From 8b2043c7b1924d47cc9d5871649929ca0c437ff8 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 14 Apr 2020 16:43:40 +0200 Subject: [PATCH 01/62] introducing List generic container for Relation specific properties. Ref ticket https://issue.openaire.research-infrastructures.eu/issues/5512 --- .../eu/dnetlib/dhp/schema/oaf/Relation.java | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java index 6871c01972..3b45c4f7d1 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java @@ -6,20 +6,49 @@ import java.util.stream.Stream; import static com.google.common.base.Preconditions.checkArgument; +/** + * Relation aims to model any edge between two nodes in the OpenAIRE graph. It has a source id and a target id + * pointing to graph node identifiers and it is further characterised by the semantic of the link throught the fields + * relType, subRelType and relClass. Provenance information is modeled according to the dataInfo element and collectedFrom, + * while individual relationship types can provide extra information via the properties field. + */ public class Relation extends Oaf { + /** + * Main relationship classifier, values include 'resultResult', 'resultProject', 'resultOrganization', etc. + */ private String relType; + /** + * Further classifies a relationship, values include 'affiliation', 'similarity', 'supplement', etc. + */ private String subRelType; + /** + * Indicates the direction of the relationship, values include 'isSupplementTo', 'isSupplementedBy', 'merges, 'isMergedIn'. + */ private String relClass; + /** + * The source entity id. + */ private String source; + /** + * The target entity id. + */ private String target; + /** + * The list of datasource id/name pairs providing this relationship. + */ private List collectedFrom = new ArrayList<>(); + /** + * List of relation specific properties. Values values include 'similarityLevel', indicating the similarity score between a pair of publications. + */ + private List properties = new ArrayList<>(); + public String getRelType() { return relType; } @@ -68,6 +97,14 @@ public class Relation extends Oaf { this.collectedFrom = collectedFrom; } + public List getProperties() { + return properties; + } + + public void setProperties(List properties) { + this.properties = properties; + } + public void mergeFrom(final Relation r) { checkArgument(Objects.equals(getSource(), r.getSource()),"source ids must be equal"); From cc67dbff819594b3b05a3eedefe05a058bcfb15d Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 14 Apr 2020 17:11:55 +0200 Subject: [PATCH 02/62] typo in text --- .../src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java index 3b45c4f7d1..d8d1508317 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java @@ -45,7 +45,7 @@ public class Relation extends Oaf { private List collectedFrom = new ArrayList<>(); /** - * List of relation specific properties. Values values include 'similarityLevel', indicating the similarity score between a pair of publications. + * List of relation specific properties. Values include 'similarityLevel', indicating the similarity score between a pair of publications. */ private List properties = new ArrayList<>(); From 11938dac5e39ba083842e6cd2401e1ddee29a196 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 4 May 2020 16:47:07 +0200 Subject: [PATCH 03/62] this commit adds: validated/validationDate to relationships; measure type and simple unit test to indicate the relative serialization --- .../eu/dnetlib/dhp/schema/oaf/Measure.java | 52 +++++++++++++++++++ .../eu/dnetlib/dhp/schema/oaf/Relation.java | 40 ++++++++++++++ .../eu/dnetlib/dhp/schema/oaf/Result.java | 12 +++++ .../dnetlib/dhp/schema/oaf/MeasureTest.java | 37 +++++++++++++ 4 files changed, 141 insertions(+) diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Measure.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Measure.java index 98adffd2a0..c37e760618 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Measure.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Measure.java @@ -1,4 +1,56 @@ package eu.dnetlib.dhp.schema.oaf; +import com.google.common.base.Objects; + +import java.util.List; + +/** + * Represent a measure, must be further described by a system available resource providing name and descriptions. + */ public class Measure { + + /** + * Unique measure identifier. + */ + private String id; + + /** + * List of units associated with this measure. KeyValue provides a pair to store the laber (key) and the value, + * plus common provenance information. + */ + private List unit; + + public String getId() { + return id; + } + + public void setId(String id) { + this.id = id; + } + + public List getUnit() { + return unit; + } + + public void setUnit(List unit) { + this.unit = unit; + } + + public void mergeFrom(Measure m) { + //TODO + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + Measure measure = (Measure) o; + return Objects.equal(id, measure.id) && + Objects.equal(unit, measure.unit); + } + + @Override + public int hashCode() { + return Objects.hashCode(id, unit); + } } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java index 76503f8853..d77bd7d733 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java @@ -40,6 +40,21 @@ public class Relation extends Oaf { */ private String target; + /** + * Was this relationship authoritatively validated? + */ + private Boolean validated; + + /** + * When was this relationship authoritatively validated. + */ + private String validationDate; + + /** + * List of relation specific properties. Values include 'similarityLevel', indicating the similarity score between a pair of publications. + */ + private List properties = new ArrayList<>(); + public String getRelType() { return relType; } @@ -80,6 +95,30 @@ public class Relation extends Oaf { this.target = target; } + public List getProperties() { + return properties; + } + + public void setProperties(List properties) { + this.properties = properties; + } + + public Boolean getValidated() { + return validated; + } + + public void setValidated(Boolean validated) { + this.validated = validated; + } + + public String getValidationDate() { + return validationDate; + } + + public void setValidationDate(String validationDate) { + this.validationDate = validationDate; + } + public void mergeFrom(final Relation r) { checkArgument(Objects.equals(getSource(), r.getSource()), "source ids must be equal"); @@ -122,4 +161,5 @@ public class Relation extends Oaf { public int hashCode() { return Objects.hash(relType, subRelType, relClass, source, target, collectedfrom); } + } 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 711b1ca681..11316f36e4 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 @@ -7,6 +7,8 @@ import java.util.List; public class Result extends OafEntity implements Serializable { + private List measures; + private List author; // resulttype allows subclassing results into publications | datasets | software @@ -51,6 +53,14 @@ public class Result extends OafEntity implements Serializable { private List instance; + public List getMeasures() { + return measures; + } + + public void setMeasures(List measures) { + this.measures = measures; + } + public List getAuthor() { return author; } @@ -229,6 +239,8 @@ public class Result extends OafEntity implements Serializable { Result r = (Result) e; + //TODO consider merging also Measures + instance = mergeLists(instance, r.getInstance()); if (r.getBestaccessright() != null && compareTrust(this, r) < 0) diff --git a/dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/oaf/MeasureTest.java b/dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/oaf/MeasureTest.java index 26376349c7..25d929db22 100644 --- a/dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/oaf/MeasureTest.java +++ b/dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/oaf/MeasureTest.java @@ -1,4 +1,41 @@ package eu.dnetlib.dhp.schema.oaf; +import com.fasterxml.jackson.annotation.JsonInclude; +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.ObjectMapper; +import com.google.common.collect.Lists; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; + +import java.io.IOException; + public class MeasureTest { + + public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper() + .setSerializationInclusion(JsonInclude.Include.NON_NULL); + + @Test + public void testMeasureSerialization() throws IOException { + + Measure m = new Measure(); + + m.setId("popularity"); + m.setUnit(Lists.newArrayList( + unit("score", "0.5"))); + + String s = OBJECT_MAPPER.writeValueAsString(m); + System.out.println(s); + + Measure mm = OBJECT_MAPPER.readValue(s, Measure.class); + + Assertions.assertNotNull(mm); + } + + private KeyValue unit(String key, String value) { + KeyValue unit = new KeyValue(); + unit.setKey(key); + unit.setValue(value); + return unit; + } + } From c54d7ca18c1c4a4f8fe64b05d94d3e74fb25b4a0 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 4 May 2020 17:02:40 +0200 Subject: [PATCH 04/62] example measures in serialization test --- .../dnetlib/dhp/schema/oaf/MeasureTest.java | 19 +++++++++++++------ 1 file changed, 13 insertions(+), 6 deletions(-) diff --git a/dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/oaf/MeasureTest.java b/dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/oaf/MeasureTest.java index 25d929db22..4275e2c56e 100644 --- a/dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/oaf/MeasureTest.java +++ b/dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/oaf/MeasureTest.java @@ -1,13 +1,14 @@ package eu.dnetlib.dhp.schema.oaf; import com.fasterxml.jackson.annotation.JsonInclude; -import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.core.type.TypeReference; import com.fasterxml.jackson.databind.ObjectMapper; import com.google.common.collect.Lists; import org.junit.jupiter.api.Assertions; import org.junit.jupiter.api.Test; import java.io.IOException; +import java.util.List; public class MeasureTest { @@ -17,16 +18,22 @@ public class MeasureTest { @Test public void testMeasureSerialization() throws IOException { - Measure m = new Measure(); - - m.setId("popularity"); - m.setUnit(Lists.newArrayList( + Measure popularity = new Measure(); + popularity.setId("popularity"); + popularity.setUnit(Lists.newArrayList( unit("score", "0.5"))); + Measure influence = new Measure(); + influence.setId("influence"); + influence.setUnit(Lists.newArrayList( + unit("score", "0.3"))); + + List m = Lists.newArrayList(popularity, influence); + String s = OBJECT_MAPPER.writeValueAsString(m); System.out.println(s); - Measure mm = OBJECT_MAPPER.readValue(s, Measure.class); + List mm = OBJECT_MAPPER.readValue(s, new TypeReference>() { }); Assertions.assertNotNull(mm); } From 22cb9e0da7ce016853c741017f98ca300e4197ab Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 15 May 2020 18:18:01 +0200 Subject: [PATCH 05/62] simple code to get file from URL --- .../eu/dnetlib/dhp/schema/oaf/Programme.java | 4 + .../dhp/actionset/h2020programme/GetFile.java | 53 +++++++++ .../h2020programme/action_set_parameters.json | 0 .../oozie_app/lib/scripts/getprogrammefile.sh | 0 .../oozie_app/lib/scripts/getprojectfile.sh | 0 .../h2020programme/oozie_app/workflow.xml | 112 ++++++++++++++++++ .../actionset/h2020programme/parameters.json | 86 ++++++++++++++ 7 files changed, 255 insertions(+) create mode 100644 dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Programme.java create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionset/h2020programme/GetFile.java create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionset/h2020programme/action_set_parameters.json create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionset/h2020programme/oozie_app/lib/scripts/getprogrammefile.sh create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionset/h2020programme/oozie_app/lib/scripts/getprojectfile.sh create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionset/h2020programme/oozie_app/workflow.xml create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionset/h2020programme/parameters.json diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Programme.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Programme.java new file mode 100644 index 0000000000..f913336163 --- /dev/null +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Programme.java @@ -0,0 +1,4 @@ +package eu.dnetlib.dhp.schema.oaf; + +public class Programme { +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionset/h2020programme/GetFile.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionset/h2020programme/GetFile.java new file mode 100644 index 0000000000..2fed1a0e36 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionset/h2020programme/GetFile.java @@ -0,0 +1,53 @@ + +package eu.dnetlib.dhp.actionset.h2020programme; + +import java.io.*; +import java.net.URL; + +import org.apache.commons.io.IOUtils; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FSDataOutputStream; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; + +public class GetFile { + + private static final Log log = LogFactory.getLog(GetFile.class); + + public static void main(final String[] args) throws Exception { + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + GetFile.class + .getResourceAsStream( + "/eu/dnetlib/dhp/actionset/h2020programme/parameters.json"))); + + Configuration conf = new Configuration(); + + parser.parseArgument(args); + + final String fileURL = parser.get("fileURL"); + final String hdfsPath = parser.get("hdfsPath"); + final String hdfsNameNode = parser.get("hdfsNameNode"); + + conf.set("fs.defaultFS", hdfsNameNode); + FileSystem fileSystem = FileSystem.get(conf); + Path hdfsWritePath = new Path(hdfsPath); + FSDataOutputStream fsDataOutputStream = null; + if (fileSystem.exists(hdfsWritePath)) { + fsDataOutputStream = fileSystem.append(hdfsWritePath); + } else { + fsDataOutputStream = fileSystem.create(hdfsWritePath); + } + + InputStream is = new BufferedInputStream(new URL(fileURL).openStream()); + + org.apache.hadoop.io.IOUtils.copyBytes(is, fsDataOutputStream, 4096, true); + + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionset/h2020programme/action_set_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionset/h2020programme/action_set_parameters.json new file mode 100644 index 0000000000..e69de29bb2 diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionset/h2020programme/oozie_app/lib/scripts/getprogrammefile.sh b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionset/h2020programme/oozie_app/lib/scripts/getprogrammefile.sh new file mode 100644 index 0000000000..e69de29bb2 diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionset/h2020programme/oozie_app/lib/scripts/getprojectfile.sh b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionset/h2020programme/oozie_app/lib/scripts/getprojectfile.sh new file mode 100644 index 0000000000..e69de29bb2 diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionset/h2020programme/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionset/h2020programme/oozie_app/workflow.xml new file mode 100644 index 0000000000..3e7f684012 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionset/h2020programme/oozie_app/workflow.xml @@ -0,0 +1,112 @@ + + + + sequenceFilePath + the path to store the sequence file of the native metadata collected + + + + mdStorePath + the path of the native mdstore + + + + apiDescription + A json encoding of the API Description class + + + + dataSourceInfo + A json encoding of the Datasource Info + + + identifierPath + An xpath to retrieve the metadata idnentifier for the generation of DNet Identifier + + + + metadataEncoding + The type of the metadata XML/JSON + + + + timestamp + The timestamp of the collection date + + + + workflowId + The identifier of the workflow + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.dhp.collection.worker.DnetCollectorWorker + -p${sequenceFilePath} + -a${apiDescription} + -n${nameNode} + -rh${rmq_host} + -ru${rmq_user} + -rp${rmq_pwd} + -rr${rmq_report} + -ro${rmq_ongoing} + -usandro.labruzzo + -w${workflowId} + + + + + + + ${jobTracker} + ${nameNode} + yarn + cluster + GenerateNativeStoreSparkJob + eu.dnetlib.dhp.collection.GenerateNativeStoreSparkJob + dhp-aggregations-1.0.0-SNAPSHOT.jar + --num-executors 50 --conf spark.yarn.jars="hdfs://hadoop-rm1.garr-pa1.d4science.org:8020/user/oozie/share/lib/lib_20180405103059/spark2" + --encoding ${metadataEncoding} + --dateOfCollection ${timestamp} + --provenance ${dataSourceInfo} + --xpath${identifierPath} + --input${sequenceFilePath} + --output${mdStorePath} + -rh${rmq_host} + -ru${rmq_user} + -rp${rmq_pwd} + -rr${rmq_report} + -ro${rmq_ongoing} + -w${workflowId} + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionset/h2020programme/parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionset/h2020programme/parameters.json new file mode 100644 index 0000000000..4a6aec5ee1 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionset/h2020programme/parameters.json @@ -0,0 +1,86 @@ +[ + { + "paramName": "issm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "when true will stop SparkSession after job execution", + "paramRequired": false + }, + { + "paramName": "e", + "paramLongName": "encoding", + "paramDescription": "the encoding of the input record should be JSON or XML", + "paramRequired": true + }, + { + "paramName": "d", + "paramLongName": "dateOfCollection", + "paramDescription": "the date when the record has been stored", + "paramRequired": true + }, + { + "paramName": "p", + "paramLongName": "provenance", + "paramDescription": "the infos about the provenance of the collected records", + "paramRequired": true + }, + { + "paramName": "x", + "paramLongName": "xpath", + "paramDescription": "the xpath to identify the record identifier", + "paramRequired": true + }, + { + "paramName": "i", + "paramLongName": "input", + "paramDescription": "the path of the sequencial file to read", + "paramRequired": true + }, + { + "paramName": "o", + "paramLongName": "output", + "paramDescription": "the path of the result DataFrame on HDFS", + "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": "t", + "paramLongName": "isTest", + "paramDescription": "the name of the report queue", + "paramRequired": false + } +] \ No newline at end of file From 83c262a483a4ecc4d7a12d6ddab2086c2f447387 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 15 May 2020 18:18:31 +0200 Subject: [PATCH 06/62] workflow to download the files --- .../h2020programme/oozie_app/workflow.xml | 145 +++++++----------- 1 file changed, 57 insertions(+), 88 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionset/h2020programme/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionset/h2020programme/oozie_app/workflow.xml index 3e7f684012..9b200c2a9c 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionset/h2020programme/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionset/h2020programme/oozie_app/workflow.xml @@ -1,112 +1,81 @@ - + - sequenceFilePath - the path to store the sequence file of the native metadata collected + projectFileURL + the url where to get the projects file - mdStorePath - the path of the native mdstore + programmeFileURL + the url where to get the programme file - apiDescription - A json encoding of the API Description class - - - - dataSourceInfo - A json encoding of the Datasource Info - - - identifierPath - An xpath to retrieve the metadata idnentifier for the generation of DNet Identifier - - - - metadataEncoding - The type of the metadata XML/JSON - - - - timestamp - The timestamp of the collection date - - - - workflowId - The identifier of the workflow + outputPath + path where to store the action set - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - + - - - - + + - + - - - ${jobTracker} - ${nameNode} - eu.dnetlib.dhp.collection.worker.DnetCollectorWorker - -p${sequenceFilePath} - -a${apiDescription} - -n${nameNode} - -rh${rmq_host} - -ru${rmq_user} - -rp${rmq_pwd} - -rr${rmq_report} - -ro${rmq_ongoing} - -usandro.labruzzo - -w${workflowId} - - - - - - - ${jobTracker} - ${nameNode} - yarn - cluster - GenerateNativeStoreSparkJob - eu.dnetlib.dhp.collection.GenerateNativeStoreSparkJob - dhp-aggregations-1.0.0-SNAPSHOT.jar - --num-executors 50 --conf spark.yarn.jars="hdfs://hadoop-rm1.garr-pa1.d4science.org:8020/user/oozie/share/lib/lib_20180405103059/spark2" - --encoding ${metadataEncoding} - --dateOfCollection ${timestamp} - --provenance ${dataSourceInfo} - --xpath${identifierPath} - --input${sequenceFilePath} - --output${mdStorePath} - -rh${rmq_host} - -ru${rmq_user} - -rp${rmq_pwd} - -rr${rmq_report} - -ro${rmq_ongoing} - -w${workflowId} - - - - - - - - - + + + eu.dnetlib.dhp.actionset.h2020programme.GetFile + --hdfsNameNode${nameNode} + --fileUrl${projectFileURL} + --hdfsPath${workingDir}/projects.csv + + + + + eu.dnetlib.dhp.actionset.h2020programme.GetFile + --hdfsNameNode${nameNode} + --fileUrl${programmeFileURL} + --hdfsPath${workingDir}/programme.csv + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file From 5a648016ef7061354f4ae795c0ab8c558c52ccff Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 15 May 2020 18:18:50 +0200 Subject: [PATCH 07/62] parameters from the GetFile class --- .../actionset/h2020programme/parameters.json | 91 +++---------------- 1 file changed, 13 insertions(+), 78 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionset/h2020programme/parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionset/h2020programme/parameters.json index 4a6aec5ee1..40ad5bf361 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionset/h2020programme/parameters.json +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionset/h2020programme/parameters.json @@ -1,86 +1,21 @@ [ + { - "paramName": "issm", - "paramLongName": "isSparkSessionManaged", - "paramDescription": "when true will stop SparkSession after job execution", - "paramRequired": false + "paramName": "fu", + "paramLongName" : "fileURL", + "paramDescription" : "the url of the file to download", + "paramRequired" : true }, { - "paramName": "e", - "paramLongName": "encoding", - "paramDescription": "the encoding of the input record should be JSON or XML", - "paramRequired": true + "paramName": "hp", + "paramLongName" : "hdfsPath", + "paramDescription" : "where to save the file", + "paramRequired" : true }, { - "paramName": "d", - "paramLongName": "dateOfCollection", - "paramDescription": "the date when the record has been stored", - "paramRequired": true - }, - { - "paramName": "p", - "paramLongName": "provenance", - "paramDescription": "the infos about the provenance of the collected records", - "paramRequired": true - }, - { - "paramName": "x", - "paramLongName": "xpath", - "paramDescription": "the xpath to identify the record identifier", - "paramRequired": true - }, - { - "paramName": "i", - "paramLongName": "input", - "paramDescription": "the path of the sequencial file to read", - "paramRequired": true - }, - { - "paramName": "o", - "paramLongName": "output", - "paramDescription": "the path of the result DataFrame on HDFS", - "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": "t", - "paramLongName": "isTest", - "paramDescription": "the name of the report queue", - "paramRequired": false + "paramName": "hnn", + "paramLongName" : "hdfsNameNode", + "paramDescription" : "the name node", + "paramRequired" : true } ] \ No newline at end of file From abc45f2708e7497cd16d1cc09041737be6d07f55 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 18 May 2020 13:04:06 +0200 Subject: [PATCH 08/62] added dnet-45 HttpConnector and related Classes, produced the POJO for projects and programme --- .../project/CollectorPluginErrorLogList.java | 20 ++ .../project/CollectorServiceException.java | 20 ++ .../project}/GetFile.java | 4 +- .../actionmanager/project/HttpConnector.java | 240 ++++++++++++++++++ .../project/PrepareProjects.java | 139 ++++++++++ .../dhp/actionmanager/project/Programme.java | 52 ++++ .../dhp/actionmanager/project/Project.java | 196 ++++++++++++++ .../project/SparkAtomicActionJob.java | 74 ++++++ .../project/action_set_parameters.json | 26 ++ .../project}/oozie_app/workflow.xml | 4 +- .../project}/parameters.json | 0 .../h2020programme/action_set_parameters.json | 0 12 files changed, 771 insertions(+), 4 deletions(-) create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/CollectorPluginErrorLogList.java create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/CollectorServiceException.java rename dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/{actionset/h2020programme => actionmanager/project}/GetFile.java (92%) create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/HttpConnector.java create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/PrepareProjects.java create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/Programme.java create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/Project.java create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/SparkAtomicActionJob.java create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/action_set_parameters.json rename dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/{actionset/h2020programme => actionmanager/project}/oozie_app/workflow.xml (95%) rename dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/{actionset/h2020programme => actionmanager/project}/parameters.json (100%) delete mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionset/h2020programme/action_set_parameters.json diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/CollectorPluginErrorLogList.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/CollectorPluginErrorLogList.java new file mode 100644 index 0000000000..bc00e4604c --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/CollectorPluginErrorLogList.java @@ -0,0 +1,20 @@ + +package eu.dnetlib.dhp.actionmanager.project; + +import java.util.LinkedList; + +public class CollectorPluginErrorLogList extends LinkedList { + + private static final long serialVersionUID = -6925786561303289704L; + + @Override + public String toString() { + String log = new String(); + int index = 0; + for (String errorMessage : this) { + log += String.format("Retry #%s: %s / ", index++, errorMessage); + } + return log; + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/CollectorServiceException.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/CollectorServiceException.java new file mode 100644 index 0000000000..a417de50d7 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/CollectorServiceException.java @@ -0,0 +1,20 @@ + +package eu.dnetlib.dhp.actionmanager.project; + +public class CollectorServiceException extends Exception { + + private static final long serialVersionUID = 7523999812098059764L; + + public CollectorServiceException(String string) { + super(string); + } + + public CollectorServiceException(String string, Throwable exception) { + super(string, exception); + } + + public CollectorServiceException(Throwable exception) { + super(exception); + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionset/h2020programme/GetFile.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/GetFile.java similarity index 92% rename from dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionset/h2020programme/GetFile.java rename to dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/GetFile.java index 2fed1a0e36..bbf59a20f3 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionset/h2020programme/GetFile.