management( για ανάπτυξη και εφαρμογή ενός πληροφοριακού συστήματος| και ανάπτυξη συστήματος)?$", + "(?i)^Consultants' contract(s)?$", + "(?i)^Upute autorima$", + "(?i)^Bijdrage tot de Kennis van den Godsdienst der Dajaks van Lan(d|f)ak en Tajan$", + "^Joshi shin kokubun$", + "^Kōtō shōgaku dokuhon nōson'yō$", + "^Jinjō shōgaku shōka$", + "^Shōgaku shūjichō$", + "^Nihon joshi dokuhon$", + "^Joshi shin dokuhon$", + "^Chūtō kanbun dokuhon$", + "^Wabun dokuhon$", + "(?i)^(Analysis of economy selected village or town|Rozbor hospodaření vybrané obce či města)$", + "(?i)^cardiac rehabilitation$", + "(?i)^Analytical summary$", + "^Thesaurus resolutionum Sacrae Congregationis Concilii$", + "(?i)^Sumario analítico(\\s{1})?(Analitic summary)?$", + "^Prikazi i osvrti$", + "^Rodinný dům s provozovnou$", + "^Family house with an establishment$", + "^Shinsei chūtō shin kokugun$", + "^Pulmonary alveolar proteinosis(\\.?)$", + "^Shinshū kanbun$", + "^Viñeta(s?) de Rodríguez$", + "(?i)^RUBRIKA UREDNIKA$", + "^A Matching Model of the Academic Publication Market$", + "^Yōgaku kōyō$", + "^Internetový marketing$", + "^Internet marketing$", + "^Chūtō kokugo dokuhon$", + "^Kokugo dokuhon$", + "^Antibiotic Cover for Dental Extraction(s?)$", + "^Strategie podniku$", + "^Strategy of an Enterprise$", + "(?i)^respiratory disease(s?)(\\.?)$", + "^Award(s?) for Gallantry in Civil Defence$", + "^Podniková kultura$", + "^Corporate Culture$", + "^Severe hyponatraemia in hospital inpatient(s?)(\\.?)$", + "^Pracovní motivace$", + "^Work Motivation$", + "^Kaitei kōtō jogaku dokuhon$", + "^Konsolidovaná účetní závěrka$", + "^Consolidated Financial Statements$", + "(?i)^intracranial tumour(s?)$", + "^Climate Change Mitigation Options and Directed Technical Change: A Decentralized Equilibrium Analysis$", + "^\\[CERVECERIAS MAHOU(\\.|\\:) INTERIOR\\] \\[Material gráfico\\]$", + "^Housing Market Dynamics(\\:|\\.) 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Zootaxa 144: 1-4, DOI: 10.5281/zenodo.156314","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}}}],"dateofacceptance":{"value":"","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}}},"publisher":{"value":"Zenodo","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}}},"embargoenddate":{"value":"","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}}},"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":{"classid":"","classname":"","schemeid":"","schemename":""},"coverage":[],"refereed":{"value":"","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}}},"context":[],"id":"50|scholexplore::ceb3a5d32107897a0df1178211e3e9ca","originalId":[],"collectedfrom":[{"key":"10|openaire____::e034d6a11054f5ade9221ebac484e864","value":"scholExplorer","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}}}],"pid":[{"value":"10.5281/zenodo.156314","qualifier":{"classid":"doi","classname":"doi","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}}}],"extraInfo":[],"dataInfo":{"invisible":false,"inferred":true,"deletedbyinference":true,"inferenceprovenance":"dedup-similarity-result-levenstein","provenanceaction":{"classid":"sysimport:actionset","classname":"sysimport:actionset","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":0} diff --git a/dhp-workflows/docs/oozie-installer.markdown b/dhp-workflows/docs/oozie-installer.markdown index b9486ad5e..b1953a54e 100644 --- a/dhp-workflows/docs/oozie-installer.markdown +++ b/dhp-workflows/docs/oozie-installer.markdown @@ -73,7 +73,7 @@ Workflow definition requirements This property can be set using maven `-D` switch. -`[oozie_app]` is the default directory name however it can be set to any value as soon as `oozieAppDir` property is provided with directory name as value. +`[oozie_app]` is the default directory name however it can be set to any value as soon as `oozieAppDir` property is provided with directory name as value. Subworkflows are supported as well and subworkflow directories should be nested within `[oozie_app]` directory. diff --git a/dhp-workflows/pom.xml b/dhp-workflows/pom.xml index 7aa581523..cf71190a4 100644 --- a/dhp-workflows/pom.xml +++ b/dhp-workflows/pom.xml @@ -17,6 +17,7 @@ dhp-aggregation dhp-distcp dhp-graph-mapper + dhp-dedup @@ -310,6 +311,7 @@ + @@ -523,6 +525,7 @@ org.apache.maven.plugins maven-failsafe-plugin + ${maven.failsave.plugin.version} default-integration-test diff --git a/pom.xml b/pom.xml index e385ff6eb..aedf5ebff 100644 --- a/pom.xml +++ b/pom.xml @@ -114,6 +114,12 @@ ${dhp.spark.version} provided + + org.apache.spark + spark-graphx_2.11 + ${dhp.spark.version} + provided + org.apache.commons @@ -177,6 +183,7 @@ ${dhp.jackson.version} provided + com.fasterxml.jackson.core jackson-annotations @@ -190,6 +197,12 @@ provided + + eu.dnetlib + dnet-pace-core + 4.0.0-SNAPSHOT + + javax.persistence @@ -203,6 +216,21 @@ amqp-client 5.6.0 + + com.jayway.jsonpath + json-path + 2.4.0 + + + com.arakelian + java-jq + 0.10.1 + + + edu.cmu + secondstring + 1.0.0 + org.apache.oozie @@ -230,7 +258,7 @@ org.apache.maven.plugins maven-compiler-plugin - 3.6.0 + ${maven.compiler.plugin.version} 1.8 1.8 @@ -259,27 +287,6 @@ - - eu.dnetlib - protoc-jar-maven-plugin - 1.1.0 - - - generate-sources - - run - - - ${google.protobuf.version} - - src/main/resources - - src/gen/java - - - - - org.apache.maven.plugins maven-surefire-plugin @@ -342,6 +349,31 @@ + + net.alchim31.maven + scala-maven-plugin + 4.0.1 + + + scala-compile-first + initialize + + add-source + compile + + + + scala-test-compile + process-test-resources + + testCompile + + + + + ${scala.version} + + @@ -380,14 +412,15 @@ UTF-8 UTF-8 - + 3.6.0 + 2.22.2 cdh5.9.2 2.6.0-${dhp.cdh.version} 4.1.0-${dhp.cdh.version} 2.4.0.cloudera2 2.9.6 3.5 - 2.11.8 + 2.11.12