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/GetFile.java @@ -1,5 +1,5 @@ -package eu.dnetlib.dhp.actionset.h2020programme; +package eu.dnetlib.dhp.actionmanager.project; import java.io.*; import java.net.URL; @@ -24,7 +24,7 @@ public class GetFile { .toString( GetFile.class .getResourceAsStream( - "/eu/dnetlib/dhp/actionset/h2020programme/parameters.json"))); + "/eu/dnetlib/dhp/actionmanager/project/parameters.json"))); Configuration conf = new Configuration(); diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/HttpConnector.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/HttpConnector.java new file mode 100644 index 0000000000..63f67f145a --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/HttpConnector.java @@ -0,0 +1,240 @@ + +package eu.dnetlib.dhp.actionmanager.project; + +import java.io.IOException; +import java.io.InputStream; +import java.net.*; +import java.security.GeneralSecurityException; +import java.security.cert.X509Certificate; +import java.util.List; +import java.util.Map; + +import javax.net.ssl.HttpsURLConnection; +import javax.net.ssl.SSLContext; +import javax.net.ssl.TrustManager; +import javax.net.ssl.X509TrustManager; + +import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.math.NumberUtils; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; + +/** + * @author jochen, michele, andrea + */ +public class HttpConnector { + + private static final Log log = LogFactory.getLog(HttpConnector.class); + + private int maxNumberOfRetry = 6; + private int defaultDelay = 120; // seconds + private int readTimeOut = 120; // seconds + + private String responseType = null; + + private String userAgent = "Mozilla/5.0 (compatible; OAI; +http://www.openaire.eu)"; + + public HttpConnector() { + CookieHandler.setDefault(new CookieManager(null, CookiePolicy.ACCEPT_ALL)); + } + + /** + * Given the URL returns the content via HTTP GET + * + * @param requestUrl the URL + * @return the content of the downloaded resource + * @throws CollectorServiceException when retrying more than maxNumberOfRetry times + */ + public String getInputSource(final String requestUrl) throws CollectorServiceException { + return attemptDownlaodAsString(requestUrl, 1, new CollectorPluginErrorLogList()); + } + + /** + * Given the URL returns the content as a stream via HTTP GET + * + * @param requestUrl the URL + * @return the content of the downloaded resource as InputStream + * @throws CollectorServiceException when retrying more than maxNumberOfRetry times + */ + public InputStream getInputSourceAsStream(final String requestUrl) throws CollectorServiceException { + return attemptDownload(requestUrl, 1, new CollectorPluginErrorLogList()); + } + + private String attemptDownlaodAsString(final String requestUrl, final int retryNumber, + final CollectorPluginErrorLogList errorList) + throws CollectorServiceException { + try { + InputStream s = attemptDownload(requestUrl, 1, new CollectorPluginErrorLogList()); + try { + return IOUtils.toString(s); + } catch (IOException e) { + log.error("error while retrieving from http-connection occured: " + requestUrl, e); + Thread.sleep(defaultDelay * 1000); + errorList.add(e.getMessage()); + return attemptDownlaodAsString(requestUrl, retryNumber + 1, errorList); + } finally { + IOUtils.closeQuietly(s); + } + } catch (InterruptedException e) { + throw new CollectorServiceException(e); + } + } + + private InputStream attemptDownload(final String requestUrl, final int retryNumber, + final CollectorPluginErrorLogList errorList) + throws CollectorServiceException { + + if (retryNumber > maxNumberOfRetry) { + throw new CollectorServiceException("Max number of retries exceeded. Cause: \n " + errorList); + } + + log.debug("Downloading " + requestUrl + " - try: " + retryNumber); + try { + InputStream input = null; + + try { + final HttpURLConnection urlConn = (HttpURLConnection) new URL(requestUrl).openConnection(); + urlConn.setInstanceFollowRedirects(false); + urlConn.setReadTimeout(readTimeOut * 1000); + urlConn.addRequestProperty("User-Agent", userAgent); + + if (log.isDebugEnabled()) { + logHeaderFields(urlConn); + } + + int retryAfter = obtainRetryAfter(urlConn.getHeaderFields()); + if (retryAfter > 0 && urlConn.getResponseCode() == HttpURLConnection.HTTP_UNAVAILABLE) { + log.warn("waiting and repeating request after " + retryAfter + " sec."); + Thread.sleep(retryAfter * 1000); + errorList.add("503 Service Unavailable"); + urlConn.disconnect(); + return attemptDownload(requestUrl, retryNumber + 1, errorList); + } else if ((urlConn.getResponseCode() == HttpURLConnection.HTTP_MOVED_PERM) + || (urlConn.getResponseCode() == HttpURLConnection.HTTP_MOVED_TEMP)) { + final String newUrl = obtainNewLocation(urlConn.getHeaderFields()); + log.debug("The requested url has been moved to " + newUrl); + errorList + .add( + String + .format( + "%s %s. Moved to: %s", urlConn.getResponseCode(), urlConn.getResponseMessage(), + newUrl)); + urlConn.disconnect(); + return attemptDownload(newUrl, retryNumber + 1, errorList); + } else if (urlConn.getResponseCode() != HttpURLConnection.HTTP_OK) { + log + .error( + String + .format("HTTP error: %s %s", urlConn.getResponseCode(), urlConn.getResponseMessage())); + Thread.sleep(defaultDelay * 1000); + errorList.add(String.format("%s %s", urlConn.getResponseCode(), urlConn.getResponseMessage())); + urlConn.disconnect(); + return attemptDownload(requestUrl, retryNumber + 1, errorList); + } else { + input = urlConn.getInputStream(); + responseType = urlConn.getContentType(); + return input; + } + } catch (IOException e) { + log.error("error while retrieving from http-connection occured: " + requestUrl, e); + Thread.sleep(defaultDelay * 1000); + errorList.add(e.getMessage()); + return attemptDownload(requestUrl, retryNumber + 1, errorList); + } + } catch (InterruptedException e) { + throw new CollectorServiceException(e); + } + } + + private void logHeaderFields(final HttpURLConnection urlConn) throws IOException { + log.debug("StatusCode: " + urlConn.getResponseMessage()); + + for (Map.Entry> e : urlConn.getHeaderFields().entrySet()) { + if (e.getKey() != null) { + for (String v : e.getValue()) { + log.debug(" key: " + e.getKey() + " - value: " + v); + } + } + } + } + + private int obtainRetryAfter(final Map> headerMap) { + for (String key : headerMap.keySet()) { + if ((key != null) && key.toLowerCase().equals("retry-after") && (headerMap.get(key).size() > 0) + && NumberUtils.isCreatable(headerMap.get(key).get(0))) { + return Integer + .parseInt(headerMap.get(key).get(0)) + 10; + } + } + return -1; + } + + private String obtainNewLocation(final Map> headerMap) throws CollectorServiceException { + for (String key : headerMap.keySet()) { + if ((key != null) && key.toLowerCase().equals("location") && (headerMap.get(key).size() > 0)) { + return headerMap.get(key).get(0); + } + } + throw new CollectorServiceException("The requested url has been MOVED, but 'location' param is MISSING"); + } + + /** + * register for https scheme; this is a workaround and not intended for the use in trusted environments + */ + public void initTrustManager() { + final X509TrustManager tm = new X509TrustManager() { + + @Override + public void checkClientTrusted(final X509Certificate[] xcs, final String string) { + } + + @Override + public void checkServerTrusted(final X509Certificate[] xcs, final String string) { + } + + @Override + public X509Certificate[] getAcceptedIssuers() { + return null; + } + }; + try { + final SSLContext ctx = SSLContext.getInstance("TLS"); + ctx.init(null, new TrustManager[] { + tm + }, null); + HttpsURLConnection.setDefaultSSLSocketFactory(ctx.getSocketFactory()); + } catch (GeneralSecurityException e) { + log.fatal(e); + throw new IllegalStateException(e); + } + } + + public int getMaxNumberOfRetry() { + return maxNumberOfRetry; + } + + public void setMaxNumberOfRetry(final int maxNumberOfRetry) { + this.maxNumberOfRetry = maxNumberOfRetry; + } + + public int getDefaultDelay() { + return defaultDelay; + } + + public void setDefaultDelay(final int defaultDelay) { + this.defaultDelay = defaultDelay; + } + + public int getReadTimeOut() { + return readTimeOut; + } + + public void setReadTimeOut(final int readTimeOut) { + this.readTimeOut = readTimeOut; + } + + public String getResponseType() { + return responseType; + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/PrepareProjects.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/PrepareProjects.java new file mode 100644 index 0000000000..8955edeb4e --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/PrepareProjects.java @@ -0,0 +1,139 @@ + +package eu.dnetlib.dhp.actionmanager.project; + +import java.io.BufferedWriter; +import java.io.Closeable; +import java.io.IOException; +import java.io.OutputStreamWriter; +import java.nio.charset.StandardCharsets; +import java.sql.ResultSet; +import java.util.Arrays; +import java.util.List; +import java.util.Set; + +import org.apache.commons.csv.CSVParser; +import org.apache.commons.csv.CSVFormat; + +import org.apache.commons.io.IOUtils; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FSDataOutputStream; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.common.RelationInverse; +import eu.dnetlib.dhp.schema.oaf.Relation; + +public class PrepareProjects implements Closeable { + private static final Log log = LogFactory.getLog(PrepareProjects.class); + private final Configuration conf; + private final BufferedWriter writer; + private final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + private final HttpConnector httpConnector; + + public static void main(final String[] args) throws Exception { + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + PrepareProjects.class + .getResourceAsStream( + "/eu/dnetlib/dhp/actionmanager/project/parameters.json"))); + + parser.parseArgument(args); + + final String fileURL = parser.get("fileURL"); + final String hdfsPath = parser.get("hdfsPath"); + final String hdfsNameNode = parser.get("hdfsNameNode"); + + try (final PrepareProjects prepareProjects = new PrepareProjects(hdfsPath, hdfsNameNode)) { + + log.info("Getting projects..."); + prepareProjects.execute(fileURL); + + } + } + + public void execute(final String fileURL) throws Exception { + + String projects = httpConnector.getInputSource(fileURL); + final CSVFormat format = CSVFormat.EXCEL + .withHeader() + .withDelimiter(';') + .withQuote('"') + .withTrim(); + final CSVParser parser = CSVParser.parse(projects, format); + final Set headers = parser.getHeaderMap().keySet(); + } + + public List processBlacklistEntry(ResultSet rs) { + try { + Relation direct = new Relation(); + Relation inverse = new Relation(); + + String source_prefix = ModelSupport.entityIdPrefix.get(rs.getString("source_type")); + String target_prefix = ModelSupport.entityIdPrefix.get(rs.getString("target_type")); + + String source_direct = source_prefix + "|" + rs.getString("source"); + direct.setSource(source_direct); + inverse.setTarget(source_direct); + + String target_direct = target_prefix + "|" + rs.getString("target"); + direct.setTarget(target_direct); + inverse.setSource(target_direct); + + String encoding = rs.getString("relationship"); + RelationInverse ri = ModelSupport.relationInverseMap.get(encoding); + direct.setRelClass(ri.getRelation()); + inverse.setRelClass(ri.getInverse()); + direct.setRelType(ri.getRelType()); + inverse.setRelType(ri.getRelType()); + direct.setSubRelType(ri.getSubReltype()); + inverse.setSubRelType(ri.getSubReltype()); + + return Arrays.asList(direct, inverse); + + } catch (final Exception e) { + throw new RuntimeException(e); + } + } + + @Override + public void close() throws IOException { + writer.close(); + } + + public PrepareProjects( + final String hdfsPath, String hdfsNameNode) + throws Exception { + + this.conf = new Configuration(); + this.conf.set("fs.defaultFS", hdfsNameNode); + this.httpConnector = new HttpConnector(); + FileSystem fileSystem = FileSystem.get(this.conf); + Path hdfsWritePath = new Path(hdfsPath); + FSDataOutputStream fsDataOutputStream = null; + if (fileSystem.exists(hdfsWritePath)) { + fsDataOutputStream = fileSystem.append(hdfsWritePath); + } else { + fsDataOutputStream = fileSystem.create(hdfsWritePath); + } + + this.writer = new BufferedWriter(new OutputStreamWriter(fsDataOutputStream, StandardCharsets.UTF_8)); + + } + + protected void writeRelation(final Relation r) { + try { + writer.write(OBJECT_MAPPER.writeValueAsString(r)); + writer.newLine(); + } catch (final Exception e) { + throw new RuntimeException(e); + } + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/Programme.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/Programme.java new file mode 100644 index 0000000000..20877b1a10 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/Programme.java @@ -0,0 +1,52 @@ + +package eu.dnetlib.dhp.actionmanager.project; + +import java.io.Serializable; + +public class Programme implements Serializable { + private String rcn; + private String code; + private String title; + private String shortTitle; + private String language; + + public String getRcn() { + return rcn; + } + + public void setRcn(String rcn) { + this.rcn = rcn; + } + + public String getCode() { + return code; + } + + public void setCode(String code) { + this.code = code; + } + + public String getTitle() { + return title; + } + + public void setTitle(String title) { + this.title = title; + } + + public String getShortTitle() { + return shortTitle; + } + + public void setShortTitle(String shortTitle) { + this.shortTitle = shortTitle; + } + + public String getLanguage() { + return language; + } + + public void setLanguage(String language) { + this.language = language; + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/Project.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/Project.java new file mode 100644 index 0000000000..abee7f8616 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/Project.java @@ -0,0 +1,196 @@ + +package eu.dnetlib.dhp.actionmanager.project; + +import java.io.Serializable; + +public class Project implements Serializable { + private String rcn; + private String id; + private String acronym; + private String status; + private String programme; + private String topics; + private String frameworkProgramme; + private String title; + private String startDate; + private String endDate; + private String projectUrl; + private String objective; + private String totalCost; + private String ecMaxContribution; + private String call; + private String fundingScheme; + private String coordinator; + private String coordinatorCountry; + private String participants; + private String participantCountries; + private String subjects; + + public String getRcn() { + return rcn; + } + + public void setRcn(String rcn) { + this.rcn = rcn; + } + + public String getId() { + return id; + } + + public void setId(String id) { + this.id = id; + } + + public String getAcronym() { + return acronym; + } + + public void setAcronym(String acronym) { + this.acronym = acronym; + } + + public String getStatus() { + return status; + } + + public void setStatus(String status) { + this.status = status; + } + + public String getProgramme() { + return programme; + } + + public void setProgramme(String programme) { + this.programme = programme; + } + + public String getTopics() { + return topics; + } + + public void setTopics(String topics) { + this.topics = topics; + } + + public String getFrameworkProgramme() { + return frameworkProgramme; + } + + public void setFrameworkProgramme(String frameworkProgramme) { + this.frameworkProgramme = frameworkProgramme; + } + + public String getTitle() { + return title; + } + + public void setTitle(String title) { + this.title = title; + } + + public String getStartDate() { + return startDate; + } + + public void setStartDate(String startDate) { + this.startDate = startDate; + } + + public String getEndDate() { + return endDate; + } + + public void setEndDate(String endDate) { + this.endDate = endDate; + } + + public String getProjectUrl() { + return projectUrl; + } + + public void setProjectUrl(String projectUrl) { + this.projectUrl = projectUrl; + } + + public String getObjective() { + return objective; + } + + public void setObjective(String objective) { + this.objective = objective; + } + + public String getTotalCost() { + return totalCost; + } + + public void setTotalCost(String totalCost) { + this.totalCost = totalCost; + } + + public String getEcMaxContribution() { + return ecMaxContribution; + } + + public void setEcMaxContribution(String ecMaxContribution) { + this.ecMaxContribution = ecMaxContribution; + } + + public String getCall() { + return call; + } + + public void setCall(String call) { + this.call = call; + } + + public String getFundingScheme() { + return fundingScheme; + } + + public void setFundingScheme(String fundingScheme) { + this.fundingScheme = fundingScheme; + } + + public String getCoordinator() { + return coordinator; + } + + public void setCoordinator(String coordinator) { + this.coordinator = coordinator; + } + + public String getCoordinatorCountry() { + return coordinatorCountry; + } + + public void setCoordinatorCountry(String coordinatorCountry) { + this.coordinatorCountry = coordinatorCountry; + } + + public String getParticipants() { + return participants; + } + + public void setParticipants(String participants) { + this.participants = participants; + } + + public String getParticipantCountries() { + return participantCountries; + } + + public void setParticipantCountries(String participantCountries) { + this.participantCountries = participantCountries; + } + + public String getSubjects() { + return subjects; + } + + public void setSubjects(String subjects) { + this.subjects = subjects; + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/SparkAtomicActionJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/SparkAtomicActionJob.java new file mode 100644 index 0000000000..b8703378ec --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/SparkAtomicActionJob.java @@ -0,0 +1,74 @@ + +package eu.dnetlib.dhp.actionmanager.project; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.util.Optional; + +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.sql.SparkSession; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.HdfsSupport; + +public class SparkAtomicActionJob { + private static final Logger log = LoggerFactory.getLogger(SparkAtomicActionJob.class); + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + public static void main(String[] args) throws Exception { + + String jsonConfiguration = IOUtils + .toString( + SparkAtomicActionJob.class + .getResourceAsStream( + "/eu/dnetlib/dhp/actionmanager/project/action_set_parameters.json")); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + + parser.parseArgument(args); + + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + String projectPath = parser.get("projectPath"); + log.info("projectPath: {}", projectPath); + + final String outputPath = parser.get("outputPath"); + log.info("outputPath {}: ", outputPath); + + final String programmePath = parser.get("programmePath"); + log.info("programmePath {}: ", programmePath); + + SparkConf conf = new SparkConf(); + + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + removeOutputDir(spark, outputPath); + getAtomicActions( + spark, + projectPath, + programmePath, + outputPath); + }); + } + + private static void removeOutputDir(SparkSession spark, String path) { + HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); + } + + private static void getAtomicActions(SparkSession spark, String projectPatj, String programmePath, + String outputPath) { + + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/action_set_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/action_set_parameters.json new file mode 100644 index 0000000000..ca9ae9e97b --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/action_set_parameters.json @@ -0,0 +1,26 @@ +[ + { + "paramName": "issm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "when true will stop SparkSession after job execution", + "paramRequired": false +}, +{ +"paramName": "pjfu", +"paramLongName": "projectsFileURL", +"paramDescription": "the URL from where to get the projects file", +"paramRequired": true +}, +{ +"paramName": "pfu", +"paramLongName": "programmeFileURL", +"paramDescription": "the URL from where to get the programme file", +"paramRequired": true +}, +{ +"paramName": "o", +"paramLongName": "outputPath", +"paramDescription": "the path of the new ActionSet", +"paramRequired": true +} +] \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionset/h2020programme/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/oozie_app/workflow.xml similarity index 95% rename from dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionset/h2020programme/oozie_app/workflow.xml rename to dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/oozie_app/workflow.xml index 9b200c2a9c..5bfa2e7c42 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionset/h2020programme/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/oozie_app/workflow.xml @@ -33,7 +33,7 @@ eu.dnetlib.dhp.actionset.h2020programme.GetFile --hdfsNameNode${nameNode} - --fileUrl${projectFileURL} + --fileURL${projectFileURL} --hdfsPath${workingDir}/projects.csv @@ -44,7 +44,7 @@ eu.dnetlib.dhp.actionset.h2020programme.GetFile --hdfsNameNode${nameNode} - --fileUrl${programmeFileURL} + --fileURL${programmeFileURL} --hdfsPath${workingDir}/programme.csv diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionset/h2020programme/parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/parameters.json similarity index 100% rename from dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionset/h2020programme/parameters.json rename to dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/parameters.json diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionset/h2020programme/action_set_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionset/h2020programme/action_set_parameters.json deleted file mode 100644 index e69de29bb2..0000000000 From 4f1ff7ba73690c64f2f35fca03a959ac605d4247 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 18 May 2020 13:04:39 +0200 Subject: [PATCH 09/62] added dependency to org.apache.commons common-csv --- dhp-workflows/dhp-aggregation/pom.xml | 50 ++++----------------------- 1 file changed, 6 insertions(+), 44 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/pom.xml b/dhp-workflows/dhp-aggregation/pom.xml index 1c5465c14a..361517af94 100644 --- a/dhp-workflows/dhp-aggregation/pom.xml +++ b/dhp-workflows/dhp-aggregation/pom.xml @@ -38,48 +38,6 @@ ${project.version} - - eu.dnetlib - dnet-actionmanager-common - - - eu.dnetlib - dnet-openaireplus-mapping-utils - - - saxonica - saxon - - - saxonica - saxon-dom - - - jgrapht - jgrapht - - - net.sf.ehcache - ehcache - - - org.springframework - spring-test - - - org.apache.* - * - - - apache - * - - - - - eu.dnetlib - dnet-openaire-data-protos - net.sf.saxon @@ -100,11 +58,15 @@ jaxen + - org.apache.hadoop - hadoop-distcp + org.apache.commons + commons-csv + 1.8 + + From 23bbac7d7cb20f9cadb0d68fcfcaf2dafe094b9b Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 18 May 2020 13:05:03 +0200 Subject: [PATCH 10/62] - --- .../dhp/actionmanager/project/action_set_parameters.json | 8 ++++---- .../dhp/actionmanager/project/oozie_app/workflow.xml | 6 +++--- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/action_set_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/action_set_parameters.json index ca9ae9e97b..a0856e10ef 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/action_set_parameters.json +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/action_set_parameters.json @@ -6,14 +6,14 @@ "paramRequired": false }, { -"paramName": "pjfu", -"paramLongName": "projectsFileURL", +"paramName": "pjp", +"paramLongName": "projectPath", "paramDescription": "the URL from where to get the projects file", "paramRequired": true }, { -"paramName": "pfu", -"paramLongName": "programmeFileURL", +"paramName": "pp", +"paramLongName": "programmePath", "paramDescription": "the URL from where to get the programme file", "paramRequired": true }, diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/oozie_app/workflow.xml index 5bfa2e7c42..992c2ded11 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/oozie_app/workflow.xml @@ -31,7 +31,7 @@ - eu.dnetlib.dhp.actionset.h2020programme.GetFile + eu.dnetlib.dhp.actionmanager.project.GetFile --hdfsNameNode${nameNode} --fileURL${projectFileURL} --hdfsPath${workingDir}/projects.csv @@ -42,7 +42,7 @@ - eu.dnetlib.dhp.actionset.h2020programme.GetFile + eu.dnetlib.dhp.actionmanager.project.GetFile --hdfsNameNode${nameNode} --fileURL${programmeFileURL} --hdfsPath${workingDir}/programme.csv @@ -56,7 +56,7 @@ - + From f0f14caf996828237e7ce6bd4a3720c7ae01ae0f Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 18 May 2020 13:06:16 +0200 Subject: [PATCH 11/62] removed script files for shell actions not performed --- .../h2020programme/oozie_app/lib/scripts/getprogrammefile.sh | 0 .../h2020programme/oozie_app/lib/scripts/getprojectfile.sh | 0 2 files changed, 0 insertions(+), 0 deletions(-) delete mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionset/h2020programme/oozie_app/lib/scripts/getprogrammefile.sh delete mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionset/h2020programme/oozie_app/lib/scripts/getprojectfile.sh diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionset/h2020programme/oozie_app/lib/scripts/getprogrammefile.sh b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionset/h2020programme/oozie_app/lib/scripts/getprogrammefile.sh deleted file mode 100644 index e69de29bb2..0000000000 diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionset/h2020programme/oozie_app/lib/scripts/getprojectfile.sh b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionset/h2020programme/oozie_app/lib/scripts/getprojectfile.sh deleted file mode 100644 index e69de29bb2..0000000000 From 9447d78ef38abc918e6f0b7bb4f338ebe9f02c86 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 19 May 2020 18:42:50 +0200 Subject: [PATCH 12/62] added preparation classes --- .../dhp/actionmanager/project/GetFile.java | 53 ----- .../project/PrepareProgramme.java | 124 ++++++++++++ .../project/PrepareProjects.java | 189 ++++++++---------- .../project/SparkAtomicActionJob.java | 61 +++++- .../project/csvutils/CSVParser.java | 37 ++++ .../CSVProgramme.java} | 4 +- .../CSVProject.java} | 5 +- .../project/csvutils/ReadCSV.java | 98 +++++++++ .../CollectorPluginErrorLogList.java | 2 +- .../CollectorServiceException.java | 2 +- .../{ => httpconnector}/HttpConnector.java | 2 +- .../project/prepare_programme_parameters.json | 26 +++ .../project/prepare_project_parameters.json | 20 ++ .../actionmanager/project/CSVParserTest.java | 43 ++++ .../project/PrepareProgrammeTest.java | 4 + .../project/SparkUpdateProjectTest.java | 4 + .../httpconnector/HttpConnectorTest.java | 4 + .../preparedProgramme_whole.json | 0 .../dhp/actionmanager/project/programme.csv | 0 .../dhp/actionmanager/projects_subset.json | 0 .../dhp/actionmanager/whole_programme.json | 0 21 files changed, 507 insertions(+), 171 deletions(-) delete mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/GetFile.java create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/PrepareProgramme.java create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/csvutils/CSVParser.java rename dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/{Programme.java => csvutils/CSVProgramme.java} (87%) rename dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/{Project.java => csvutils/CSVProject.java} (97%) create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/csvutils/ReadCSV.java rename dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/{ => httpconnector}/CollectorPluginErrorLogList.java (86%) rename dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/{ => httpconnector}/CollectorServiceException.java (86%) rename dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/{ => httpconnector}/HttpConnector.java (99%) create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/prepare_programme_parameters.json create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/prepare_project_parameters.json create mode 100644 dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/CSVParserTest.java create mode 100644 dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/PrepareProgrammeTest.java create mode 100644 dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/SparkUpdateProjectTest.java create mode 100644 dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/httpconnector/HttpConnectorTest.java create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/preparedProgramme_whole.json create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/project/programme.csv create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/projects_subset.json create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/whole_programme.json diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/GetFile.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/GetFile.java deleted file mode 100644 index bbf59a20f3..0000000000 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/GetFile.java +++ /dev/null @@ -1,53 +0,0 @@ - -package eu.dnetlib.dhp.actionmanager.project; - -import java.io.*; -import java.net.URL; - -import org.apache.commons.io.IOUtils; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; -import org.apache.hadoop.conf.Configuration; -import org.apache.hadoop.fs.FSDataOutputStream; -import org.apache.hadoop.fs.FileSystem; -import org.apache.hadoop.fs.Path; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; - -public class GetFile { - - private static final Log log = LogFactory.getLog(GetFile.class); - - public static void main(final String[] args) throws Exception { - final ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils - .toString( - GetFile.class - .getResourceAsStream( - "/eu/dnetlib/dhp/actionmanager/project/parameters.json"))); - - Configuration conf = new Configuration(); - - parser.parseArgument(args); - - final String fileURL = parser.get("fileURL"); - final String hdfsPath = parser.get("hdfsPath"); - final String hdfsNameNode = parser.get("hdfsNameNode"); - - conf.set("fs.defaultFS", hdfsNameNode); - FileSystem fileSystem = FileSystem.get(conf); - Path hdfsWritePath = new Path(hdfsPath); - FSDataOutputStream fsDataOutputStream = null; - if (fileSystem.exists(hdfsWritePath)) { - fsDataOutputStream = fileSystem.append(hdfsWritePath); - } else { - fsDataOutputStream = fileSystem.create(hdfsWritePath); - } - - InputStream is = new BufferedInputStream(new URL(fileURL).openStream()); - - org.apache.hadoop.io.IOUtils.copyBytes(is, fsDataOutputStream, 4096, true); - - } - -} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/PrepareProgramme.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/PrepareProgramme.java new file mode 100644 index 0000000000..a5abb9ea7d --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/PrepareProgramme.java @@ -0,0 +1,124 @@ + +package eu.dnetlib.dhp.actionmanager.project; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.util.HashMap; +import java.util.Optional; + +import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.*; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.actionmanager.project.csvutils.CSVProgramme; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.HdfsSupport; +import scala.Tuple2; + +public class PrepareProgramme { + + private static final Logger log = LoggerFactory.getLogger(PrepareProgramme.class); + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + private static final HashMap programmeMap = new HashMap<>(); + + public static void main(String[] args) throws Exception { + + String jsonConfiguration = IOUtils + .toString( + PrepareProgramme.class + .getResourceAsStream( + "/eu/dnetlib/dhp/actionmanager/project/prepare_programme_parameters.json")); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + + parser.parseArgument(args); + + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + final String programmePath = parser.get("programmePath"); + log.info("programmePath {}: ", programmePath); + + final String outputPath = parser.get("outputPath"); + log.info("outputPath {}: ", outputPath); + + SparkConf conf = new SparkConf(); + + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + removeOutputDir(spark, outputPath); + exec(spark, programmePath, outputPath); + }); + } + + private static void removeOutputDir(SparkSession spark, String path) { + HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); + } + + private static void exec(SparkSession spark, String programmePath, String outputPath) { + Dataset programme = readPath(spark, programmePath, CSVProgramme.class); + + programme + .toJavaRDD() + .filter(p -> !p.getCode().contains("FP7")) + .mapToPair(csvProgramme -> new Tuple2<>(csvProgramme.getCode(), csvProgramme)) + .reduceByKey((a, b) -> { + if (StringUtils.isEmpty(a.getShortTitle())) { + if (StringUtils.isEmpty(b.getShortTitle())) { + if (StringUtils.isEmpty(a.getTitle())) { + if (StringUtils.isNotEmpty(b.getTitle())) { + a.setShortTitle(b.getTitle()); + a.setLanguage(b.getLanguage()); + } + } else {// notIsEmpty a.getTitle + if (StringUtils.isEmpty(b.getTitle())) { + a.setShortTitle(a.getTitle()); + } else { + if (b.getLanguage().equalsIgnoreCase("en")) { + a.setShortTitle(b.getTitle()); + a.setLanguage(b.getLanguage()); + } else { + a.setShortTitle(a.getTitle()); + } + } + } + } else {// not isEmpty b.getShortTitle + a.setShortTitle(b.getShortTitle()); + // a.setLanguage(b.getLanguage()); + } + } + return a; + + }) + .map(p -> { + CSVProgramme csvProgramme = p._2(); + if (StringUtils.isEmpty(csvProgramme.getShortTitle())) { + csvProgramme.setShortTitle(csvProgramme.getTitle()); + } + return OBJECT_MAPPER.writeValueAsString(csvProgramme); + }) + .saveAsTextFile(outputPath); + + } + + public static Dataset readPath( + SparkSession spark, String inputPath, Class clazz) { + return spark + .read() + .textFile(inputPath) + .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz)); + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/PrepareProjects.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/PrepareProjects.java index 8955edeb4e..1c98199f82 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/PrepareProjects.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/PrepareProjects.java @@ -1,139 +1,108 @@ package eu.dnetlib.dhp.actionmanager.project; -import java.io.BufferedWriter; -import java.io.Closeable; -import java.io.IOException; -import java.io.OutputStreamWriter; -import java.nio.charset.StandardCharsets; -import java.sql.ResultSet; -import java.util.Arrays; -import java.util.List; -import java.util.Set; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; -import org.apache.commons.csv.CSVParser; -import org.apache.commons.csv.CSVFormat; +import java.util.ArrayList; +import java.util.HashMap; +import java.util.List; +import java.util.Optional; import org.apache.commons.io.IOUtils; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; -import org.apache.hadoop.conf.Configuration; -import org.apache.hadoop.fs.FSDataOutputStream; -import org.apache.hadoop.fs.FileSystem; -import org.apache.hadoop.fs.Path; +import org.apache.commons.lang3.StringUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SparkSession; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.actionmanager.project.csvutils.CSVProgramme; +import eu.dnetlib.dhp.actionmanager.project.csvutils.CSVProject; import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.schema.common.ModelSupport; -import eu.dnetlib.dhp.schema.common.RelationInverse; -import eu.dnetlib.dhp.schema.oaf.Relation; +import eu.dnetlib.dhp.common.HdfsSupport; +import scala.Tuple2; -public class PrepareProjects implements Closeable { - private static final Log log = LogFactory.getLog(PrepareProjects.class); - private final Configuration conf; - private final BufferedWriter writer; - private final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - private final HttpConnector httpConnector; +public class PrepareProjects { - public static void main(final String[] args) throws Exception { - final ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils - .toString( - PrepareProjects.class - .getResourceAsStream( - "/eu/dnetlib/dhp/actionmanager/project/parameters.json"))); + private static final Logger log = LoggerFactory.getLogger(PrepareProgramme.class); + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + private static final HashMap programmeMap = new HashMap<>(); + + public static void main(String[] args) throws Exception { + + String jsonConfiguration = IOUtils + .toString( + PrepareProjects.class + .getResourceAsStream( + "/eu/dnetlib/dhp/actionmanager/project/prepare_project_parameters.json")); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); parser.parseArgument(args); - final String fileURL = parser.get("fileURL"); - final String hdfsPath = parser.get("hdfsPath"); - final String hdfsNameNode = parser.get("hdfsNameNode"); + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); - try (final PrepareProjects prepareProjects = new PrepareProjects(hdfsPath, hdfsNameNode)) { + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - log.info("Getting projects..."); - prepareProjects.execute(fileURL); + final String projectPath = parser.get("projectPath"); + log.info("projectPath {}: ", projectPath); - } + final String outputPath = parser.get("outputPath"); + log.info("outputPath {}: ", outputPath); + + SparkConf conf = new SparkConf(); + + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + removeOutputDir(spark, outputPath); + exec(spark, projectPath, outputPath); + }); } - public void execute(final String fileURL) throws Exception { - - String projects = httpConnector.getInputSource(fileURL); - final CSVFormat format = CSVFormat.EXCEL - .withHeader() - .withDelimiter(';') - .withQuote('"') - .withTrim(); - final CSVParser parser = CSVParser.parse(projects, format); - final Set headers = parser.getHeaderMap().keySet(); + private static void removeOutputDir(SparkSession spark, String path) { + HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); } - public List processBlacklistEntry(ResultSet rs) { - try { - Relation direct = new Relation(); - Relation inverse = new Relation(); + private static void exec(SparkSession spark, String progjectPath, String outputPath) { + Dataset project = readPath(spark, progjectPath, CSVProject.class); - String source_prefix = ModelSupport.entityIdPrefix.get(rs.getString("source_type")); - String target_prefix = ModelSupport.entityIdPrefix.get(rs.getString("target_type")); + project + .toJavaRDD() + .flatMap(p -> { + List csvProjectList = new ArrayList<>(); + String[] programme = p.getProgramme().split(";"); + if (programme.length > 1) { + for (int i = 0; i < programme.length; i++) { + CSVProject csvProject = new CSVProject(); + csvProject.setProgramme(programme[i]); + csvProjectList.add(csvProject); + } + } else { + csvProjectList.add(p); + } - String source_direct = source_prefix + "|" + rs.getString("source"); - direct.setSource(source_direct); - inverse.setTarget(source_direct); - - String target_direct = target_prefix + "|" + rs.getString("target"); - direct.setTarget(target_direct); - inverse.setSource(target_direct); - - String encoding = rs.getString("relationship"); - RelationInverse ri = ModelSupport.relationInverseMap.get(encoding); - direct.setRelClass(ri.getRelation()); - inverse.setRelClass(ri.getInverse()); - direct.setRelType(ri.getRelType()); - inverse.setRelType(ri.getRelType()); - direct.setSubRelType(ri.getSubReltype()); - inverse.setSubRelType(ri.getSubReltype()); - - return Arrays.asList(direct, inverse); - - } catch (final Exception e) { - throw new RuntimeException(e); - } - } - - @Override - public void close() throws IOException { - writer.close(); - } - - public PrepareProjects( - final String hdfsPath, String hdfsNameNode) - throws Exception { - - this.conf = new Configuration(); - this.conf.set("fs.defaultFS", hdfsNameNode); - this.httpConnector = new HttpConnector(); - FileSystem fileSystem = FileSystem.get(this.conf); - Path hdfsWritePath = new Path(hdfsPath); - FSDataOutputStream fsDataOutputStream = null; - if (fileSystem.exists(hdfsWritePath)) { - fsDataOutputStream = fileSystem.append(hdfsWritePath); - } else { - fsDataOutputStream = fileSystem.create(hdfsWritePath); - } - - this.writer = new BufferedWriter(new OutputStreamWriter(fsDataOutputStream, StandardCharsets.UTF_8)); + return csvProjectList.iterator(); + }) + .map(p -> OBJECT_MAPPER.writeValueAsString(p)) + .saveAsTextFile(outputPath); } - protected void writeRelation(final Relation r) { - try { - writer.write(OBJECT_MAPPER.writeValueAsString(r)); - writer.newLine(); - } catch (final Exception e) { - throw new RuntimeException(e); - } + public static Dataset readPath( + SparkSession spark, String inputPath, Class clazz) { + return spark + .read() + .textFile(inputPath) + .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz)); } - } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/SparkAtomicActionJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/SparkAtomicActionJob.java index b8703378ec..61bd952db2 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/SparkAtomicActionJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/SparkAtomicActionJob.java @@ -3,22 +3,35 @@ package eu.dnetlib.dhp.actionmanager.project; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; +import java.util.Arrays; +import java.util.HashMap; import java.util.Optional; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.actionmanager.project.csvutils.CSVProgramme; +import eu.dnetlib.dhp.actionmanager.project.csvutils.CSVProject; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.oaf.Programme; +import eu.dnetlib.dhp.schema.oaf.Project; +import eu.dnetlib.dhp.utils.DHPUtils; public class SparkAtomicActionJob { private static final Logger log = LoggerFactory.getLogger(SparkAtomicActionJob.class); private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + private static final HashMap programmeMap = new HashMap<>(); public static void main(String[] args) throws Exception { @@ -67,8 +80,54 @@ public class SparkAtomicActionJob { HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); } - private static void getAtomicActions(SparkSession spark, String projectPatj, String programmePath, + private static void getAtomicActions(SparkSession spark, String projectPatH, + String programmePath, String outputPath) { + Dataset project = readPath(spark, projectPatH, CSVProject.class); + Dataset programme = readPath(spark, programmePath, CSVProgramme.class); + + project + .joinWith(programme, project.col("programme").equalTo(programme.col("code")), "left") + .map(c -> { + CSVProject csvProject = c._1(); + Optional csvProgramme = Optional.ofNullable(c._2()); + if (csvProgramme.isPresent()) { + Project p = new Project(); + p + .setId( + createOpenaireId( + ModelSupport.entityIdPrefix.get("project"), + "corda__h2020", csvProject.getId())); + Programme pm = new Programme(); + pm.setCode(csvProject.getProgramme()); + pm.setDescription(csvProgramme.get().getShortTitle()); + p.setProgramme(Arrays.asList(pm)); + return p; + } + + return null; + }, Encoders.bean(Project.class)) + .filter(p -> !(p == null)) + // .map(p -> new AtomicAction<>(Project.class, p), Encoders.bean(AtomicAction.class)) + .write() + .option("compression", "gzip") + .mode(SaveMode.Overwrite) + .json(outputPath); + } + + public static Dataset readPath( + SparkSession spark, String inputPath, Class clazz) { + return spark + .read() + .textFile(inputPath) + .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz)); + } + + public static String createOpenaireId( + final String prefix, final String nsPrefix, final String id) { + + return String.format("%s|%s::%s", prefix, nsPrefix, DHPUtils.md5(id)); + } } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/csvutils/CSVParser.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/csvutils/CSVParser.java new file mode 100644 index 0000000000..ef29a6b6a6 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/csvutils/CSVParser.java @@ -0,0 +1,37 @@ + +package eu.dnetlib.dhp.actionmanager.project.csvutils; + +import java.io.IOException; +import java.util.ArrayList; +import java.util.List; +import java.util.Set; + +import org.apache.commons.csv.CSVFormat; +import org.apache.commons.csv.CSVRecord; +import org.apache.commons.lang.reflect.FieldUtils; + +public class CSVParser { + + public List parse(String csvFile, String classForName) + throws ClassNotFoundException, IOException, IllegalAccessException, InstantiationException { + final CSVFormat format = CSVFormat.EXCEL + .withHeader() + .withDelimiter(';') + .withQuote('"') + .withTrim(); + List ret = new ArrayList<>(); + final org.apache.commons.csv.CSVParser parser = org.apache.commons.csv.CSVParser.parse(csvFile, format); + final Set headers = parser.getHeaderMap().keySet(); + Class clazz = Class.forName(classForName); + for (CSVRecord csvRecord : parser.getRecords()) { + final Object cc = clazz.newInstance(); + for (String header : headers) { + FieldUtils.writeField(cc, header, csvRecord.get(header), true); + + } + ret.add((R) cc); + } + + return ret; + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/Programme.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/csvutils/CSVProgramme.java similarity index 87% rename from dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/Programme.java rename to dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/csvutils/CSVProgramme.java index 20877b1a10..a9069e5104 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/Programme.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/csvutils/CSVProgramme.java @@ -1,9 +1,9 @@ -package eu.dnetlib.dhp.actionmanager.project; +package eu.dnetlib.dhp.actionmanager.project.csvutils; import java.io.Serializable; -public class Programme implements Serializable { +public class CSVProgramme implements Serializable { private String rcn; private String code; private String title; diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/Project.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/csvutils/CSVProject.java similarity index 97% rename from dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/Project.java rename to dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/csvutils/CSVProject.java index abee7f8616..ff18c6260e 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/Project.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/csvutils/CSVProject.java @@ -1,9 +1,9 @@ -package eu.dnetlib.dhp.actionmanager.project; +package eu.dnetlib.dhp.actionmanager.project.csvutils; import java.io.Serializable; -public class Project implements Serializable { +public class CSVProject implements Serializable { private String rcn; private String id; private String acronym; @@ -193,4 +193,5 @@ public class Project implements Serializable { public void setSubjects(String subjects) { this.subjects = subjects; } + } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/csvutils/ReadCSV.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/csvutils/ReadCSV.java new file mode 100644 index 0000000000..9051942321 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/csvutils/ReadCSV.java @@ -0,0 +1,98 @@ + +package eu.dnetlib.dhp.actionmanager.project.csvutils; + +import java.io.BufferedWriter; +import java.io.Closeable; +import java.io.IOException; +import java.io.OutputStreamWriter; +import java.nio.charset.StandardCharsets; + +import org.apache.commons.io.IOUtils; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FSDataOutputStream; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.actionmanager.project.httpconnector.HttpConnector; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; + +public class ReadCSV implements Closeable { + private static final Log log = LogFactory.getLog(ReadCSV.class); + private final Configuration conf; + private final BufferedWriter writer; + private final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + private String csvFile; + + public static void main(final String[] args) throws Exception { + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + ReadCSV.class + .getResourceAsStream( + "/eu/dnetlib/dhp/actionmanager/project/parameters.json"))); + + parser.parseArgument(args); + + final String fileURL = parser.get("fileURL"); + final String hdfsPath = parser.get("hdfsPath"); + final String hdfsNameNode = parser.get("hdfsNameNode"); + final String classForName = parser.get("classForName"); + + try (final ReadCSV readCSV = new ReadCSV(hdfsPath, hdfsNameNode, fileURL)) { + + log.info("Getting CSV file..."); + readCSV.execute(classForName); + + } + } + + public void execute(final String classForName) throws Exception { + CSVParser csvParser = new CSVParser(); + csvParser + .parse(csvFile, classForName) + .stream() + .forEach(p -> write(p)); + + } + + @Override + public void close() throws IOException { + writer.close(); + } + + public ReadCSV( + final String hdfsPath, + final String hdfsNameNode, + final String fileURL) + throws Exception { + this.conf = new Configuration(); + this.conf.set("fs.defaultFS", hdfsNameNode); + HttpConnector httpConnector = new HttpConnector(); + FileSystem fileSystem = FileSystem.get(this.conf); + Path hdfsWritePath = new Path(hdfsPath); + FSDataOutputStream fsDataOutputStream = null; + if (fileSystem.exists(hdfsWritePath)) { + fsDataOutputStream = fileSystem.append(hdfsWritePath); + } else { + fsDataOutputStream = fileSystem.create(hdfsWritePath); + } + + this.writer = new BufferedWriter(new OutputStreamWriter(fsDataOutputStream, StandardCharsets.UTF_8)); + this.csvFile = httpConnector.getInputSource(fileURL); + ; + } + + protected void write(final Object p) { + try { + writer.write(OBJECT_MAPPER.writeValueAsString(p)); + writer.newLine(); + } catch (final Exception e) { + throw new RuntimeException(e); + } + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/CollectorPluginErrorLogList.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/httpconnector/CollectorPluginErrorLogList.java similarity index 86% rename from dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/CollectorPluginErrorLogList.java rename to dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/httpconnector/CollectorPluginErrorLogList.java index bc00e4604c..9d3f882651 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/CollectorPluginErrorLogList.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/httpconnector/CollectorPluginErrorLogList.java @@ -1,5 +1,5 @@ -package eu.dnetlib.dhp.actionmanager.project; +package eu.dnetlib.dhp.actionmanager.project.httpconnector; import java.util.LinkedList; diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/CollectorServiceException.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/httpconnector/CollectorServiceException.java similarity index 86% rename from dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/CollectorServiceException.java rename to dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/httpconnector/CollectorServiceException.java index a417de50d7..9167d97b4c 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/CollectorServiceException.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/httpconnector/CollectorServiceException.java @@ -1,5 +1,5 @@ -package eu.dnetlib.dhp.actionmanager.project; +package eu.dnetlib.dhp.actionmanager.project.httpconnector; public class CollectorServiceException extends Exception { diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/HttpConnector.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/httpconnector/HttpConnector.java similarity index 99% rename from dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/HttpConnector.java rename to dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/httpconnector/HttpConnector.java index 63f67f145a..e20518b559 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/HttpConnector.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/httpconnector/HttpConnector.java @@ -1,5 +1,5 @@ -package eu.dnetlib.dhp.actionmanager.project; +package eu.dnetlib.dhp.actionmanager.project.httpconnector; import java.io.IOException; import java.io.InputStream; diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/prepare_programme_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/prepare_programme_parameters.json new file mode 100644 index 0000000000..a0856e10ef --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/prepare_programme_parameters.json @@ -0,0 +1,26 @@ +[ + { + "paramName": "issm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "when true will stop SparkSession after job execution", + "paramRequired": false +}, +{ +"paramName": "pjp", +"paramLongName": "projectPath", +"paramDescription": "the URL from where to get the projects file", +"paramRequired": true +}, +{ +"paramName": "pp", +"paramLongName": "programmePath", +"paramDescription": "the URL from where to get the programme file", +"paramRequired": true +}, +{ +"paramName": "o", +"paramLongName": "outputPath", +"paramDescription": "the path of the new ActionSet", +"paramRequired": true +} +] \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/prepare_project_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/prepare_project_parameters.json new file mode 100644 index 0000000000..54083e1089 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/prepare_project_parameters.json @@ -0,0 +1,20 @@ +[ + { + "paramName": "issm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "when true will stop SparkSession after job execution", + "paramRequired": false +}, +{ +"paramName": "pp", +"paramLongName": "programmePath", +"paramDescription": "the URL from where to get the programme file", +"paramRequired": true +}, +{ +"paramName": "o", +"paramLongName": "outputPath", +"paramDescription": "the path of the new ActionSet", +"paramRequired": true +} +] \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/CSVParserTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/CSVParserTest.java new file mode 100644 index 0000000000..d344f31186 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/CSVParserTest.java @@ -0,0 +1,43 @@ +package eu.dnetlib.dhp.actionmanager.project; + +import org.apache.commons.io.IOUtils; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; + +public class ReadCSVTest { + + private static Path workingDir; + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files.createTempDirectory(eu.dnetlib.dhp.actionmanager.project.ReadCSVTest.class.getSimpleName()); + + + } + @Test + public void readProgrammeTest() throws Exception { + + String programmecsv = IOUtils.toString(getClass() + .getClassLoader().getResourceAsStream("eu/dnetlib/dhp/actionmanager/project/programme.csv")); + ReadCSV + .main( + new String[] { + "-fileURL", + "http://cordis.europa.eu/data/reference/cordisref-H2020programmes.csv", + "-outputPath", + workingDir.toString() + "/project", + "-hdfsPath", + getClass().getResource("/eu/dnetlib/dhp/blacklist/blacklist").getPath(), + "-mergesPath", + getClass().getResource("/eu/dnetlib/dhp/blacklist/mergesRelOneMerge").getPath(), + }); + + + + + } +} diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/PrepareProgrammeTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/PrepareProgrammeTest.java new file mode 100644 index 0000000000..b22e6bd6d7 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/PrepareProgrammeTest.java @@ -0,0 +1,4 @@ +package eu.dnetlib.dhp.actionmanager.project; + +public class PrepareProgrammeTest { +} diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/SparkUpdateProjectTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/SparkUpdateProjectTest.java new file mode 100644 index 0000000000..f7d271fe02 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/SparkUpdateProjectTest.java @@ -0,0 +1,4 @@ +package eu.dnetlib.dhp.actionmanager.project; + +public class SparkUpdateProjectSet { +} diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/httpconnector/HttpConnectorTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/httpconnector/HttpConnectorTest.java new file mode 100644 index 0000000000..29e9a6cce9 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/httpconnector/HttpConnectorTest.java @@ -0,0 +1,4 @@ +package eu.dnetlib.dhp.actionmanager.project.httpconnector; + +public class HttpConnectorTest { +} diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/preparedProgramme_whole.json b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/preparedProgramme_whole.json new file mode 100644 index 0000000000..e69de29bb2 diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/project/programme.csv b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/project/programme.csv new file mode 100644 index 0000000000..e69de29bb2 diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/projects_subset.json b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/projects_subset.json new file mode 100644 index 0000000000..e69de29bb2 diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/whole_programme.json b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/whole_programme.json new file mode 100644 index 0000000000..e69de29bb2 From 457293ccc0c86f1cb5e51b179772302102b18c81 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 19 May 2020 18:43:42 +0200 Subject: [PATCH 13/62] test for the variuos steps of project update with programme --- .../actionmanager/project/CSVParserTest.java | 50 +++++----- .../project/PrepareProgrammeTest.java | 90 ++++++++++++++++++ .../project/SparkUpdateProjectTest.java | 92 ++++++++++++++++++- .../httpconnector/HttpConnectorTest.java | 35 +++++++ 4 files changed, 240 insertions(+), 27 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/CSVParserTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/CSVParserTest.java index d344f31186..17fdd45111 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/CSVParserTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/CSVParserTest.java @@ -1,43 +1,41 @@ + package eu.dnetlib.dhp.actionmanager.project; +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.List; + import org.apache.commons.io.IOUtils; import org.junit.jupiter.api.BeforeAll; import org.junit.jupiter.api.Test; -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; +import eu.dnetlib.dhp.actionmanager.project.csvutils.CSVParser; -public class ReadCSVTest { +public class CSVParserTest { - private static Path workingDir; + private static Path workingDir; - @BeforeAll - public static void beforeAll() throws IOException { - workingDir = Files.createTempDirectory(eu.dnetlib.dhp.actionmanager.project.ReadCSVTest.class.getSimpleName()); + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files.createTempDirectory(CSVParserTest.class.getSimpleName()); + } - } - @Test - public void readProgrammeTest() throws Exception { + @Test + public void readProgrammeTest() throws Exception { - String programmecsv = IOUtils.toString(getClass() - .getClassLoader().getResourceAsStream("eu/dnetlib/dhp/actionmanager/project/programme.csv")); - ReadCSV - .main( - new String[] { - "-fileURL", - "http://cordis.europa.eu/data/reference/cordisref-H2020programmes.csv", - "-outputPath", - workingDir.toString() + "/project", - "-hdfsPath", - getClass().getResource("/eu/dnetlib/dhp/blacklist/blacklist").getPath(), - "-mergesPath", - getClass().getResource("/eu/dnetlib/dhp/blacklist/mergesRelOneMerge").getPath(), - }); + String programmecsv = IOUtils + .toString( + getClass() + .getClassLoader() + .getResourceAsStream("eu/dnetlib/dhp/actionmanager/project/programme.csv")); + CSVParser csvParser = new CSVParser(); + List pl = csvParser.parse(programmecsv, "eu.dnetlib.dhp.actionmanager.project.csvutils.CSVProgramme"); + System.out.println(pl.size()); - } + } } diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/PrepareProgrammeTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/PrepareProgrammeTest.java index b22e6bd6d7..50804f75e0 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/PrepareProgrammeTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/PrepareProgrammeTest.java @@ -1,4 +1,94 @@ + package eu.dnetlib.dhp.actionmanager.project; +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; + +import org.apache.commons.io.FileUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.actionmanager.project.csvutils.CSVProgramme; + public class PrepareProgrammeTest { + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static final ClassLoader cl = eu.dnetlib.dhp.actionmanager.project.PrepareProgrammeTest.class + .getClassLoader(); + + private static SparkSession spark; + + private static Path workingDir; + private static final Logger log = LoggerFactory + .getLogger(eu.dnetlib.dhp.actionmanager.project.PrepareProgrammeTest.class); + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files + .createTempDirectory(eu.dnetlib.dhp.actionmanager.project.PrepareProgrammeTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(eu.dnetlib.dhp.actionmanager.project.PrepareProgrammeTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + + spark = SparkSession + .builder() + .appName(PrepareProgrammeTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + public void numberDistinctProgrammeTest() throws Exception { + PrepareProgramme + .main( + new String[] { + "-isSparkSessionManaged", + Boolean.FALSE.toString(), + "-programmePath", + getClass().getResource("/eu/dnetlib/dhp/actionmanager/whole_programme.json").getPath(), + "-outputPath", + workingDir.toString() + "/preparedProgramme" + }); + + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/preparedProgramme") + .map(item -> OBJECT_MAPPER.readValue(item, CSVProgramme.class)); + + Assertions.assertEquals(277, tmp.count()); + + Dataset verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(CSVProgramme.class)); + + Assertions.assertEquals(0, verificationDataset.filter("shortTitle =''").count()); + } + } diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/SparkUpdateProjectTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/SparkUpdateProjectTest.java index f7d271fe02..d488848429 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/SparkUpdateProjectTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/SparkUpdateProjectTest.java @@ -1,4 +1,94 @@ + package eu.dnetlib.dhp.actionmanager.project; -public class SparkUpdateProjectSet { +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; + +import org.apache.commons.io.FileUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.schema.oaf.Project; + +public class SparkUpdateProjectTest { + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static final ClassLoader cl = eu.dnetlib.dhp.actionmanager.project.SparkUpdateProjectTest.class + .getClassLoader(); + + private static SparkSession spark; + + private static Path workingDir; + private static final Logger log = LoggerFactory + .getLogger(eu.dnetlib.dhp.actionmanager.project.SparkUpdateProjectTest.class); + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files + .createTempDirectory(eu.dnetlib.dhp.actionmanager.project.SparkUpdateProjectTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(eu.dnetlib.dhp.actionmanager.project.SparkUpdateProjectTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + + spark = SparkSession + .builder() + .appName(SparkUpdateProjectTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + public void numberDistinctProgrammeTest() throws Exception { + SparkAtomicActionJob + .main( + new String[] { + "-isSparkSessionManaged", + Boolean.FALSE.toString(), + "-programmePath", + getClass().getResource("/eu/dnetlib/dhp/actionmanager/preparedProgramme_whole.json").getPath(), + "-projectPath", + getClass().getResource("/eu/dnetlib/dhp/actionmanager/projects_subset.json").getPath(), + "-outputPath", + workingDir.toString() + "/actionSet" + }); + + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/actionSet") + .map(item -> OBJECT_MAPPER.readValue(item, Project.class)); + + Assertions.assertEquals(14, tmp.count()); + +// Dataset verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(CSVProgramme.class)); +// +// Assertions.assertEquals(0, verificationDataset.filter("shortTitle =''").count()); + } } diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/httpconnector/HttpConnectorTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/httpconnector/HttpConnectorTest.java index 29e9a6cce9..51a7019cac 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/httpconnector/HttpConnectorTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/httpconnector/HttpConnectorTest.java @@ -1,4 +1,39 @@ + package eu.dnetlib.dhp.actionmanager.project.httpconnector; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.apache.http.conn.ssl.SSLConnectionSocketFactory; +import org.apache.http.ssl.SSLContextBuilder; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; + public class HttpConnectorTest { + + private static final Log log = LogFactory.getLog(HttpConnectorTest.class); + private static HttpConnector connector; + + private static final String URL = "http://cordis.europa.eu/data/reference/cordisref-H2020programmes.csv"; + private static final String URL_MISCONFIGURED_SERVER = "https://www.alexandria.unisg.ch/cgi/oai2?verb=Identify"; + private static final String URL_GOODSNI_SERVER = "https://air.unimi.it/oai/openaire?verb=Identify"; + + private static final SSLContextBuilder sslContextBuilder = new SSLContextBuilder(); + private static SSLConnectionSocketFactory sslSocketFactory; + + @BeforeAll + public static void setUp() { + connector = new HttpConnector(); + } + + @Test + + public void testGetInputSource() throws CollectorServiceException { + System.out.println(connector.getInputSource(URL)); + } + + @Test + public void testGoodServers() throws CollectorServiceException { + System.out.println(connector.getInputSource(URL_GOODSNI_SERVER)); + } + } From 08218d2f3f9fd64423907ebf31508b8213745249 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 19 May 2020 18:44:25 +0200 Subject: [PATCH 14/62] new workflow with added steps --- .../project/oozie_app/workflow.xml | 114 +++++++++++++----- 1 file changed, 82 insertions(+), 32 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/oozie_app/workflow.xml index 992c2ded11..cd4d79ab77 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/oozie_app/workflow.xml @@ -24,6 +24,7 @@ + @@ -31,51 +32,100 @@ - eu.dnetlib.dhp.actionmanager.project.GetFile + eu.dnetlib.dhp.actionmanager.project.csvutils.ReadCSV --hdfsNameNode${nameNode} --fileURL${projectFileURL} - --hdfsPath${workingDir}/projects.csv + --hdfsPath${workingDir}/projects + --classForNameeu.dnetlib.dhp.actionmanager.project.csvutils.CSVProject - + - + - eu.dnetlib.dhp.actionmanager.project.GetFile + eu.dnetlib.dhp.actionmanager.project.csvutils.ReadCSV --hdfsNameNode${nameNode} --fileURL${programmeFileURL} - --hdfsPath${workingDir}/programme.csv + --hdfsPath${workingDir}/programme + --classForNameeu.dnetlib.dhp.actionmanager.project.csvutils.CSVProgramme + + + + + + + yarn + cluster + PrepareProgramme + eu.dnetlib.dhp.actionmanager.project.PrepareProgramme + dhp-aggregation-${projectVersion}.jar + + --executor-cores=${sparkExecutorCores} + --executor-memory=${sparkExecutorMemory} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=3840 + + --programmePath${workingDir}/programme + --outputPath${workingDir}/preparedProgramme + + + + + + + + yarn + cluster + PrepareProgramme + eu.dnetlib.dhp.actionmanager.project.PrepareProjects + dhp-aggregation-${projectVersion}.jar + + --executor-cores=${sparkExecutorCores} + --executor-memory=${sparkExecutorMemory} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=3840 + + --projectPath${workingDir}/projects + --outputPath${workingDir}/preparedProjects + + + + + + + + yarn + cluster + ProjectProgrammeAS + eu.dnetlib.dhp.actionmanager.project.SparkAtomicActionJob + dhp-aggregation-${projectVersion}.jar + + --executor-cores=${sparkExecutorCores} + --executor-memory=${sparkExecutorMemory} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=3840 + + --projectPath${workingDir}/preparedProjects + --programmePath${workingDir}/preparedProgramme + --outputPath/tmp/h2020programme + - - - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file From eb0e47ba53d22e130740215d20a1636144c9071a Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 20 May 2020 10:26:44 +0200 Subject: [PATCH 15/62] parameters for h2020 programme --- .../project/oozie_app/config-default.xml | 54 +++++++++++++++++++ .../dhp/actionmanager/project/parameters.json | 10 +++- .../project/prepare_programme_parameters.json | 6 --- .../project/prepare_project_parameters.json | 4 +- 4 files changed, 65 insertions(+), 9 deletions(-) create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/oozie_app/config-default.xml diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/oozie_app/config-default.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/oozie_app/config-default.xml new file mode 100644 index 0000000000..fe82ae1940 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/oozie_app/config-default.xml @@ -0,0 +1,54 @@ + + + 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 + + + spark2YarnHistoryServerAddress + http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089 + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + + + sparkExecutorNumber + 4 + + + spark2EventLogDir + /user/spark/spark2ApplicationHistory + + + sparkDriverMemory + 15G + + + sparkExecutorMemory + 6G + + + sparkExecutorCores + 1 + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/parameters.json index 40ad5bf361..dd3de70f6e 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/parameters.json +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/parameters.json @@ -17,5 +17,13 @@ "paramLongName" : "hdfsNameNode", "paramDescription" : "the name node", "paramRequired" : true - } + }, + { + "paramName": "cfn", + "paramLongName" : "classForName", + "paramDescription" : "the name of the class to deserialize the csv to", + "paramRequired" : true +} + + ] \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/prepare_programme_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/prepare_programme_parameters.json index a0856e10ef..54083e1089 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/prepare_programme_parameters.json +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/prepare_programme_parameters.json @@ -6,12 +6,6 @@ "paramRequired": false }, { -"paramName": "pjp", -"paramLongName": "projectPath", -"paramDescription": "the URL from where to get the projects file", -"paramRequired": true -}, -{ "paramName": "pp", "paramLongName": "programmePath", "paramDescription": "the URL from where to get the programme file", diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/prepare_project_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/prepare_project_parameters.json index 54083e1089..5fc88ce8e9 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/prepare_project_parameters.json +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/prepare_project_parameters.json @@ -6,8 +6,8 @@ "paramRequired": false }, { -"paramName": "pp", -"paramLongName": "programmePath", +"paramName": "pjp", +"paramLongName": "projectPath", "paramDescription": "the URL from where to get the programme file", "paramRequired": true }, From d323100af09a8301694a6a712753547dcaecd127 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 20 May 2020 10:27:27 +0200 Subject: [PATCH 16/62] added the new Programme POJO. It contains the code and the description of the programme --- .../eu/dnetlib/dhp/schema/oaf/Programme.java | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Programme.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Programme.java index f913336163..69223ab019 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Programme.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Programme.java @@ -1,4 +1,23 @@ + package eu.dnetlib.dhp.schema.oaf; public class Programme { + private String code; + private String description; + + public String getCode() { + return code; + } + + public void setCode(String code) { + this.code = code; + } + + public String getDescription() { + return description; + } + + public void setDescription(String description) { + this.description = description; + } } From 24daa1deaaa1b78a14556c4fb53570a5db478aa4 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 20 May 2020 10:28:16 +0200 Subject: [PATCH 17/62] added to the Project class a new field that is the list of programmes --- .../main/java/eu/dnetlib/dhp/schema/oaf/Project.java | 10 ++++++++++ 1 file changed, 10 insertions(+) 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 924c08cc9c..1eae3e8eeb 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 @@ -58,6 +58,8 @@ public class Project extends OafEntity implements Serializable { private Float fundedamount; + private List programme; + public Field getWebsiteurl() { return websiteurl; } @@ -266,6 +268,14 @@ public class Project extends OafEntity implements Serializable { this.fundedamount = fundedamount; } + public List getProgramme() { + return programme; + } + + public void setProgramme(List programme) { + this.programme = programme; + } + @Override public void mergeFrom(OafEntity e) { super.mergeFrom(e); From 75491482de353bbc9f5d7a415028061267d2f43e Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 20 May 2020 10:28:56 +0200 Subject: [PATCH 18/62] added a new preparation step to replicate each project for the programme it is associated to --- .../eu/dnetlib/dhp/actionmanager/project/PrepareProjects.java | 2 ++ 1 file changed, 2 insertions(+) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/PrepareProjects.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/PrepareProjects.java index 1c98199f82..df37f92863 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/PrepareProjects.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/PrepareProjects.java @@ -82,9 +82,11 @@ public class PrepareProjects { List csvProjectList = new ArrayList<>(); String[] programme = p.getProgramme().split(";"); if (programme.length > 1) { + String id = p.getId(); for (int i = 0; i < programme.length; i++) { CSVProject csvProject = new CSVProject(); csvProject.setProgramme(programme[i]); + csvProject.setId(id); csvProjectList.add(csvProject); } } else { From faed7521bf100bca898ada798dc76abe96f02e80 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 20 May 2020 10:29:29 +0200 Subject: [PATCH 19/62] added resources for testing --- .../preparedProgramme_whole.json.gz | Bin 0 -> 14212 bytes .../dhp/actionmanager/whole_programme.json.gz | Bin 0 -> 34620 bytes 2 files changed, 0 insertions(+), 0 deletions(-) create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/preparedProgramme_whole.json.gz create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/whole_programme.json.gz diff --git 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zY5#eb(?aQcppZrhtC!s$wREi8Gc#b%Zx;kYB-zgdrIXnJrC0MdTe-K@|Mtzfkx;FGRlc|C$M+m^^*hnr7Wj~F;9V!ec;Zup>D z52o&nJ^ilq{FlLK8kBSGC2+s}ge*`TOE9Fw1?hrJWa#&TcFg!*6M6P@u` zLF3|;TBH71WJ`1@WlCShd%r$?^5k0weE}yYM$ou0T=~kqEWv`P&L>DBhl{{`pBQ3E zl!;Y9DhG|W8mYVly23H!mq1cNWMp+Y`A9ackc$95oQTDgnIR+IOf121-2!BTrGb>L zL;l{{uLC&tRi_ooF@CC#Ee2^55X;%{Nul$Xa8Pnz$~4 ztCn;P-~2@`%jT2I?G{FjzH~_nMy8#Z(9<+U099O1m0y^pabzhQGFLUtwoDZqHeM2` zxAee}k`89hOBg!CjvJZ(#gN?1hfxc)EhjG>t)kUs?wxh}Nhd=1I~>d8@%hd>P+?RV)K&C!u!q7vye|=$oZjC{477?4hSXmws4hJl1WJ#cs9gi ziojvdeC`p0=fd6m*{AP!_yY9h9JR%Wg^a_k$LW#g6dm&^nX6bGP4#a15$-s5Y`}yn z0uEw{2onQ>V~OK2WMYT3rt%$hW!1`BUl0&=Dh(``EEk6^_w!kD71OPdtOc?7Z Date: Wed, 20 May 2020 10:29:57 +0200 Subject: [PATCH 20/62] tests --- .../dhp/actionmanager/project/PrepareProgrammeTest.java | 2 +- .../dhp/actionmanager/project/SparkUpdateProjectTest.java | 6 ++---- 2 files changed, 3 insertions(+), 5 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/PrepareProgrammeTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/PrepareProgrammeTest.java index 50804f75e0..e9755c8584 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/PrepareProgrammeTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/PrepareProgrammeTest.java @@ -73,7 +73,7 @@ public class PrepareProgrammeTest { "-isSparkSessionManaged", Boolean.FALSE.toString(), "-programmePath", - getClass().getResource("/eu/dnetlib/dhp/actionmanager/whole_programme.json").getPath(), + getClass().getResource("/eu/dnetlib/dhp/actionmanager/whole_programme.json.gz").getPath(), "-outputPath", workingDir.toString() + "/preparedProgramme" }); diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/SparkUpdateProjectTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/SparkUpdateProjectTest.java index d488848429..c41daf2ccb 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/SparkUpdateProjectTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/SparkUpdateProjectTest.java @@ -9,8 +9,6 @@ import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.sql.Dataset; -import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SparkSession; import org.junit.jupiter.api.AfterAll; import org.junit.jupiter.api.Assertions; @@ -72,7 +70,7 @@ public class SparkUpdateProjectTest { "-isSparkSessionManaged", Boolean.FALSE.toString(), "-programmePath", - getClass().getResource("/eu/dnetlib/dhp/actionmanager/preparedProgramme_whole.json").getPath(), + getClass().getResource("/eu/dnetlib/dhp/actionmanager/preparedProgramme_whole.json.gz").getPath(), "-projectPath", getClass().getResource("/eu/dnetlib/dhp/actionmanager/projects_subset.json").getPath(), "-outputPath", @@ -85,7 +83,7 @@ public class SparkUpdateProjectTest { .textFile(workingDir.toString() + "/actionSet") .map(item -> OBJECT_MAPPER.readValue(item, Project.class)); - Assertions.assertEquals(14, tmp.count()); + Assertions.assertEquals(16, tmp.count()); // Dataset verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(CSVProgramme.class)); // From c0d9e0234050929097896b56a2824a50e262aa9d Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 20 May 2020 10:30:25 +0200 Subject: [PATCH 21/62] zipped test resources that are too big --- .../dhp/actionmanager/project/programme.csv | 25 +++++++++++++++++++ .../dhp/actionmanager/projects_subset.json | 16 ++++++++++++ 2 files changed, 41 insertions(+) diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/project/programme.csv b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/project/programme.csv index e69de29bb2..6a9c855a03 100644 --- a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/project/programme.csv +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/project/programme.csv @@ -0,0 +1,25 @@ +rcn;code;title;shortTitle;language +664331;H2020-EU.3.3.2.;Un approvisionnement en électricité à faible coût et à faibles émissions de carbone;Low-cost, low-carbon energy supply;fr +664355;H2020-EU.3.3.7.;Absorción por el mercado de la innovación energética - explotación del Programa Energía Inteligente - Europa Europe;Market uptake of energy innovation;es +664323;H2020-EU.3.3.1.;Ridurre il consumo di energia e le emissioni di carbonio grazie all'uso intelligente e sostenibile;Reducing energy consumption and carbon footprint;it +664233;H2020-EU.2.3.2.3.;Wsparcie innowacji rynkowych;Supporting market-driven innovation;pl +664199;H2020-EU.2.1.5.1.;Tecnologías para las fábricas del futuro;Technologies for Factories of the Future;es +664235;H2020-EU.3.;PRIORITÉ «Défis de société»;Societal Challenges;fr +664355;H2020-EU.3.3.7.;"Assorbimento di mercato dell'innovazione energetica - iniziative fondate sul programma ""Energia intelligente - Europa""";Market uptake of energy innovation;it +664355;H2020-EU.3.3.7.;"Markteinführung von Energieinnovationen – Aufbau auf ""Intelligente Energie – Europa";Market uptake of energy innovation;de +664235;H2020-EU.3.;"PRIORIDAD ""Retos de la sociedad""";Societal Challenges;es +664231;H2020-EU.2.3.2.2.;Mejorar la capacidad de innovación de las PYME;Enhancing the innovation capacity of SMEs;es +664223;H2020-EU.2.3.;LIDERAZGO INDUSTRIAL - Innovación en la pequeña y mediana empresa;Innovation in SMEs;es +664323;H2020-EU.3.3.1.;Réduire la consommation d'énergie et l'empreinte carbone en utilisant l'énergie de manière intelligente et durable;Reducing energy consumption and carbon footprint;fr +664323;H2020-EU.3.3.1.;Reducir el consumo de energía y la huella de carbono mediante un uso inteligente y sostenible;Reducing energy consumption and carbon footprint;es +664215;H2020-EU.2.1.6.4.;Beitrag der europäischen Forschung zu internationalen Weltraumpartnerschaften;Research in support of international space partnerships;de +664213;H2020-EU.2.1.6.3.;Permettere lo sfruttamento dei dati spaziali;;it +664213;H2020-EU.2.1.6.3.;Permettre l'exploitation des données spatiales;Enabling exploitation of space data;fr +664231;H2020-EU.2.3.2.2.;Zwiększenie zdolności MŚP pod względem innowacji;Enhancing the innovation capacity of SMEs;pl +664231;H2020-EU.2.3.2.2.;Rafforzare la capacità di innovazione delle PMI;Enhancing the innovation capacity of SMEs;it +664213;H2020-EU.2.1.6.3.;Grundlagen für die Nutzung von Weltraumdaten;Enabling exploitation of space data;de +664211;H2020-EU.2.1.6.2.;Favorecer los avances en las tecnologías espaciales;Enabling advances in space technology;es +664209;H2020-EU.2.1.6.1.;Assurer la compétitivité et l'indépendance de l'Europe et promouvoir l'innovation dans le secteur spatial européen;Competitiveness, non-dependence and innovation;fr +664231;H2020-EU.2.3.2.2.;Renforcement de la capacité d'innovation des PME;Enhancing the innovation capacity of SMEs;fr +664203;H2020-EU.2.1.5.3.;Tecnologías sostenibles, eficientes en su utilización de recursos y de baja emisión de carbono en las industrias de transformación de gran consumo energético;Sustainable, resource-efficient and low-carbon technologies in energy-intensive process industries;es +664103;H2020-EU.1.2.1.;FET Open;FET Open;es \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/projects_subset.json b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/projects_subset.json index e69de29bb2..b8805b2db5 100644 --- a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/projects_subset.json +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/projects_subset.json @@ -0,0 +1,16 @@ +{"rcn":"229267","id":"894593","acronym":"ICARUS","status":"SIGNED","programme":"H2020-EU.3.4.7.","topics":"SESAR-ER4-31-2019","frameworkProgramme":"H2020","title":"INTEGRATED COMMON ALTITUDE REFERENCE SYSTEM FOR U-SPACE","startDate":"2020-05-01","endDate":"2022-07-31","projectUrl":"","objective":"ICARUS project proposes an innovative solution to the challenge of the Common Altitude Reference inside VLL airspaces with the definition of a new U-space service and its validation in a real operational environment. In manned aviation, the methods of determining the altitude of an aircraft are based on pressure altitude difference measurements (e.g. QFE, QNH and FL) referred to a common datum. \nThe UA flights superimpose a new challenge, since a small drone may take off and land almost from everywhere, hence reducing the original significance of QFE settings, introduced on behalf of manned pilots to display on the altimeter the 0-height at touchdown on the local runway. In fact, the possibility for n drones to take off at n different places would generate a series of n different QFE corresponding to different heights of ground pressures referred to the take-off “Home points”. Therefore for a large number drones, new methodologies and procedures shall be put in place. The ICARUS defines a new U-space U3 service tightly coupled with the interface of the existing U-space services (e.g. Tracking, and Flight Planning services). The users of ICARUS service shall be remote pilots competent to fly in BVLOS in the specific category of UAS operations and ultralight GA pilots potentially sharing the same VLL airspace. \nThe ICARUS proposed approach foresees the realization of DTM service embedded in an Application Program Interface (API) that can be queried by UAS pilot/operator (or by drone itself) based on the actual positioning of the UA along its trajectory, computed by the (E)GNSS receiver. The output of the DTM service would provide information on distance from ground/obstacles in combination with the common altitude reference.\nAccuracy, continuity, integrity and availability requirements for GNSS-based altimetry together with accuracy and resolution requirements of the DTM to be provided by ICARUS service are key topics of the study.","totalCost":"1385286,25","ecMaxContribution":"1144587,5","call":"H2020-SESAR-2019-2","fundingScheme":"SESAR-RIA","coordinator":"E-GEOS SPA","coordinatorCountry":"IT","participants":"TOPVIEW SRL;TELESPAZIO SPA;DRONERADAR SP Z O.O.;EUROCONTROL - EUROPEAN ORGANISATION FOR THE SAFETY OF AIR NAVIGATION;EUROUSC ESPANA SL;POLITECNICO DI MILANO;UNIVERSITA DEGLI STUDI DI ROMA LA SAPIENZA","participantCountries":"IT;PL;BE;ES","subjects":""} +{"rcn":"229284","id":"897004","acronym":"ISLand","status":"SIGNED","programme":"H2020-EU.1.3.2.","topics":"MSCA-IF-2019","frameworkProgramme":"H2020","title":"Isolation and Segregation Landscape. Archaeology of quarantine in the Indian Ocean World","startDate":"2020-11-01","endDate":"2023-10-31","projectUrl":"","objective":"The proposed research presents an experimental and completely novel investigation within the historical archaeology,\napplied to isolated contexts. The main objective of ISLand is to provide a new way of thinking about human interactions\nwithin colonial empires and bringing colonial studies into dialogue with medical history and the emerging concept of\nhealthscaping. It seeks to do so by studying quarantine facilities in the Indian Ocean World during the long nineteenth\ncentury, a crucial period for the history of European empires in that region and a flashpoint for the conceptualization of\nmodern public health. Quarantine, traditionally viewed as merely a mechanism for the control of disease, will be analyzed as\nthe outward material response to important changes taking place socially, ecologically, and politically at the time.\nThe project is a part of an international, interdisciplinary effort, combining history, archaeology, and anthropology. The\nresearcher will tap numerous archival sources and archaeological data from selected sites, examine them through social and\nspatial analysis, and systematically analyze a test case in Mauritius through the most innovative methods that target\nlandscape and standing archaeology.\nThe broader impacts of ISLand have relevance for current European approaches to the migration crisis, where the threat of\ndisease has been ignited as a potentially debilitating consequence of immigration from extra-European countries. The\ntraining-through-research project at the Stanford University, the top institution where acquiring knowledge and skills in\nhistorical archaeology, will allow the applicant to develop into a position of professional maturity with a specific\ninterdisciplinary set of skills. With the support of the host institutions in EU, the researcher will promote historical archaeology\nin European academy, stimulating new approaches in usual archaeological research and an interdisciplinary approach with\ncultural anthropology.","totalCost":"253052,16","ecMaxContribution":"253052,16","call":"H2020-MSCA-IF-2019","fundingScheme":"MSCA-IF-GF","coordinator":"UNIVERSITEIT VAN AMSTERDAM","coordinatorCountry":"NL","participants":"","participantCountries":"","subjects":""} +{"rcn":"229281","id":"896300","acronym":"STRETCH","status":"SIGNED","programme":"H2020-EU.1.3.2.","topics":"MSCA-IF-2019","frameworkProgramme":"H2020","title":"Smart Textiles for RETrofitting and Monitoring of Cultural Heritage Buildings","startDate":"2020-09-01","endDate":"2022-08-31","projectUrl":"","objective":"This project aims to develop novel techniques using smart multifunctional materials for the combined seismic-plus-energy retrofitting, and Structural Health Monitoring (SHM) of the European cultural heritage buildings (CHB). The need for upgrading the existing old and CHB is becoming increasingly important for the EU countries, due to: (1) their poor structural performance during recent earthquakes (e.g. Italy, Greece) or other natural hazards (e.g. extreme weather conditions) that have resulted in significant economic losses, and loss of human lives; and (2) their low energy performance which increases significantly their energy consumption (buildings are responsible for 40% of EU energy consumption). Moreover, the SHM of the existing buildings is crucial for assessing continuously their structural integrity and thus to provide information for planning cost effective and sustainable maintenance decisions. Since replacing the old buildings with new is not financially feasible, and even it is not allowed for CHB, their lifetime extension requires considering simultaneously both structural and energy retrofitting. It is noted that the annual cost of repair and maintenance of existing European building stock is estimated to be about 50% of the total construction budget, currently standing at more than €300 billion. To achieve cost effectiveness, STRETCH explores a novel approach, which integrates technical textile reinforcement with thermal insulation systems and strain sensors to provide simultaneous structural-plus-energy retrofitting combined with SHM, tailored for masonry cultural heritage building envelopes. The effectiveness of the proposed retrofitting system will be validated experimentally and analytically. Moreover, draft guidelines and recommendations for determining future research on the use of smart composite materials for the concurrent retrofitting (structural-plus-energy) and SHM of the existing cultural heritage buildings envelopes will be proposed.","totalCost":"183473,28","ecMaxContribution":"183473,28","call":"H2020-MSCA-IF-2019","fundingScheme":"MSCA-IF-EF-ST","coordinator":"JRC -JOINT RESEARCH CENTRE- EUROPEAN COMMISSION","coordinatorCountry":"BE","participants":"","participantCountries":"","subjects":""} +{"rcn":"229265","id":"892890","acronym":"RhythmicPrediction","status":"SIGNED","programme":"H2020-EU.1.3.2.","topics":"MSCA-IF-2019","frameworkProgramme":"H2020","title":"Rhythmic prediction in speech perception: are our brain waves in sync with our native language?","startDate":"2021-01-01","endDate":"2022-12-31","projectUrl":"","objective":"Speech has rhythmic properties that widely differ across languages. When we listen to foreign languages, we may perceive them to be more musical, or rather more rap-like than our own. Even if we are unaware of it, the rhythm and melody of language, i.e. prosody, reflects its linguistic structure. On the one hand, prosody emphasizes content words and new information with stress and accents. On the other hand, it is aligned to phrase edges, marking them with boundary tones. Prosody hence helps the listener to focus on important words and to chunk sentences into phrases, and phrases into words. In fact, prosody is even used predictively, for instance to time the onset of the next word, the next piece of new information, or the total remaining length of the utterance, so the listener can seamlessly start their own speaking turn. \nSo, the listener, or rather their brain, is actively predicting when important speech events will happen, using prosody. How prosodic rhythms are exploited to predict speech timing, however, is unclear. No link between prosody and neural predictive processing has yet been empirically made. One hypothesis is that rhythm, such as the alternation of stressed and unstressed syllables, helps listeners time their attention. Similar behavior is best captured by the notion of an internal oscillator which can be set straight by attentional spikes. While neuroscientific evidence for the relation of neural oscillators to speech processing is starting to emerge, no link to the use of prosody nor predictive listening exists, yet. Furthermore, it is still unknown how native language knowledge affects cortical oscillations, and how oscillations are affected by cross-linguistic differences in rhythmic structure. The current project combines the standing knowledge of prosodic typology with the recent advances in neuroscience on cortical oscillations, to investigate the role of internal oscillators on native prosody perception, and active speech prediction.","totalCost":"191149,44","ecMaxContribution":"191149,44","call":"H2020-MSCA-IF-2019","fundingScheme":"MSCA-IF-EF-ST","coordinator":"UNIVERSITE DE GENEVE","coordinatorCountry":"CH","participants":"","participantCountries":"","subjects":""} +{"rcn":"229235","id":"886828","acronym":"ASAP","status":"SIGNED","programme":"H2020-EU.1.3.2.","topics":"MSCA-IF-2019","frameworkProgramme":"H2020","title":"Advanced Solutions for Asphalt Pavements","startDate":"2021-09-01","endDate":"2023-08-31","projectUrl":"","objective":"The Advanced Solutions for Asphalt Pavements (ASAP) project involves the development of a unique road paving technology which will use a bio-bitumen rejuvenator to rejuvenate aged asphalt bitumen. This technology will help to extend the lifespan of asphalt pavements (roads) and will reduce the environmental and economic impact of roads and road maintenance processes. Recycling and self-healing processes will replace fossil fuel dependent technology. Self-healing will involve rejuvenating aged asphalt bitumen using a bio-rejuvenator developed using microalgae oils (rejuvenating bio-oil). Microalgae has been selected because of its fast growth, versatility and ability to survive within hostile environments, such as wastewater. \n\nASAP will utilise microalgae, cultivated within the wastewater treatment process, as a source of the rejuvenating bio-oil. The solvent (Soxhlet) processes will be used to extract the oil from the microalgae. To ensure the efficiency of the oil extraction process, an ultrasonication process will be used to pre-treat the microalgae. The suitability of rejuvenating bio-oil as a replacement for the bitumen rejuvenator (fossil fuel based) will be ascertained via a series of standard bituminous and accelerated tests. A rejuvenator-binder diffusion numerical model will be developed, based on the Delft Lattice concrete diffusion model, to determine the conditions required for rejuvenation to occur and to ascertain the healing rate of the asphalt binder. These parameters will facilitate the selection and optimisation of the asphalt self-healing systems (specifically the amount of bio-oil rejuvenator and time required) to achieve full rejuvenation. \n\nThis novel approach will benchmark the effectiveness of this intervention against existing asphalt design and maintenance processes and assess feasibility. The ASAP project presents an opportunity to revolutionise road design and maintenance processes and reduce its environmental and financial costs.","totalCost":"187572,48","ecMaxContribution":"187572,48","call":"H2020-MSCA-IF-2019","fundingScheme":"MSCA-IF-EF-ST","coordinator":"NEDERLANDSE ORGANISATIE VOOR TOEGEPAST NATUURWETENSCHAPPELIJK ONDERZOEK TNO","coordinatorCountry":"NL","participants":"","participantCountries":"","subjects":""} +{"rcn":null,"id":"886776","acronym":null,"status":null,"programme":"H2020-EU.2.1.4.","topics":null,"frameworkProgramme":"H2020","title":"BIO-Based pESTicides production for sustainable agriculture management plan","startDate":"2020-05-01","endDate":"2023-04-30","projectUrl":"","objective":"The BIOBESTicide project will validate and demonstrate the production of an effective and cost-efficient biopesticide. The demonstration will be based on an innovative bio-based value chain starting from the valorisation of sustainable biomasses, i.e. beet pulp and sugar molasses and will exploit the properties of the oomycete Pythium oligandrum strain I-5180 to increase natural plant defenses, to produce an highly effective and eco-friendly biopesticide solution for vine plants protection. \nBIOVITIS, the project coordinator, has developed, at laboratory level (TRL4), an effective method to biocontrol one of the major causes of worldwide vineyards destruction, the Grapevine Trunk Diseases (GTDs). The protection system is based on the oomycete Pythium oligandrum strain I-5180 that, at applied at optimal time and concentration, colonises the root of vines and stimulates the natural plant defences against GTDs, providing a protection that ranges between 40% and 60%. \nBIOBESTicide project will respond to the increasing demands for innovative solutions for crop protection agents, transferring the technology to a DEMO Plant able to produce more than 10 T of a high-quality oomycete-based biopesticide product per year (TRL7). \nThe BIOBESTicide project will validate the efficiency of the formulated product on vineyards of different geographical areas.\nTo assure the safety of products under both health and environmental points of view, a full and complete approval dossier for Pythium oligandrum strain I-5180 will be submitted in all the European countries. \nA Life Cycle Sustainability Assessment (LCSA) will be conducted to assess the environmental, economic and social impacts of the developed products.\nThe adoption of the effective and cost-efficient biopesticide will have significant impacts with a potential ROI of 30 % in just 5 years and a total EBITDA of more than € 6,400,000.","totalCost":"4402772,5","ecMaxContribution":"3069653","call":"H2020-BBI-JTI-2019","fundingScheme":"BBI-IA-DEMO","coordinator":"BIOVITIS","coordinatorCountry":"FR","participants":"MERCIER FRERES SARL;FUNDACION TECNALIA RESEARCH & INNOVATION;LAMBERTI SPA;EURION CONSULTING;CIAOTECH Srl;STOWARZYSZENIE ZACHODNIOPOMORSKI KLASTER CHEMICZNY ZIELONA CHEMIA;NORDZUCKER AG;INSTITUT NATIONAL DE RECHERCHE POUR L'AGRICULTURE, L'ALIMENTATION ET L'ENVIRONNEMENT;INSTITUT FRANCAIS DE LA VIGNE ET DU VIN","participantCountries":"FR;ES;IT;PL;DE","subjects":""} +{"rcn":null,"id":"886776","acronym":null,"status":null,"programme":"H2020-EU.3.2.6.","topics":"BBI-2019-SO3-D4","frameworkProgramme":"H2020","title":"BIO-Based pESTicides production for sustainable agriculture management plan","startDate":"2020-05-01","endDate":"2023-04-30","projectUrl":"","objective":"The BIOBESTicide project will validate and demonstrate the production of an effective and cost-efficient biopesticide. The demonstration will be based on an innovative bio-based value chain starting from the valorisation of sustainable biomasses, i.e. beet pulp and sugar molasses and will exploit the properties of the oomycete Pythium oligandrum strain I-5180 to increase natural plant defenses, to produce an highly effective and eco-friendly biopesticide solution for vine plants protection. \nBIOVITIS, the project coordinator, has developed, at laboratory level (TRL4), an effective method to biocontrol one of the major causes of worldwide vineyards destruction, the Grapevine Trunk Diseases (GTDs). The protection system is based on the oomycete Pythium oligandrum strain I-5180 that, at applied at optimal time and concentration, colonises the root of vines and stimulates the natural plant defences against GTDs, providing a protection that ranges between 40% and 60%. \nBIOBESTicide project will respond to the increasing demands for innovative solutions for crop protection agents, transferring the technology to a DEMO Plant able to produce more than 10 T of a high-quality oomycete-based biopesticide product per year (TRL7). \nThe BIOBESTicide project will validate the efficiency of the formulated product on vineyards of different geographical areas.\nTo assure the safety of products under both health and environmental points of view, a full and complete approval dossier for Pythium oligandrum strain I-5180 will be submitted in all the European countries. \nA Life Cycle Sustainability Assessment (LCSA) will be conducted to assess the environmental, economic and social impacts of the developed products.\nThe adoption of the effective and cost-efficient biopesticide will have significant impacts with a potential ROI of 30 % in just 5 years and a total EBITDA of more than € 6,400,000.","totalCost":"4402772,5","ecMaxContribution":"3069653","call":"H2020-BBI-JTI-2019","fundingScheme":"BBI-IA-DEMO","coordinator":"BIOVITIS","coordinatorCountry":"FR","participants":"MERCIER FRERES SARL;FUNDACION TECNALIA RESEARCH & INNOVATION;LAMBERTI SPA;EURION CONSULTING;CIAOTECH Srl;STOWARZYSZENIE ZACHODNIOPOMORSKI KLASTER CHEMICZNY ZIELONA CHEMIA;NORDZUCKER AG;INSTITUT NATIONAL DE RECHERCHE POUR L'AGRICULTURE, L'ALIMENTATION ET L'ENVIRONNEMENT;INSTITUT FRANCAIS DE LA VIGNE ET DU VIN","participantCountries":"FR;ES;IT;PL;DE","subjects":""} +{"rcn":"229276","id":"895426","acronym":"DisMoBoH","status":"SIGNED","programme":"H2020-EU.1.3.2.","topics":"MSCA-IF-2019","frameworkProgramme":"H2020","title":"Dissecting the molecular building principles of locally formed transcriptional hubs","startDate":"2021-09-01","endDate":"2023-08-31","projectUrl":"","objective":"Numerous DNA variants have already been identified that modulate inter-individual molecular traits – most prominently gene expression. However, since finding mechanistic interpretations relating genotype to phenotype has proven challenging, the focus has shifted to higher-order regulatory features, i.e. chromatin accessibility, transcription factor (TF) binding and 3D chromatin interactions. This revealed at least two enhancer types: “lead” enhancers in which the presence of genetic variants modulates the activity of entire chromatin domains, and “dependent” ones in which variants induce subtle changes, affecting DNA accessibility, but not transcription. Although cell type-specific TFs are likely important, it remains unclear which sequence features are required to establish such enhancer hierarchies, and under which circumstances genetic variation results in altered enhancer-promoter contacts and differential gene expression. Here, we propose to investigate the molecular mechanisms that link DNA variation to TF binding, chromatin topology, and gene expression response. We will leverage data on enhancer hierarchy and sequence-specific TF binding to identify the sequence signatures that define “lead” enhancers. The results will guide the design of a synthetic locus that serves as an in vivo platform to systematically vary the building blocks of local transcriptional units: i) DNA sequence – including variations in TF binding site affinity and syntax, ii) molecular interactions between TFs, and iii) chromatin conformation. To validate our findings, we will perform optical reconstruction of chromatin architecture for a select number of DNA variants. By simultaneously perturbing co-dependent features, this proposal will provide novel mechanistic insights into the formation of local transcriptional hubs.","totalCost":"191149,44","ecMaxContribution":"191149,44","call":"H2020-MSCA-IF-2019","fundingScheme":"MSCA-IF-EF-RI","coordinator":"ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE","coordinatorCountry":"CH","participants":"","participantCountries":"","subjects":""} +{"rcn":"229288","id":"898218","acronym":"devUTRs","status":"SIGNED","programme":"H2020-EU.1.3.2.","topics":"MSCA-IF-2019","frameworkProgramme":"H2020","title":"Uncovering the roles of 5′UTRs in translational control during early zebrafish development","startDate":"2021-09-01","endDate":"2023-08-31","projectUrl":"","objective":"Following fertilisation, metazoan embryos are transcriptionally silent, and embryogenesis is controlled by maternally deposited factors. Developmental progression requires the synthesis of new mRNAs and proteins in a coordinated fashion. Many posttranscriptional mechanisms regulate the fate of maternal mRNAs, but it is less understood how translational control shapes early embryogenesis. In eukaryotes, translation starts at the mRNA 5′ end, consisting of the 5′ cap and 5′ untranslated region (UTR). Protein synthesis is primarily regulated at the translation initiation step by elements within the 5′UTR. However, the role of 5′UTRs in regulating the dynamics of mRNA translation during vertebrate embryogenesis remains unexplored. For example, all vertebrate ribosomal protein (RP) mRNAs harbor a conserved terminal oligopyrimidine tract (TOP) in their 5′UTR. RP levels must be tightly controlled to ensure proper organismal development, but if and how the TOP motif mediates RP mRNA translational regulation during embryogenesis is unclear. Overall, we lack a systematic understanding of the regulatory information contained in 5′UTRs. In this work, I aim to uncover the 5′UTR in vivo rules for mRNA translational regulation during zebrafish embryogenesis. I propose to apply imaging and biochemical approaches to characterise the role of the TOP motif in RP mRNA translational regulation during embryogenesis and identify the trans-acting factor(s) that bind(s) to it (Aim 1). To systematically assess the contribution of 5′UTRs to mRNA translational regulation during zebrafish embryogenesis, I will couple a massively parallel reporter assay of 5′UTRs to polysome profiling (Aim 2). By integrating the translational behaviour of 5′UTR reporters throughout embryogenesis with sequence-based regression models, I anticipate to uncover novel cis-regulatory elements in 5′UTRs with developmental roles.","totalCost":"191149,44","ecMaxContribution":"191149,44","call":"H2020-MSCA-IF-2019","fundingScheme":"MSCA-IF-EF-ST","coordinator":"UNIVERSITAT BASEL","coordinatorCountry":"CH","participants":"","participantCountries":"","subjects":""} +{"rcn":"229261","id":"893787","acronym":"HOLYHOST","status":"SIGNED","programme":"H2020-EU.1.3.2.","topics":"MSCA-IF-2019","frameworkProgramme":"H2020","title":"Welfare and Hosting buildings in the “Holy Land” between the 4th and the 7th c. AD","startDate":"2020-10-01","endDate":"2022-09-30","projectUrl":"","objective":"Between the 4th and the 7th century AD, many hospices dedicated to the poor, elderly, strangers and travelers were built in the countryside, along roads, around and inside cities. They were commissioned by the Church, rich pious men and women concerned by the redeem of their sins, as well as emperors who saw this as a guarantee of social stability. Welfare is thus an important phenomena of Late Antiquity, abundantly mentioned by ancient literary sources and inscriptions, particularly in the eastern part of the Empire. However, the buildings that provided shelter and care to the needy have not yet received sufficient attention from archaeologists. Except for buildings which were identified by their inventors as hostels dedicated to pilgrims, they are still invisible in the field. \nThe aim of the HOLYHOST research project is to bring this social history’s main topic on the field of archaeology. It will address the welfare issue through the archaeological and architectural survey and study of Ancient welfare and hosting establishments’ remains, in the Holy Land (Palestine and Jordan) and around. This work will contribute to a better understanding of the practices linked to hospitality, welfare, accommodation and care in Antiquity. Moreover, such establishments served as models for medieval and modern Islamic, Jewish and Christian waqf institutions (religious endowment), and welfare continues to be highly relevant nowadays, through issues still at the heart of contemporary challenges debated in Europe: poverty, social exclusion, migrant crisis, principle of reception and hospitality. This interdisciplinary and diachronic research project will thus offer many new research perspectives, in terms of history of architecture, evolution of care practices, social and political regulations.","totalCost":"196707,84","ecMaxContribution":"196707,84","call":"H2020-MSCA-IF-2019","fundingScheme":"MSCA-IF-EF-ST","coordinator":"UNIVERSITE PARIS I PANTHEON-SORBONNE","coordinatorCountry":"FR","participants":"","participantCountries":"","subjects":""} +{"rcn":"229282","id":"896189","acronym":"MICADO","status":"SIGNED","programme":"H2020-EU.1.3.2.","topics":"MSCA-IF-2019","frameworkProgramme":"H2020","title":"Microbial contribution to continental wetland carbon budget","startDate":"2021-01-04","endDate":"2023-01-03","projectUrl":"","objective":"Continental wetlands are major carbon dioxide sinks but the second largest source of methane. Monitoring of wetland methane emissions revealed large inter-site variability that is hard to explain in the framework of current biogeochemical theories. Methane production in wetlands is an anaerobic microbial driven process involving a complex set of microbial metabolisms depending on the availability of (i) energy (via the presence of specific redox couples), (ii) organic substrates and (iii) specific microbial communities. To understand the complexity of microbial drivers on wetland methane emissions and quantify their contribution, the MICADO project will set up a multidisciplinary approach linking isotope organic geochemistry and environmental microbiology to assess microbial functioning in situ. As an organic geochemist I have developed an innovative approach to trace in situ microbial activity via compound specific carbon isotope analysis of microbe macromolecules and organic metabolites. The host institution is a leader in France in environmental microbiology and biogeochemistry developing high-throughput metagenomics and microbial rate assessments, for which I will be trained during the MICADO project. These techniques are highly complementary and combined they will provide a comprehensive knowledge on microbial metabolisms involved in organic matter degradation encompassing their complexity and interactions. This will revisit the relationships between organic substrate availability and microbial communities and will contribute at estimating the impact of microbial activity on wetland methane emissions. This project will give me the opportunity to acquire fundamental knowledge and to develop original lines of research that will consolidate my position as an independent scientist in biogeochemistry.","totalCost":"196707,84","ecMaxContribution":"196707,84","call":"H2020-MSCA-IF-2019","fundingScheme":"MSCA-IF-EF-ST","coordinator":"CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE CNRS","coordinatorCountry":"FR","participants":"","participantCountries":"","subjects":""} +{"rcn":"229249","id":"891624","acronym":"CuTAN","status":"SIGNED","programme":"H2020-EU.1.3.2.","topics":"MSCA-IF-2019","frameworkProgramme":"H2020","title":"Copper-Catalyzed Multicomponent Reactions in Tandem Processes for Target Molecule Synthesis","startDate":"2021-02-01","endDate":"2023-01-31","projectUrl":"","objective":"The invention of processes that can form several bonds, stereocentres and rings in a single process is key to a sustainable future in synthetic chemistry. Multicomponent reactions and tandem procedures are two strategies that enable the rapid build-up of molecular complexity from simple reagents. By combining these two strategies into a single procedure, the diversity, complexity and value of products can be further enhanced along with the efficiency and economy of their construction. In this project, Dr Satpathi will develop novel copper-catalyzed multicomponent couplings of unsaturated hydrocarbons (e.g. allenes, enynes) with imines and boron reagents. These procedures will provide high-value amine products with universally high regio-, diastero- and enantiocontrol. The products will bear a variety of synthetic handles, for example, amino, alkynyl/alkenyl, and boryl groups, thus the products are primed for subsequent transformation. Dr Satpathi will exploit this functionality in tandem intramolecular couplings (e.g. intramolecular Suzuki/Buchwald-Hartwig reactions) to provide core cyclic structures of drug molecules and natural products. Thus, through a tandem procedure of; 1) copper-catalyzed borofunctionalization, and; 2) subsequent transition-metal catalyzed cyclization, he will gain efficient access to highly sought-after complex molecules. Overall, the process will provide high-value, chiral, cyclic motifs from abundant, achiral, linear substrates. Finally, Dr Satpathi has identified the phthalide-isoquinoline family of alkaloids as target molecules to display the power of his tandem methodology. Dr Satpathi has devised a novel route, which begins with our tandem multifunctionalization/cyclization reaction, to provide a range of these important alkaloids. The chosen alkaloids are of particular interest as they display a range of bioactivities – for example as natural products, receptor antagonists and on-market drugs.","totalCost":"212933,76","ecMaxContribution":"212933,76","call":"H2020-MSCA-IF-2019","fundingScheme":"MSCA-IF-EF-ST","coordinator":"THE UNIVERSITY OF MANCHESTER","coordinatorCountry":"UK","participants":"","participantCountries":"","subjects":""} +{"rcn":"229239","id":"887259","acronym":"ALEHOOP","status":"SIGNED","programme":"H2020-EU.2.1.4.","topics":"BBI-2019-SO3-D3","frameworkProgramme":"H2020","title":"Biorefineries for the valorisation of macroalgal residual biomass and legume processing by-products to obtain new protein value chains for high-value food and feed applications","startDate":"2020-06-01","endDate":"2024-05-31","projectUrl":"","objective":"ALEHOOP provides the demonstration at pilot scale of both sustainable macroalgae and legume-based biorefineries for the recovery of low-cost dietary proteins from alga-based and plant residual biomass and their validation to meet market requirements of consumers and industry in the food and feed sectors. In these sectors, consumers are demanding affordable functional natural proteins from alternative sources and industry is demanding low-cost bio-based protein formulations with better performance and higher sustainability. \nCurrent protein demand for the 7.3 billion inhabitants of the world is approximately 202 Mt. Due to the rise in meat consumption more proteins are therefore required for animal feeding. To satisfy the current protein demand, Europe imports over 30 Mt of soy from the Americas each year mainly for animal feeding, entailing 95% dependency of EU on imported soy. Current sources of proteins are becoming unsustainable from an economic and environmental perspective for Europe resulting in concerns for sustainability and food security and leading to search for new alternative proteins. \nALEHOOP addresses the obtaining of proteins from green macroalgal blooms, brown seaweed by-products from algae processors and legume processing by-products (peas, lupines, beans and lentils) as alternative protein sources for animal feeding (case of green seaweed) and food applications (case of brown seaweed and legume by-products), since they are low cost and under-exploited biomass that do not compete with traditional food crops for space and resources. This will reduce EU´s dependency on protein imports and contribute to our raw material security. The new proteins will be validated in foods for elderly, sporty and overweight people, vegetarians and healthy consumers as well as for animal feed creating cross-sectorial interconnection between these value chains and supporting the projected business plan.","totalCost":"6718370","ecMaxContribution":"5140274,41","call":"H2020-BBI-JTI-2019","fundingScheme":"BBI-IA-DEMO","coordinator":"CONTACTICA S.L.","coordinatorCountry":"ES","participants":"CENTIV GMBH;ALGINOR ASA;FUNDACION TECNALIA RESEARCH & INNOVATION;INDUKERN,S.A.;ASOCIACION NACIONAL DE FABRICANTES DE CONSERVAS DE PESCADOS Y MARISCOS-CENTRO TECNICO NACIONAL DE CONSERVACION DE PRODUCTOS DE LA PESCA;BIOZOON GMBH;EIGEN VERMOGEN VAN HET INSTITUUT VOOR LANDBOUW- EN VISSERIJONDERZOEK;BIOSURYA SL;VYZKUMNY USTAV VETERINARNIHO LEKARSTVI;NUTRITION SCIENCES;TECHNOLOGICAL UNIVERSITY DUBLIN;GARLAN, S.COOP.;ISANATUR SPAIN SL;UNIVERSIDAD DE VIGO;UNIVERSIDAD DE CADIZ","participantCountries":"DE;NO;ES;BE;CZ;IE","subjects":""} +{"rcn":"229239","id":"887259","acronym":"ALEHOOP","status":"SIGNED","programme":"H2020-EU.3.2.6.","topics":"BBI-2019-SO3-D3","frameworkProgramme":"H2020","title":"Biorefineries for the valorisation of macroalgal residual biomass and legume processing by-products to obtain new protein value chains for high-value food and feed applications","startDate":"2020-06-01","endDate":"2024-05-31","projectUrl":"","objective":"ALEHOOP provides the demonstration at pilot scale of both sustainable macroalgae and legume-based biorefineries for the recovery of low-cost dietary proteins from alga-based and plant residual biomass and their validation to meet market requirements of consumers and industry in the food and feed sectors. In these sectors, consumers are demanding affordable functional natural proteins from alternative sources and industry is demanding low-cost bio-based protein formulations with better performance and higher sustainability. \nCurrent protein demand for the 7.3 billion inhabitants of the world is approximately 202 Mt. Due to the rise in meat consumption more proteins are therefore required for animal feeding. To satisfy the current protein demand, Europe imports over 30 Mt of soy from the Americas each year mainly for animal feeding, entailing 95% dependency of EU on imported soy. Current sources of proteins are becoming unsustainable from an economic and environmental perspective for Europe resulting in concerns for sustainability and food security and leading to search for new alternative proteins. \nALEHOOP addresses the obtaining of proteins from green macroalgal blooms, brown seaweed by-products from algae processors and legume processing by-products (peas, lupines, beans and lentils) as alternative protein sources for animal feeding (case of green seaweed) and food applications (case of brown seaweed and legume by-products), since they are low cost and under-exploited biomass that do not compete with traditional food crops for space and resources. This will reduce EU´s dependency on protein imports and contribute to our raw material security. The new proteins will be validated in foods for elderly, sporty and overweight people, vegetarians and healthy consumers as well as for animal feed creating cross-sectorial interconnection between these value chains and supporting the projected business plan.","totalCost":"6718370","ecMaxContribution":"5140274,41","call":"H2020-BBI-JTI-2019","fundingScheme":"BBI-IA-DEMO","coordinator":"CONTACTICA S.L.","coordinatorCountry":"ES","participants":"CENTIV GMBH;ALGINOR ASA;FUNDACION TECNALIA RESEARCH & INNOVATION;INDUKERN,S.A.;ASOCIACION NACIONAL DE FABRICANTES DE CONSERVAS DE PESCADOS Y MARISCOS-CENTRO TECNICO NACIONAL DE CONSERVACION DE PRODUCTOS DE LA PESCA;BIOZOON GMBH;EIGEN VERMOGEN VAN HET INSTITUUT VOOR LANDBOUW- EN VISSERIJONDERZOEK;BIOSURYA SL;VYZKUMNY USTAV VETERINARNIHO LEKARSTVI;NUTRITION SCIENCES;TECHNOLOGICAL UNIVERSITY DUBLIN;GARLAN, S.COOP.;ISANATUR SPAIN SL;UNIVERSIDAD DE VIGO;UNIVERSIDAD DE CADIZ","participantCountries":"DE;NO;ES;BE;CZ;IE","subjects":""} +{"rcn":"229258","id":"892834","acronym":"DENVPOC","status":"SIGNED","programme":"H2020-EU.1.3.2.","topics":"MSCA-IF-2019","frameworkProgramme":"H2020","title":"qPCR Microfluidics point-of-care platform for dengue diagnosis","startDate":"2020-05-18","endDate":"2022-05-17","projectUrl":"","objective":"As a result of Global climate change and fast urbanization, global outbreaks of Dengue (DENV)/ Zika(ZIKV)/Chikungunya(CHIKV) virus have the potential to occur. The most common pathway of these infections in humans is through the female Aedes mosquito vector. DENV is an exanthematous febrile disease with varied clinical manifestations and progressions . Due to similarities in symptoms between DENV and ZIKV and CHIKV, it is difficult to make a differential diagnosis, impeding appropriate, timely medical intervention. Furthermore, cross-reactivity with ZIKV, which was recently related to microcephaly, is a serious issue. In 2016, in Brazil alone, there were 4180 microcephaly cases reported instead of 163 cases, more in line with yearly expected projections , , Thus, the sooner an accurate diagnostic which differentiates DENV from the other manifestations is critical; most especially at the early stages of the infection, to have a reliable diagnosis in pregnant women. In 2016, the OMS emergency committee declared that the outbreaks and the potentially resultant neurological disorders in Brazil were an important international state of emergency in public health, as a result of the associated secondary effects; these diseases became a Global concern. This project allows developing a highly and fast Multiplex qPCR POC platform by using FASTGENE technology with a minimal amount of patient serotype. It would reduce the time of analysis (30 to 90’ for a standard) and costs. Additionally, the sample preprocessing and thermalization will shorten real-time PCR amplification time and will be integrated within the microfluidic systems. This platform can result in a commercialized product whereupon a main market target would be pregnant women and people living or traveling through/from outbreak risk areas.","totalCost":"196707,84","ecMaxContribution":"196707,84","call":"H2020-MSCA-IF-2019","fundingScheme":"MSCA-IF-EF-SE","coordinator":"BFORCURE","coordinatorCountry":"FR","participants":"","participantCountries":"","subjects":""} +{"rcn":"229280","id":"895716","acronym":"DoMiCoP","status":"SIGNED","programme":"H2020-EU.1.3.2.","topics":"MSCA-IF-2019","frameworkProgramme":"H2020","title":"The Diffusion of Migration Control Practice. Actors, Processes and Effects.","startDate":"2021-03-01","endDate":"2023-02-28","projectUrl":"","objective":"DoMiCoP develops new understandings and perspectives to study migration control in practice in the European Union by asking one main question: how and why do communities of practice develop and diffuse the knowledge required to put migration control into action? Unlike the nexus between expert knowledge, epistemic communities and policy formulation, the nexus between everyday knowledge, communities of practice and policy implementation has not yet received systematic scholarly attention. My project bridges that gap by focusing on intermediate arenas in which communities of practice take shape most notably the meetings and trainings that gather state and non-state actors involved in putting asylum, detention and removal into practice. By building on field-based methodologies (interviews and participant observations), DoMiCoP sheds ethnographic light on the role that ‘learning from abroad’ plays in the implementation of migration control in the EU. My project’s aim is threefold: 1) Identifying arenas at intermediate levels in which communities of practice take shape; 2) Analysing the communities of practice by focusing on the configurations of actors and organizations involved, the motivations underlying their involvement, the process of knowledge development in interaction, the conflicts and negotiations; 3) Revealing the role of non-state organizations (private for profit and not-for-profit). From a theoretical point of view, this project goes beyond the classical view of the implementation as a test to assess the effectiveness of policy transfers towards an analysis of policy transfer at that level of policy-making. From an empirical point of view, the project expands knowledge about less-studied venues of policy-making and provides original thick descriptions. From a methodological point of view, the project engages with qualitative methods for the study of policy diffusion and aims at responding to their main challenges through participant observation.","totalCost":"163673,28","ecMaxContribution":"163673,28","call":"H2020-MSCA-IF-2019","fundingScheme":"MSCA-IF-EF-ST","coordinator":"EUROPEAN UNIVERSITY INSTITUTE","coordinatorCountry":"IT","participants":"","participantCountries":"","subjects":""} \ No newline at end of file From 3c0eb12d3ea6ea7cb0cd074391e0e5a1d5521658 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 20 May 2020 10:31:05 +0200 Subject: [PATCH 22/62] removed the not zipped files --- .../eu/dnetlib/dhp/actionmanager/preparedProgramme_whole.json | 0 .../resources/eu/dnetlib/dhp/actionmanager/whole_programme.json | 0 2 files changed, 0 insertions(+), 0 deletions(-) delete mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/preparedProgramme_whole.json delete mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/whole_programme.json diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/preparedProgramme_whole.json b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/preparedProgramme_whole.json deleted file mode 100644 index e69de29bb2..0000000000 diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/whole_programme.json b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/whole_programme.json deleted file mode 100644 index e69de29bb2..0000000000 From 67ba4fde57d0bd6763c46cc3aaf09af5c51405e3 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 20 May 2020 13:53:08 +0200 Subject: [PATCH 23/62] added test for prepare projects step --- .../project/PrepareProjectTest.java | 94 ++++++++++++++++++ .../preparedProgramme_whole.json.gz | Bin .../prepared_projects.json} | 0 .../project/projects_subset.json | 0 .../{ => project}/whole_programme.json.gz | Bin 5 files changed, 94 insertions(+) create mode 100644 dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/PrepareProjectTest.java rename dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/{ => project}/preparedProgramme_whole.json.gz (100%) rename dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/{projects_subset.json => project/prepared_projects.json} (100%) create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/project/projects_subset.json rename dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/{ => project}/whole_programme.json.gz (100%) diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/PrepareProjectTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/PrepareProjectTest.java new file mode 100644 index 0000000000..fa9e32fd57 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/PrepareProjectTest.java @@ -0,0 +1,94 @@ + +package eu.dnetlib.dhp.actionmanager.project; + +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.actionmanager.project.csvutils.CSVProgramme; +import eu.dnetlib.dhp.actionmanager.project.csvutils.CSVProject; +import org.apache.commons.io.FileUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; + +public class PrepareProjectTest { + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static final ClassLoader cl = PrepareProjectTest.class + .getClassLoader(); + + private static SparkSession spark; + + private static Path workingDir; + private static final Logger log = LoggerFactory + .getLogger(PrepareProjectTest.class); + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files + .createTempDirectory(PrepareProjectTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(PrepareProjectTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + + spark = SparkSession + .builder() + .appName(PrepareProjectTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + public void numberDistinctProgrammeTest() throws Exception { + PrepareProjects + .main( + new String[] { + "-isSparkSessionManaged", + Boolean.FALSE.toString(), + "-projectPath", + getClass().getResource("/eu/dnetlib/dhp/actionmanager/project/projects_subset.json").getPath(), + "-outputPath", + workingDir.toString() + "/preparedProjects" + }); + + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/preparedProjects") + .map(item -> OBJECT_MAPPER.readValue(item, CSVProject.class)); + + Assertions.assertEquals(20, tmp.count()); + + Dataset verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(CSVProject.class)); + + Assertions.assertEquals(0, verificationDataset.filter("length(id) = 0").count()); + Assertions.assertEquals(0, verificationDataset.filter("length(programme) = 0").count()); + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/preparedProgramme_whole.json.gz b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/project/preparedProgramme_whole.json.gz similarity index 100% rename from dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/preparedProgramme_whole.json.gz rename to dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/project/preparedProgramme_whole.json.gz diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/projects_subset.json b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/project/prepared_projects.json similarity index 100% rename from dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/projects_subset.json rename to dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/project/prepared_projects.json diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/project/projects_subset.json b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/project/projects_subset.json new file mode 100644 index 0000000000..e69de29bb2 diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/whole_programme.json.gz b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/project/whole_programme.json.gz similarity index 100% rename from dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/whole_programme.json.gz rename to dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/project/whole_programme.json.gz From 9079bc1f6125bc687a4d144093c7125651e9176c Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 20 May 2020 13:53:32 +0200 Subject: [PATCH 24/62] - --- .../dhp/actionmanager/project/PrepareProgrammeTest.java | 2 +- .../dhp/actionmanager/project/SparkUpdateProjectTest.java | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/PrepareProgrammeTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/PrepareProgrammeTest.java index e9755c8584..7f890a8a35 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/PrepareProgrammeTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/PrepareProgrammeTest.java @@ -73,7 +73,7 @@ public class PrepareProgrammeTest { "-isSparkSessionManaged", Boolean.FALSE.toString(), "-programmePath", - getClass().getResource("/eu/dnetlib/dhp/actionmanager/whole_programme.json.gz").getPath(), + getClass().getResource("/eu/dnetlib/dhp/actionmanager/project/whole_programme.json.gz").getPath(), "-outputPath", workingDir.toString() + "/preparedProgramme" }); diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/SparkUpdateProjectTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/SparkUpdateProjectTest.java index c41daf2ccb..3e559228f7 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/SparkUpdateProjectTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/SparkUpdateProjectTest.java @@ -70,9 +70,9 @@ public class SparkUpdateProjectTest { "-isSparkSessionManaged", Boolean.FALSE.toString(), "-programmePath", - getClass().getResource("/eu/dnetlib/dhp/actionmanager/preparedProgramme_whole.json.gz").getPath(), + getClass().getResource("/eu/dnetlib/dhp/actionmanager/project/preparedProgramme_whole.json.gz").getPath(), "-projectPath", - getClass().getResource("/eu/dnetlib/dhp/actionmanager/projects_subset.json").getPath(), + getClass().getResource("/eu/dnetlib/dhp/actionmanager/project/prepared_projects.json").getPath(), "-outputPath", workingDir.toString() + "/actionSet" }); From 055eec5a77c52d5f4e1b6ec9788fa9645c800220 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 20 May 2020 13:54:10 +0200 Subject: [PATCH 25/62] added resource for prepare project test --- .../actionmanager/project/projects_subset.json | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/project/projects_subset.json b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/project/projects_subset.json index e69de29bb2..edf83fbc8c 100644 --- a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/project/projects_subset.json +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/project/projects_subset.json @@ -0,0 +1,16 @@ +{"rcn":"229267","id":"894593","acronym":"ICARUS","status":"SIGNED","programme":"H2020-EU.3.4.7.","topics":"SESAR-ER4-31-2019","frameworkProgramme":"H2020","title":"INTEGRATED COMMON ALTITUDE REFERENCE SYSTEM FOR U-SPACE","startDate":"2020-05-01","endDate":"2022-07-31","projectUrl":"","objective":"ICARUS project proposes an innovative solution to the challenge of the Common Altitude Reference inside VLL airspaces with the definition of a new U-space service and its validation in a real operational environment. In manned aviation, the methods of determining the altitude of an aircraft are based on pressure altitude difference measurements (e.g. QFE, QNH and FL) referred to a common datum. \nThe UA flights superimpose a new challenge, since a small drone may take off and land almost from everywhere, hence reducing the original significance of QFE settings, introduced on behalf of manned pilots to display on the altimeter the 0-height at touchdown on the local runway. In fact, the possibility for n drones to take off at n different places would generate a series of n different QFE corresponding to different heights of ground pressures referred to the take-off “Home points”. Therefore for a large number drones, new methodologies and procedures shall be put in place. The ICARUS defines a new U-space U3 service tightly coupled with the interface of the existing U-space services (e.g. Tracking, and Flight Planning services). The users of ICARUS service shall be remote pilots competent to fly in BVLOS in the specific category of UAS operations and ultralight GA pilots potentially sharing the same VLL airspace. \nThe ICARUS proposed approach foresees the realization of DTM service embedded in an Application Program Interface (API) that can be queried by UAS pilot/operator (or by drone itself) based on the actual positioning of the UA along its trajectory, computed by the (E)GNSS receiver. The output of the DTM service would provide information on distance from ground/obstacles in combination with the common altitude reference.\nAccuracy, continuity, integrity and availability requirements for GNSS-based altimetry together with accuracy and resolution requirements of the DTM to be provided by ICARUS service are key topics of the study.","totalCost":"1385286,25","ecMaxContribution":"1144587,5","call":"H2020-SESAR-2019-2","fundingScheme":"SESAR-RIA","coordinator":"E-GEOS SPA","coordinatorCountry":"IT","participants":"TOPVIEW SRL;TELESPAZIO SPA;DRONERADAR SP Z O.O.;EUROCONTROL - EUROPEAN ORGANISATION FOR THE SAFETY OF AIR NAVIGATION;EUROUSC ESPANA SL;POLITECNICO DI MILANO;UNIVERSITA DEGLI STUDI DI ROMA LA SAPIENZA","participantCountries":"IT;PL;BE;ES","subjects":""} +{"rcn":"229284","id":"897004","acronym":"ISLand","status":"SIGNED","programme":"H2020-EU.1.3.2.","topics":"MSCA-IF-2019","frameworkProgramme":"H2020","title":"Isolation and Segregation Landscape. Archaeology of quarantine in the Indian Ocean World","startDate":"2020-11-01","endDate":"2023-10-31","projectUrl":"","objective":"The proposed research presents an experimental and completely novel investigation within the historical archaeology,\napplied to isolated contexts. The main objective of ISLand is to provide a new way of thinking about human interactions\nwithin colonial empires and bringing colonial studies into dialogue with medical history and the emerging concept of\nhealthscaping. It seeks to do so by studying quarantine facilities in the Indian Ocean World during the long nineteenth\ncentury, a crucial period for the history of European empires in that region and a flashpoint for the conceptualization of\nmodern public health. Quarantine, traditionally viewed as merely a mechanism for the control of disease, will be analyzed as\nthe outward material response to important changes taking place socially, ecologically, and politically at the time.\nThe project is a part of an international, interdisciplinary effort, combining history, archaeology, and anthropology. The\nresearcher will tap numerous archival sources and archaeological data from selected sites, examine them through social and\nspatial analysis, and systematically analyze a test case in Mauritius through the most innovative methods that target\nlandscape and standing archaeology.\nThe broader impacts of ISLand have relevance for current European approaches to the migration crisis, where the threat of\ndisease has been ignited as a potentially debilitating consequence of immigration from extra-European countries. The\ntraining-through-research project at the Stanford University, the top institution where acquiring knowledge and skills in\nhistorical archaeology, will allow the applicant to develop into a position of professional maturity with a specific\ninterdisciplinary set of skills. With the support of the host institutions in EU, the researcher will promote historical archaeology\nin European academy, stimulating new approaches in usual archaeological research and an interdisciplinary approach with\ncultural anthropology.","totalCost":"253052,16","ecMaxContribution":"253052,16","call":"H2020-MSCA-IF-2019","fundingScheme":"MSCA-IF-GF","coordinator":"UNIVERSITEIT VAN AMSTERDAM","coordinatorCountry":"NL","participants":"","participantCountries":"","subjects":""} +{"rcn":"229281","id":"896300","acronym":"STRETCH","status":"SIGNED","programme":"H2020-EU.1.3.2.","topics":"MSCA-IF-2019","frameworkProgramme":"H2020","title":"Smart Textiles for RETrofitting and Monitoring of Cultural Heritage Buildings","startDate":"2020-09-01","endDate":"2022-08-31","projectUrl":"","objective":"This project aims to develop novel techniques using smart multifunctional materials for the combined seismic-plus-energy retrofitting, and Structural Health Monitoring (SHM) of the European cultural heritage buildings (CHB). The need for upgrading the existing old and CHB is becoming increasingly important for the EU countries, due to: (1) their poor structural performance during recent earthquakes (e.g. Italy, Greece) or other natural hazards (e.g. extreme weather conditions) that have resulted in significant economic losses, and loss of human lives; and (2) their low energy performance which increases significantly their energy consumption (buildings are responsible for 40% of EU energy consumption). Moreover, the SHM of the existing buildings is crucial for assessing continuously their structural integrity and thus to provide information for planning cost effective and sustainable maintenance decisions. Since replacing the old buildings with new is not financially feasible, and even it is not allowed for CHB, their lifetime extension requires considering simultaneously both structural and energy retrofitting. It is noted that the annual cost of repair and maintenance of existing European building stock is estimated to be about 50% of the total construction budget, currently standing at more than €300 billion. To achieve cost effectiveness, STRETCH explores a novel approach, which integrates technical textile reinforcement with thermal insulation systems and strain sensors to provide simultaneous structural-plus-energy retrofitting combined with SHM, tailored for masonry cultural heritage building envelopes. The effectiveness of the proposed retrofitting system will be validated experimentally and analytically. Moreover, draft guidelines and recommendations for determining future research on the use of smart composite materials for the concurrent retrofitting (structural-plus-energy) and SHM of the existing cultural heritage buildings envelopes will be proposed.","totalCost":"183473,28","ecMaxContribution":"183473,28","call":"H2020-MSCA-IF-2019","fundingScheme":"MSCA-IF-EF-ST","coordinator":"JRC -JOINT RESEARCH CENTRE- EUROPEAN COMMISSION","coordinatorCountry":"BE","participants":"","participantCountries":"","subjects":""} +{"rcn":"229265","id":"892890","acronym":"RhythmicPrediction","status":"SIGNED","programme":"H2020-EU.1.3.2.","topics":"MSCA-IF-2019","frameworkProgramme":"H2020","title":"Rhythmic prediction in speech perception: are our brain waves in sync with our native language?","startDate":"2021-01-01","endDate":"2022-12-31","projectUrl":"","objective":"Speech has rhythmic properties that widely differ across languages. When we listen to foreign languages, we may perceive them to be more musical, or rather more rap-like than our own. Even if we are unaware of it, the rhythm and melody of language, i.e. prosody, reflects its linguistic structure. On the one hand, prosody emphasizes content words and new information with stress and accents. On the other hand, it is aligned to phrase edges, marking them with boundary tones. Prosody hence helps the listener to focus on important words and to chunk sentences into phrases, and phrases into words. In fact, prosody is even used predictively, for instance to time the onset of the next word, the next piece of new information, or the total remaining length of the utterance, so the listener can seamlessly start their own speaking turn. \nSo, the listener, or rather their brain, is actively predicting when important speech events will happen, using prosody. How prosodic rhythms are exploited to predict speech timing, however, is unclear. No link between prosody and neural predictive processing has yet been empirically made. One hypothesis is that rhythm, such as the alternation of stressed and unstressed syllables, helps listeners time their attention. Similar behavior is best captured by the notion of an internal oscillator which can be set straight by attentional spikes. While neuroscientific evidence for the relation of neural oscillators to speech processing is starting to emerge, no link to the use of prosody nor predictive listening exists, yet. Furthermore, it is still unknown how native language knowledge affects cortical oscillations, and how oscillations are affected by cross-linguistic differences in rhythmic structure. The current project combines the standing knowledge of prosodic typology with the recent advances in neuroscience on cortical oscillations, to investigate the role of internal oscillators on native prosody perception, and active speech prediction.","totalCost":"191149,44","ecMaxContribution":"191149,44","call":"H2020-MSCA-IF-2019","fundingScheme":"MSCA-IF-EF-ST","coordinator":"UNIVERSITE DE GENEVE","coordinatorCountry":"CH","participants":"","participantCountries":"","subjects":""} +{"rcn":"229235","id":"886828","acronym":"ASAP","status":"SIGNED","programme":"H2020-EU.1.3.2.","topics":"MSCA-IF-2019","frameworkProgramme":"H2020","title":"Advanced Solutions for Asphalt Pavements","startDate":"2021-09-01","endDate":"2023-08-31","projectUrl":"","objective":"The Advanced Solutions for Asphalt Pavements (ASAP) project involves the development of a unique road paving technology which will use a bio-bitumen rejuvenator to rejuvenate aged asphalt bitumen. This technology will help to extend the lifespan of asphalt pavements (roads) and will reduce the environmental and economic impact of roads and road maintenance processes. Recycling and self-healing processes will replace fossil fuel dependent technology. Self-healing will involve rejuvenating aged asphalt bitumen using a bio-rejuvenator developed using microalgae oils (rejuvenating bio-oil). Microalgae has been selected because of its fast growth, versatility and ability to survive within hostile environments, such as wastewater. \n\nASAP will utilise microalgae, cultivated within the wastewater treatment process, as a source of the rejuvenating bio-oil. The solvent (Soxhlet) processes will be used to extract the oil from the microalgae. To ensure the efficiency of the oil extraction process, an ultrasonication process will be used to pre-treat the microalgae. The suitability of rejuvenating bio-oil as a replacement for the bitumen rejuvenator (fossil fuel based) will be ascertained via a series of standard bituminous and accelerated tests. A rejuvenator-binder diffusion numerical model will be developed, based on the Delft Lattice concrete diffusion model, to determine the conditions required for rejuvenation to occur and to ascertain the healing rate of the asphalt binder. These parameters will facilitate the selection and optimisation of the asphalt self-healing systems (specifically the amount of bio-oil rejuvenator and time required) to achieve full rejuvenation. \n\nThis novel approach will benchmark the effectiveness of this intervention against existing asphalt design and maintenance processes and assess feasibility. The ASAP project presents an opportunity to revolutionise road design and maintenance processes and reduce its environmental and financial costs.","totalCost":"187572,48","ecMaxContribution":"187572,48","call":"H2020-MSCA-IF-2019","fundingScheme":"MSCA-IF-EF-ST","coordinator":"NEDERLANDSE ORGANISATIE VOOR TOEGEPAST NATUURWETENSCHAPPELIJK ONDERZOEK TNO","coordinatorCountry":"NL","participants":"","participantCountries":"","subjects":""} +{"rcn":"229236","id":"886776","acronym":"BIOBESTicide","status":"SIGNED","programme":"H2020-EU.2.1.4.;H2020-EU.3.2.6.","topics":"BBI-2019-SO3-D4","frameworkProgramme":"H2020","title":"BIO-Based pESTicides production for sustainable agriculture management plan","startDate":"2020-05-01","endDate":"2023-04-30","projectUrl":"","objective":"The BIOBESTicide project will validate and demonstrate the production of an effective and cost-efficient biopesticide. The demonstration will be based on an innovative bio-based value chain starting from the valorisation of sustainable biomasses, i.e. beet pulp and sugar molasses and will exploit the properties of the oomycete Pythium oligandrum strain I-5180 to increase natural plant defenses, to produce an highly effective and eco-friendly biopesticide solution for vine plants protection. \nBIOVITIS, the project coordinator, has developed, at laboratory level (TRL4), an effective method to biocontrol one of the major causes of worldwide vineyards destruction, the Grapevine Trunk Diseases (GTDs). The protection system is based on the oomycete Pythium oligandrum strain I-5180 that, at applied at optimal time and concentration, colonises the root of vines and stimulates the natural plant defences against GTDs, providing a protection that ranges between 40% and 60%. \nBIOBESTicide project will respond to the increasing demands for innovative solutions for crop protection agents, transferring the technology to a DEMO Plant able to produce more than 10 T of a high-quality oomycete-based biopesticide product per year (TRL7). \nThe BIOBESTicide project will validate the efficiency of the formulated product on vineyards of different geographical areas.\nTo assure the safety of products under both health and environmental points of view, a full and complete approval dossier for Pythium oligandrum strain I-5180 will be submitted in all the European countries. \nA Life Cycle Sustainability Assessment (LCSA) will be conducted to assess the environmental, economic and social impacts of the developed products.\nThe adoption of the effective and cost-efficient biopesticide will have significant impacts with a potential ROI of 30 % in just 5 years and a total EBITDA of more than € 6,400,000.","totalCost":"4402772,5","ecMaxContribution":"3069653","call":"H2020-BBI-JTI-2019","fundingScheme":"BBI-IA-DEMO","coordinator":"BIOVITIS","coordinatorCountry":"FR","participants":"MERCIER FRERES SARL;FUNDACION TECNALIA RESEARCH & INNOVATION;LAMBERTI SPA;EURION CONSULTING;CIAOTECH Srl;STOWARZYSZENIE ZACHODNIOPOMORSKI KLASTER CHEMICZNY ZIELONA CHEMIA;NORDZUCKER AG;INSTITUT NATIONAL DE RECHERCHE POUR L'AGRICULTURE, L'ALIMENTATION ET L'ENVIRONNEMENT;INSTITUT FRANCAIS DE LA VIGNE ET DU VIN","participantCountries":"FR;ES;IT;PL;DE","subjects":""} +{"rcn":"229276","id":"895426","acronym":"DisMoBoH","status":"SIGNED","programme":"H2020-EU.1.3.2.","topics":"MSCA-IF-2019","frameworkProgramme":"H2020","title":"Dissecting the molecular building principles of locally formed transcriptional hubs","startDate":"2021-09-01","endDate":"2023-08-31","projectUrl":"","objective":"Numerous DNA variants have already been identified that modulate inter-individual molecular traits – most prominently gene expression. However, since finding mechanistic interpretations relating genotype to phenotype has proven challenging, the focus has shifted to higher-order regulatory features, i.e. chromatin accessibility, transcription factor (TF) binding and 3D chromatin interactions. This revealed at least two enhancer types: “lead” enhancers in which the presence of genetic variants modulates the activity of entire chromatin domains, and “dependent” ones in which variants induce subtle changes, affecting DNA accessibility, but not transcription. Although cell type-specific TFs are likely important, it remains unclear which sequence features are required to establish such enhancer hierarchies, and under which circumstances genetic variation results in altered enhancer-promoter contacts and differential gene expression. Here, we propose to investigate the molecular mechanisms that link DNA variation to TF binding, chromatin topology, and gene expression response. We will leverage data on enhancer hierarchy and sequence-specific TF binding to identify the sequence signatures that define “lead” enhancers. The results will guide the design of a synthetic locus that serves as an in vivo platform to systematically vary the building blocks of local transcriptional units: i) DNA sequence – including variations in TF binding site affinity and syntax, ii) molecular interactions between TFs, and iii) chromatin conformation. To validate our findings, we will perform optical reconstruction of chromatin architecture for a select number of DNA variants. By simultaneously perturbing co-dependent features, this proposal will provide novel mechanistic insights into the formation of local transcriptional hubs.","totalCost":"191149,44","ecMaxContribution":"191149,44","call":"H2020-MSCA-IF-2019","fundingScheme":"MSCA-IF-EF-RI","coordinator":"ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE","coordinatorCountry":"CH","participants":"","participantCountries":"","subjects":""} +{"rcn":"229288","id":"898218","acronym":"devUTRs","status":"SIGNED","programme":"H2020-EU.1.3.2.","topics":"MSCA-IF-2019","frameworkProgramme":"H2020","title":"Uncovering the roles of 5′UTRs in translational control during early zebrafish development","startDate":"2021-09-01","endDate":"2023-08-31","projectUrl":"","objective":"Following fertilisation, metazoan embryos are transcriptionally silent, and embryogenesis is controlled by maternally deposited factors. Developmental progression requires the synthesis of new mRNAs and proteins in a coordinated fashion. Many posttranscriptional mechanisms regulate the fate of maternal mRNAs, but it is less understood how translational control shapes early embryogenesis. In eukaryotes, translation starts at the mRNA 5′ end, consisting of the 5′ cap and 5′ untranslated region (UTR). Protein synthesis is primarily regulated at the translation initiation step by elements within the 5′UTR. However, the role of 5′UTRs in regulating the dynamics of mRNA translation during vertebrate embryogenesis remains unexplored. For example, all vertebrate ribosomal protein (RP) mRNAs harbor a conserved terminal oligopyrimidine tract (TOP) in their 5′UTR. RP levels must be tightly controlled to ensure proper organismal development, but if and how the TOP motif mediates RP mRNA translational regulation during embryogenesis is unclear. Overall, we lack a systematic understanding of the regulatory information contained in 5′UTRs. In this work, I aim to uncover the 5′UTR in vivo rules for mRNA translational regulation during zebrafish embryogenesis. I propose to apply imaging and biochemical approaches to characterise the role of the TOP motif in RP mRNA translational regulation during embryogenesis and identify the trans-acting factor(s) that bind(s) to it (Aim 1). To systematically assess the contribution of 5′UTRs to mRNA translational regulation during zebrafish embryogenesis, I will couple a massively parallel reporter assay of 5′UTRs to polysome profiling (Aim 2). By integrating the translational behaviour of 5′UTR reporters throughout embryogenesis with sequence-based regression models, I anticipate to uncover novel cis-regulatory elements in 5′UTRs with developmental roles.","totalCost":"191149,44","ecMaxContribution":"191149,44","call":"H2020-MSCA-IF-2019","fundingScheme":"MSCA-IF-EF-ST","coordinator":"UNIVERSITAT BASEL","coordinatorCountry":"CH","participants":"","participantCountries":"","subjects":""} +{"rcn":"229261","id":"893787","acronym":"HOLYHOST","status":"SIGNED","programme":"H2020-EU.1.3.2.","topics":"MSCA-IF-2019","frameworkProgramme":"H2020","title":"Welfare and Hosting buildings in the “Holy Land” between the 4th and the 7th c. AD","startDate":"2020-10-01","endDate":"2022-09-30","projectUrl":"","objective":"Between the 4th and the 7th century AD, many hospices dedicated to the poor, elderly, strangers and travelers were built in the countryside, along roads, around and inside cities. They were commissioned by the Church, rich pious men and women concerned by the redeem of their sins, as well as emperors who saw this as a guarantee of social stability. Welfare is thus an important phenomena of Late Antiquity, abundantly mentioned by ancient literary sources and inscriptions, particularly in the eastern part of the Empire. However, the buildings that provided shelter and care to the needy have not yet received sufficient attention from archaeologists. Except for buildings which were identified by their inventors as hostels dedicated to pilgrims, they are still invisible in the field. \nThe aim of the HOLYHOST research project is to bring this social history’s main topic on the field of archaeology. It will address the welfare issue through the archaeological and architectural survey and study of Ancient welfare and hosting establishments’ remains, in the Holy Land (Palestine and Jordan) and around. This work will contribute to a better understanding of the practices linked to hospitality, welfare, accommodation and care in Antiquity. Moreover, such establishments served as models for medieval and modern Islamic, Jewish and Christian waqf institutions (religious endowment), and welfare continues to be highly relevant nowadays, through issues still at the heart of contemporary challenges debated in Europe: poverty, social exclusion, migrant crisis, principle of reception and hospitality. This interdisciplinary and diachronic research project will thus offer many new research perspectives, in terms of history of architecture, evolution of care practices, social and political regulations.","totalCost":"196707,84","ecMaxContribution":"196707,84","call":"H2020-MSCA-IF-2019","fundingScheme":"MSCA-IF-EF-ST","coordinator":"UNIVERSITE PARIS I PANTHEON-SORBONNE","coordinatorCountry":"FR","participants":"","participantCountries":"","subjects":""} +{"rcn":"229282","id":"896189","acronym":"MICADO","status":"SIGNED","programme":"H2020-EU.1.3.2.","topics":"MSCA-IF-2019","frameworkProgramme":"H2020","title":"Microbial contribution to continental wetland carbon budget","startDate":"2021-01-04","endDate":"2023-01-03","projectUrl":"","objective":"Continental wetlands are major carbon dioxide sinks but the second largest source of methane. Monitoring of wetland methane emissions revealed large inter-site variability that is hard to explain in the framework of current biogeochemical theories. Methane production in wetlands is an anaerobic microbial driven process involving a complex set of microbial metabolisms depending on the availability of (i) energy (via the presence of specific redox couples), (ii) organic substrates and (iii) specific microbial communities. To understand the complexity of microbial drivers on wetland methane emissions and quantify their contribution, the MICADO project will set up a multidisciplinary approach linking isotope organic geochemistry and environmental microbiology to assess microbial functioning in situ. As an organic geochemist I have developed an innovative approach to trace in situ microbial activity via compound specific carbon isotope analysis of microbe macromolecules and organic metabolites. The host institution is a leader in France in environmental microbiology and biogeochemistry developing high-throughput metagenomics and microbial rate assessments, for which I will be trained during the MICADO project. These techniques are highly complementary and combined they will provide a comprehensive knowledge on microbial metabolisms involved in organic matter degradation encompassing their complexity and interactions. This will revisit the relationships between organic substrate availability and microbial communities and will contribute at estimating the impact of microbial activity on wetland methane emissions. This project will give me the opportunity to acquire fundamental knowledge and to develop original lines of research that will consolidate my position as an independent scientist in biogeochemistry.","totalCost":"196707,84","ecMaxContribution":"196707,84","call":"H2020-MSCA-IF-2019","fundingScheme":"MSCA-IF-EF-ST","coordinator":"CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE CNRS","coordinatorCountry":"FR","participants":"","participantCountries":"","subjects":""} +{"rcn":"229249","id":"891624","acronym":"CuTAN","status":"SIGNED","programme":"H2020-EU.1.3.2.","topics":"MSCA-IF-2019","frameworkProgramme":"H2020","title":"Copper-Catalyzed Multicomponent Reactions in Tandem Processes for Target Molecule Synthesis","startDate":"2021-02-01","endDate":"2023-01-31","projectUrl":"","objective":"The invention of processes that can form several bonds, stereocentres and rings in a single process is key to a sustainable future in synthetic chemistry. Multicomponent reactions and tandem procedures are two strategies that enable the rapid build-up of molecular complexity from simple reagents. By combining these two strategies into a single procedure, the diversity, complexity and value of products can be further enhanced along with the efficiency and economy of their construction. In this project, Dr Satpathi will develop novel copper-catalyzed multicomponent couplings of unsaturated hydrocarbons (e.g. allenes, enynes) with imines and boron reagents. These procedures will provide high-value amine products with universally high regio-, diastero- and enantiocontrol. The products will bear a variety of synthetic handles, for example, amino, alkynyl/alkenyl, and boryl groups, thus the products are primed for subsequent transformation. Dr Satpathi will exploit this functionality in tandem intramolecular couplings (e.g. intramolecular Suzuki/Buchwald-Hartwig reactions) to provide core cyclic structures of drug molecules and natural products. Thus, through a tandem procedure of; 1) copper-catalyzed borofunctionalization, and; 2) subsequent transition-metal catalyzed cyclization, he will gain efficient access to highly sought-after complex molecules. Overall, the process will provide high-value, chiral, cyclic motifs from abundant, achiral, linear substrates. Finally, Dr Satpathi has identified the phthalide-isoquinoline family of alkaloids as target molecules to display the power of his tandem methodology. Dr Satpathi has devised a novel route, which begins with our tandem multifunctionalization/cyclization reaction, to provide a range of these important alkaloids. The chosen alkaloids are of particular interest as they display a range of bioactivities – for example as natural products, receptor antagonists and on-market drugs.","totalCost":"212933,76","ecMaxContribution":"212933,76","call":"H2020-MSCA-IF-2019","fundingScheme":"MSCA-IF-EF-ST","coordinator":"THE UNIVERSITY OF MANCHESTER","coordinatorCountry":"UK","participants":"","participantCountries":"","subjects":""} +{"rcn":"229239","id":"887259","acronym":"ALEHOOP","status":"SIGNED","programme":"H2020-EU.2.1.4.;H2020-EU.3.2.6.","topics":"BBI-2019-SO3-D3","frameworkProgramme":"H2020","title":"Biorefineries for the valorisation of macroalgal residual biomass and legume processing by-products to obtain new protein value chains for high-value food and feed applications","startDate":"2020-06-01","endDate":"2024-05-31","projectUrl":"","objective":"ALEHOOP provides the demonstration at pilot scale of both sustainable macroalgae and legume-based biorefineries for the recovery of low-cost dietary proteins from alga-based and plant residual biomass and their validation to meet market requirements of consumers and industry in the food and feed sectors. In these sectors, consumers are demanding affordable functional natural proteins from alternative sources and industry is demanding low-cost bio-based protein formulations with better performance and higher sustainability. \nCurrent protein demand for the 7.3 billion inhabitants of the world is approximately 202 Mt. Due to the rise in meat consumption more proteins are therefore required for animal feeding. To satisfy the current protein demand, Europe imports over 30 Mt of soy from the Americas each year mainly for animal feeding, entailing 95% dependency of EU on imported soy. Current sources of proteins are becoming unsustainable from an economic and environmental perspective for Europe resulting in concerns for sustainability and food security and leading to search for new alternative proteins. \nALEHOOP addresses the obtaining of proteins from green macroalgal blooms, brown seaweed by-products from algae processors and legume processing by-products (peas, lupines, beans and lentils) as alternative protein sources for animal feeding (case of green seaweed) and food applications (case of brown seaweed and legume by-products), since they are low cost and under-exploited biomass that do not compete with traditional food crops for space and resources. This will reduce EU´s dependency on protein imports and contribute to our raw material security. The new proteins will be validated in foods for elderly, sporty and overweight people, vegetarians and healthy consumers as well as for animal feed creating cross-sectorial interconnection between these value chains and supporting the projected business plan.","totalCost":"6718370","ecMaxContribution":"5140274,41","call":"H2020-BBI-JTI-2019","fundingScheme":"BBI-IA-DEMO","coordinator":"CONTACTICA S.L.","coordinatorCountry":"ES","participants":"CENTIV GMBH;ALGINOR ASA;FUNDACION TECNALIA RESEARCH & INNOVATION;INDUKERN,S.A.;ASOCIACION NACIONAL DE FABRICANTES DE CONSERVAS DE PESCADOS Y MARISCOS-CENTRO TECNICO NACIONAL DE CONSERVACION DE PRODUCTOS DE LA PESCA;BIOZOON GMBH;EIGEN VERMOGEN VAN HET INSTITUUT VOOR LANDBOUW- EN VISSERIJONDERZOEK;BIOSURYA SL;VYZKUMNY USTAV VETERINARNIHO LEKARSTVI;NUTRITION SCIENCES;TECHNOLOGICAL UNIVERSITY DUBLIN;GARLAN, S.COOP.;ISANATUR SPAIN SL;UNIVERSIDAD DE VIGO;UNIVERSIDAD DE CADIZ","participantCountries":"DE;NO;ES;BE;CZ;IE","subjects":""} +{"rcn":"229258","id":"892834","acronym":"DENVPOC","status":"SIGNED","programme":"H2020-EU.1.3.2.","topics":"MSCA-IF-2019","frameworkProgramme":"H2020","title":"qPCR Microfluidics point-of-care platform for dengue diagnosis","startDate":"2020-05-18","endDate":"2022-05-17","projectUrl":"","objective":"As a result of Global climate change and fast urbanization, global outbreaks of Dengue (DENV)/ Zika(ZIKV)/Chikungunya(CHIKV) virus have the potential to occur. The most common pathway of these infections in humans is through the female Aedes mosquito vector. DENV is an exanthematous febrile disease with varied clinical manifestations and progressions . Due to similarities in symptoms between DENV and ZIKV and CHIKV, it is difficult to make a differential diagnosis, impeding appropriate, timely medical intervention. Furthermore, cross-reactivity with ZIKV, which was recently related to microcephaly, is a serious issue. In 2016, in Brazil alone, there were 4180 microcephaly cases reported instead of 163 cases, more in line with yearly expected projections , , Thus, the sooner an accurate diagnostic which differentiates DENV from the other manifestations is critical; most especially at the early stages of the infection, to have a reliable diagnosis in pregnant women. In 2016, the OMS emergency committee declared that the outbreaks and the potentially resultant neurological disorders in Brazil were an important international state of emergency in public health, as a result of the associated secondary effects; these diseases became a Global concern. This project allows developing a highly and fast Multiplex qPCR POC platform by using FASTGENE technology with a minimal amount of patient serotype. It would reduce the time of analysis (30 to 90’ for a standard) and costs. Additionally, the sample preprocessing and thermalization will shorten real-time PCR amplification time and will be integrated within the microfluidic systems. This platform can result in a commercialized product whereupon a main market target would be pregnant women and people living or traveling through/from outbreak risk areas.","totalCost":"196707,84","ecMaxContribution":"196707,84","call":"H2020-MSCA-IF-2019","fundingScheme":"MSCA-IF-EF-SE","coordinator":"BFORCURE","coordinatorCountry":"FR","participants":"","participantCountries":"","subjects":""} +{"rcn":"229280","id":"895716","acronym":"DoMiCoP","status":"SIGNED","programme":"H2020-EU.1.3.2.","topics":"MSCA-IF-2019","frameworkProgramme":"H2020","title":"The Diffusion of Migration Control Practice. Actors, Processes and Effects.","startDate":"2021-03-01","endDate":"2023-02-28","projectUrl":"","objective":"DoMiCoP develops new understandings and perspectives to study migration control in practice in the European Union by asking one main question: how and why do communities of practice develop and diffuse the knowledge required to put migration control into action? Unlike the nexus between expert knowledge, epistemic communities and policy formulation, the nexus between everyday knowledge, communities of practice and policy implementation has not yet received systematic scholarly attention. My project bridges that gap by focusing on intermediate arenas in which communities of practice take shape most notably the meetings and trainings that gather state and non-state actors involved in putting asylum, detention and removal into practice. By building on field-based methodologies (interviews and participant observations), DoMiCoP sheds ethnographic light on the role that ‘learning from abroad’ plays in the implementation of migration control in the EU. My project’s aim is threefold: 1) Identifying arenas at intermediate levels in which communities of practice take shape; 2) Analysing the communities of practice by focusing on the configurations of actors and organizations involved, the motivations underlying their involvement, the process of knowledge development in interaction, the conflicts and negotiations; 3) Revealing the role of non-state organizations (private for profit and not-for-profit). From a theoretical point of view, this project goes beyond the classical view of the implementation as a test to assess the effectiveness of policy transfers towards an analysis of policy transfer at that level of policy-making. From an empirical point of view, the project expands knowledge about less-studied venues of policy-making and provides original thick descriptions. From a methodological point of view, the project engages with qualitative methods for the study of policy diffusion and aims at responding to their main challenges through participant observation.","totalCost":"163673,28","ecMaxContribution":"163673,28","call":"H2020-MSCA-IF-2019","fundingScheme":"MSCA-IF-EF-ST","coordinator":"EUROPEAN UNIVERSITY INSTITUTE","coordinatorCountry":"IT","participants":"","participantCountries":"","subjects":""} +{"rcn":"229297","id":"954782","acronym":"MiniLLock","status":"SIGNED","programme":"H2020-EU.3.;H2020-EU.2.3.;H2020-EU.2.1.","topics":"EIC-SMEInst-2018-2020","frameworkProgramme":"H2020","title":"Mini Launch Lock devices for small satellites","startDate":"2020-05-01","endDate":"2022-04-30","projectUrl":"","objective":"Space industry is experiencing the most important paradigm shift in its history with the rise of small satellites and megaconstellations.\nSatellite miniaturization requires to reduce significantly production and orbit launching costs. To address the\nnew challenge of this manufacturing process and switch from craftsmanship to industrialization, space industry is turning\ntowards other domains looking for new solutions, disruptive technologies, and manufacturing process.\nMini Launch Lock devices for small satellites (MiniLLock) proposes innovative actuators on the cutting edge of customer\ndemand. They offer plug and play solutions that can directly be integrated into industry for satellites robotized production.\nMiniLLock is smaller, lighter, safer, with a longer lifetime and generates significantly less shocks and vibrations than\nstandard actuators such as electromagnet and pyrotechnics. MiniLLock offers performances which have never been reached\nwith any other materials.\nNimesis is the only company that can provide such cost-effective actuators suitable to small satellite with high performances\nand reliability, enabling features previously impossible.\nMiniLLock will accelerate and leverage the commercialization of Nimesis technology and ensure Europe worldwide\nleadership\nand independence in the new space emergent environment.\nNimesis ambitions to become the global leader of this domain with a turnover of € 26 million and a market share of 28% in\n2027.","totalCost":"2413543,75","ecMaxContribution":"1689480,63","call":"H2020-EIC-SMEInst-2018-2020-3","fundingScheme":"SME-2b","coordinator":"NIMESIS TECHNOLOGY SARL","coordinatorCountry":"FR","participants":"","participantCountries":"","subjects":""} +{"rcn":"229299","id":"101003374","acronym":"NOPHOS","status":"SIGNED","programme":"H2020-EU.4.","topics":"WF-02-2019","frameworkProgramme":"H2020","title":"Unravelling protein phosphorylation mechanisms and phosphoproteome changes under nitrosative stress conditions in E.coli","startDate":"2020-07-01","endDate":"2022-06-30","projectUrl":"","objective":"Currently, we face a global antibiotic resistance crisis aggravated by the slow development of more effective and anti-resistance promoting therapeutical solutions. Protein phosphorylation (PP) has recently emerged as one of the major post-translational modification in bacteria, involved in the regulation of multiple physiological processes. In this MSCA individual fellowship application we aim to bridge the current gap in the field for prokaryotes by unravelling the unknown regulatory role of PP on proteins involved in nitrosative stress (NS) detoxification in the model bacterium E.coli. We propose to examine for the first time both global protein modifications (e.g. phosphoproteomics) under nitrogen species stress, as well as characterize PP in individual proteins involved in NS response. We will construct a network model that reflect the phosphoproteomic changes upon NS in E.coli, that may pave the way for the design of new bacterial targets. Understanding how bacteria respond to the chemical weapons of the human innate system is fundamental to develop efficient therapies. We will pioneer research on the mechanism and the regulation of nitric oxide detoxification proteins already identified as phosphorylated, by analyzing how this modification influences their stability and activity in vitro and in vivo. This project opens up new research paths on bacterial detoxification systems and signalling in general, addressing for the first time the role of PP in these processes. The proposal brings together transversal and scientific skills that will enable the researcher to lead the development of this emerging field and position herself as an expert in the area, and aims at establishing the importance of PP in NO microbial response, a novelty in this field.","totalCost":"147815,04","ecMaxContribution":"147815,04","call":"H2020-WF-02-2019","fundingScheme":"MSCA-IF-EF-ST","coordinator":"UNIVERSIDADE NOVA DE LISBOA","coordinatorCountry":"PT","participants":"","participantCountries":"","subjects":""} \ No newline at end of file From 4589c428b142a833ab015990147310828d3c4832 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 21 May 2020 16:30:39 +0200 Subject: [PATCH 26/62] generate action sets and saves them in the hdfs path for the actions sets --- .../project/SparkAtomicActionJob.java | 71 ++++++++++++------- .../project/oozie_app/workflow.xml | 1 - 2 files changed, 44 insertions(+), 28 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/SparkAtomicActionJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/SparkAtomicActionJob.java index 61bd952db2..5b038b49ae 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/SparkAtomicActionJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/SparkAtomicActionJob.java @@ -3,11 +3,16 @@ package eu.dnetlib.dhp.actionmanager.project; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; +import java.io.IOException; import java.util.Arrays; import java.util.HashMap; import java.util.Optional; +import java.util.function.Consumer; +import eu.dnetlib.dhp.schema.action.AtomicAction; import org.apache.commons.io.IOUtils; +import org.apache.hadoop.fs.Path; +import org.apache.hadoop.io.IntWritable; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Dataset; @@ -28,6 +33,15 @@ import eu.dnetlib.dhp.schema.oaf.Programme; import eu.dnetlib.dhp.schema.oaf.Project; import eu.dnetlib.dhp.utils.DHPUtils; +import org.apache.hadoop.conf.Configuration; + +import org.apache.hadoop.io.SequenceFile; +import org.apache.spark.rdd.SequenceFileRDDFunctions; +import org.apache.hadoop.io.Text; +import scala.Function1; +import scala.Tuple2; +import scala.runtime.BoxedUnit; + public class SparkAtomicActionJob { private static final Logger log = LoggerFactory.getLogger(SparkAtomicActionJob.class); private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); @@ -61,6 +75,8 @@ public class SparkAtomicActionJob { final String programmePath = parser.get("programmePath"); log.info("programmePath {}: ", programmePath); + final String nameNode = parser.get("hdfsNameNode"); + SparkConf conf = new SparkConf(); runWithSparkSession( @@ -72,7 +88,8 @@ public class SparkAtomicActionJob { spark, projectPath, programmePath, - outputPath); + outputPath, + nameNode); }); } @@ -82,38 +99,38 @@ public class SparkAtomicActionJob { private static void getAtomicActions(SparkSession spark, String projectPatH, String programmePath, - String outputPath) { + String outputPath, + String nameNode) throws Exception{ Dataset project = readPath(spark, projectPatH, CSVProject.class); Dataset programme = readPath(spark, programmePath, CSVProgramme.class); project - .joinWith(programme, project.col("programme").equalTo(programme.col("code")), "left") - .map(c -> { - CSVProject csvProject = c._1(); - Optional csvProgramme = Optional.ofNullable(c._2()); - if (csvProgramme.isPresent()) { - Project p = new Project(); - p - .setId( - createOpenaireId( - ModelSupport.entityIdPrefix.get("project"), - "corda__h2020", csvProject.getId())); - Programme pm = new Programme(); - pm.setCode(csvProject.getProgramme()); - pm.setDescription(csvProgramme.get().getShortTitle()); - p.setProgramme(Arrays.asList(pm)); - return p; - } + .joinWith(programme, project.col("programme").equalTo(programme.col("code")), "left") + .map(c -> { + CSVProject csvProject = c._1(); + Optional csvProgramme = Optional.ofNullable(c._2()); + if (csvProgramme.isPresent()) { + Project p = new Project(); + p + .setId( + createOpenaireId( + ModelSupport.entityIdPrefix.get("project"), + "corda__h2020", csvProject.getId())); + Programme pm = new Programme(); + pm.setCode(csvProject.getProgramme()); + pm.setDescription(csvProgramme.get().getShortTitle()); + p.setProgramme(Arrays.asList(pm)); + return new AtomicAction<>(Project.class, p); + } + + return null; + }, Encoders.bean(AtomicAction.class)) + .filter(aa -> !(aa == null)) + .toJavaRDD() + .mapToPair(aa->new Tuple2<>(aa.getClazz().getCanonicalName(), OBJECT_MAPPER.writeValueAsString(aa))) + .saveAsHadoopFile(outputPath, Text.class, Text.class, null); - return null; - }, Encoders.bean(Project.class)) - .filter(p -> !(p == null)) - // .map(p -> new AtomicAction<>(Project.class, p), Encoders.bean(AtomicAction.class)) - .write() - .option("compression", "gzip") - .mode(SaveMode.Overwrite) - .json(outputPath); } public static Dataset readPath( diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/oozie_app/workflow.xml index cd4d79ab77..ba99fb3143 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/oozie_app/workflow.xml @@ -24,7 +24,6 @@ - From 473c6d3a23c83053ffc7c13a81a40814f531b467 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 22 May 2020 15:26:57 +0200 Subject: [PATCH 27/62] produces AtomicActions instead of Projects --- .../project/SparkAtomicActionJob.java | 71 +++++++++---------- 1 file changed, 35 insertions(+), 36 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/SparkAtomicActionJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/SparkAtomicActionJob.java index 5b038b49ae..990e50abd7 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/SparkAtomicActionJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/SparkAtomicActionJob.java @@ -9,12 +9,17 @@ import java.util.HashMap; import java.util.Optional; import java.util.function.Consumer; -import eu.dnetlib.dhp.schema.action.AtomicAction; import org.apache.commons.io.IOUtils; +import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.fs.Path; import org.apache.hadoop.io.IntWritable; +import org.apache.hadoop.io.SequenceFile; +import org.apache.hadoop.io.Text; +import org.apache.hadoop.mapred.SequenceFileOutputFormat; +import org.apache.hadoop.mapred.TextOutputFormat; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.rdd.SequenceFileRDDFunctions; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SaveMode; @@ -28,16 +33,11 @@ import eu.dnetlib.dhp.actionmanager.project.csvutils.CSVProgramme; import eu.dnetlib.dhp.actionmanager.project.csvutils.CSVProject; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.schema.action.AtomicAction; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.Programme; import eu.dnetlib.dhp.schema.oaf.Project; import eu.dnetlib.dhp.utils.DHPUtils; - -import org.apache.hadoop.conf.Configuration; - -import org.apache.hadoop.io.SequenceFile; -import org.apache.spark.rdd.SequenceFileRDDFunctions; -import org.apache.hadoop.io.Text; import scala.Function1; import scala.Tuple2; import scala.runtime.BoxedUnit; @@ -75,8 +75,6 @@ public class SparkAtomicActionJob { final String programmePath = parser.get("programmePath"); log.info("programmePath {}: ", programmePath); - final String nameNode = parser.get("hdfsNameNode"); - SparkConf conf = new SparkConf(); runWithSparkSession( @@ -88,8 +86,7 @@ public class SparkAtomicActionJob { spark, projectPath, programmePath, - outputPath, - nameNode); + outputPath); }); } @@ -99,37 +96,39 @@ public class SparkAtomicActionJob { private static void getAtomicActions(SparkSession spark, String projectPatH, String programmePath, - String outputPath, - String nameNode) throws Exception{ + String outputPath) { Dataset project = readPath(spark, projectPatH, CSVProject.class); Dataset programme = readPath(spark, programmePath, CSVProgramme.class); project - .joinWith(programme, project.col("programme").equalTo(programme.col("code")), "left") - .map(c -> { - CSVProject csvProject = c._1(); - Optional csvProgramme = Optional.ofNullable(c._2()); - if (csvProgramme.isPresent()) { - Project p = new Project(); - p - .setId( - createOpenaireId( - ModelSupport.entityIdPrefix.get("project"), - "corda__h2020", csvProject.getId())); - Programme pm = new Programme(); - pm.setCode(csvProject.getProgramme()); - pm.setDescription(csvProgramme.get().getShortTitle()); - p.setProgramme(Arrays.asList(pm)); - return new AtomicAction<>(Project.class, p); - } + .joinWith(programme, project.col("programme").equalTo(programme.col("code")), "left") + .map(c -> { + CSVProject csvProject = c._1(); + Optional csvProgramme = Optional.ofNullable(c._2()); + if (csvProgramme.isPresent()) { + Project p = new Project(); + p + .setId( + createOpenaireId( + ModelSupport.entityIdPrefix.get("project"), + "corda__h2020", csvProject.getId())); + Programme pm = new Programme(); + pm.setCode(csvProject.getProgramme()); + pm.setDescription(csvProgramme.get().getShortTitle()); + p.setProgramme(Arrays.asList(pm)); + return p; + } - return null; - }, Encoders.bean(AtomicAction.class)) - .filter(aa -> !(aa == null)) - .toJavaRDD() - .mapToPair(aa->new Tuple2<>(aa.getClazz().getCanonicalName(), OBJECT_MAPPER.writeValueAsString(aa))) - .saveAsHadoopFile(outputPath, Text.class, Text.class, null); + return null; + }, Encoders.bean(Project.class)) + .filter(p -> !(p == null)) + .toJavaRDD() + .map(p -> new AtomicAction(Project.class, p)) + .mapToPair( + aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()), + new Text(OBJECT_MAPPER.writeValueAsString(aa)))) + .saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class); } From 50ad83b97f7190642f2e7a89e2cfbad53592b4f8 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 22 May 2020 15:27:19 +0200 Subject: [PATCH 28/62] - --- .../actionmanager/project/PrepareProjectTest.java | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/PrepareProjectTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/PrepareProjectTest.java index fa9e32fd57..73bedb741a 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/PrepareProjectTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/PrepareProjectTest.java @@ -1,9 +1,10 @@ package eu.dnetlib.dhp.actionmanager.project; -import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.actionmanager.project.csvutils.CSVProgramme; -import eu.dnetlib.dhp.actionmanager.project.csvutils.CSVProject; +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; + import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; @@ -18,9 +19,10 @@ import org.junit.jupiter.api.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.actionmanager.project.csvutils.CSVProgramme; +import eu.dnetlib.dhp.actionmanager.project.csvutils.CSVProject; public class PrepareProjectTest { From ac8025f4696d7cf5b786ef9e0bc76620350748c5 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 22 May 2020 15:29:41 +0200 Subject: [PATCH 29/62] - --- .../dhp/actionmanager/project/SparkUpdateProjectTest.java | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/SparkUpdateProjectTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/SparkUpdateProjectTest.java index 3e559228f7..f7b8722c4f 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/SparkUpdateProjectTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/SparkUpdateProjectTest.java @@ -70,7 +70,9 @@ public class SparkUpdateProjectTest { "-isSparkSessionManaged", Boolean.FALSE.toString(), "-programmePath", - getClass().getResource("/eu/dnetlib/dhp/actionmanager/project/preparedProgramme_whole.json.gz").getPath(), + getClass() + .getResource("/eu/dnetlib/dhp/actionmanager/project/preparedProgramme_whole.json.gz") + .getPath(), "-projectPath", getClass().getResource("/eu/dnetlib/dhp/actionmanager/project/prepared_projects.json").getPath(), "-outputPath", From f3dcca0dd05d3f2fd0796fe47dd98a163da62058 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 27 May 2020 17:23:34 +0200 Subject: [PATCH 30/62] added equals for programme --- .../eu/dnetlib/dhp/schema/oaf/Programme.java | 18 +++++++++++++++++- 1 file changed, 17 insertions(+), 1 deletion(-) diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Programme.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Programme.java index 69223ab019..c5259d07e5 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Programme.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Programme.java @@ -1,7 +1,10 @@ package eu.dnetlib.dhp.schema.oaf; -public class Programme { +import java.io.Serializable; +import java.util.Objects; + +public class Programme implements Serializable { private String code; private String description; @@ -20,4 +23,17 @@ public class Programme { public void setDescription(String description) { this.description = description; } + + @Override + public boolean equals(Object o) { + if (this == o) + return true; + if (o == null || getClass() != o.getClass()) + return false; + + Programme programme = (Programme) o; + return Objects.equals(code, programme.code); + } + + } From dd1e0b93b851cde75ef27e53d743a44ea901ebb5 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 27 May 2020 17:40:32 +0200 Subject: [PATCH 31/62] added merge for Programme --- .../src/main/java/eu/dnetlib/dhp/schema/oaf/Project.java | 3 +++ 1 file changed, 3 insertions(+) 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 1eae3e8eeb..1fcfb305e7 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 @@ -330,6 +330,9 @@ public class Project extends OafEntity implements Serializable { fundedamount = p.getFundedamount() != null && compareTrust(this, e) < 0 ? p.getFundedamount() : fundedamount; + + programme = mergeLists(programme, p.getProgramme()); + mergeOAFDataInfo(e); } } From 18554534340ce5ca7d53addeaed5c48c8d8ab883 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 27 May 2020 17:59:36 +0200 Subject: [PATCH 32/62] changed the outputdir of the last step --- .../eu/dnetlib/dhp/actionmanager/project/oozie_app/workflow.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/oozie_app/workflow.xml index ba99fb3143..421df460cd 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/oozie_app/workflow.xml @@ -120,7 +120,7 @@ --projectPath${workingDir}/preparedProjects --programmePath${workingDir}/preparedProgramme - --outputPath/tmp/h2020programme + --outputPath${outputPath} From 669c05c7712154e37fa5d76fc8ea1a0bec9c9d8c Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 28 May 2020 10:00:45 +0200 Subject: [PATCH 33/62] added groupBy before creating Actions --- .../project/SparkAtomicActionJob.java | 14 +++++++++++++- 1 file changed, 13 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/SparkAtomicActionJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/SparkAtomicActionJob.java index 990e50abd7..1023e2d19d 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/SparkAtomicActionJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/SparkAtomicActionJob.java @@ -6,6 +6,7 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.io.IOException; import java.util.Arrays; import java.util.HashMap; +import java.util.Objects; import java.util.Optional; import java.util.function.Consumer; @@ -19,6 +20,7 @@ import org.apache.hadoop.mapred.SequenceFileOutputFormat; import org.apache.hadoop.mapred.TextOutputFormat; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.api.java.function.MapGroupsFunction; import org.apache.spark.rdd.SequenceFileRDDFunctions; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; @@ -122,7 +124,17 @@ public class SparkAtomicActionJob { return null; }, Encoders.bean(Project.class)) - .filter(p -> !(p == null)) + .filter(Objects::nonNull) + .groupByKey( + (MapFunction) p -> p.getId(), + Encoders.STRING()) + .mapGroups((MapGroupsFunction) (s, it) -> { + Project first = it.next(); + it.forEachRemaining(p -> { + first.mergeFrom(p); + }); + return first; + }, Encoders.bean(Project.class)) .toJavaRDD() .map(p -> new AtomicAction(Project.class, p)) .mapToPair( From 96d1a3c4316f972924a7c0a76dc0d7f066a1712c Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 28 May 2020 10:04:10 +0200 Subject: [PATCH 34/62] deleted the file were to store the csv files --- .../dnetlib/dhp/actionmanager/project/csvutils/ReadCSV.java | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/csvutils/ReadCSV.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/csvutils/ReadCSV.java index 9051942321..2b72b229ad 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/csvutils/ReadCSV.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/csvutils/ReadCSV.java @@ -76,10 +76,9 @@ public class ReadCSV implements Closeable { Path hdfsWritePath = new Path(hdfsPath); FSDataOutputStream fsDataOutputStream = null; if (fileSystem.exists(hdfsWritePath)) { - fsDataOutputStream = fileSystem.append(hdfsWritePath); - } else { - fsDataOutputStream = fileSystem.create(hdfsWritePath); + fileSystem.delete(hdfsWritePath, false); } + fsDataOutputStream = fileSystem.create(hdfsWritePath); this.writer = new BufferedWriter(new OutputStreamWriter(fsDataOutputStream, StandardCharsets.UTF_8)); this.csvFile = httpConnector.getInputSource(fileURL); From 1060977272fd90449c48612a7976511d9d525154 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 28 May 2020 10:04:36 +0200 Subject: [PATCH 35/62] added fs actions to remove and the create the workingDir --- .../eu/dnetlib/dhp/actionmanager/project/oozie_app/workflow.xml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/oozie_app/workflow.xml index 421df460cd..edeb0582a0 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/oozie_app/workflow.xml @@ -24,6 +24,8 @@ + + From 87b07f4af88b5fa87d807dc5c15fad097409f7e5 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 28 May 2020 10:05:43 +0200 Subject: [PATCH 36/62] removed unused variables --- .../eu/dnetlib/dhp/actionmanager/project/PrepareProgramme.java | 1 - 1 file changed, 1 deletion(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/PrepareProgramme.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/PrepareProgramme.java index a5abb9ea7d..c6dab13a06 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/PrepareProgramme.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/PrepareProgramme.java @@ -25,7 +25,6 @@ public class PrepareProgramme { private static final Logger log = LoggerFactory.getLogger(PrepareProgramme.class); private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - private static final HashMap programmeMap = new HashMap<>(); public static void main(String[] args) throws Exception { From df44db686a8b53e2769167e6329d0f4b9d605cbf Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 28 May 2020 10:07:00 +0200 Subject: [PATCH 37/62] refactoring --- .../project/PrepareProjects.java | 20 +++++++------------ 1 file changed, 7 insertions(+), 13 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/PrepareProjects.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/PrepareProjects.java index df37f92863..7ca50b219d 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/PrepareProjects.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/PrepareProjects.java @@ -3,10 +3,7 @@ package eu.dnetlib.dhp.actionmanager.project; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; -import java.util.ArrayList; -import java.util.HashMap; -import java.util.List; -import java.util.Optional; +import java.util.*; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; @@ -81,17 +78,14 @@ public class PrepareProjects { .flatMap(p -> { List csvProjectList = new ArrayList<>(); String[] programme = p.getProgramme().split(";"); - if (programme.length > 1) { - String id = p.getId(); - for (int i = 0; i < programme.length; i++) { + Arrays + .stream(programme) + .forEach(value -> { CSVProject csvProject = new CSVProject(); - csvProject.setProgramme(programme[i]); - csvProject.setId(id); + csvProject.setProgramme(value); + csvProject.setId(p.getId()); csvProjectList.add(csvProject); - } - } else { - csvProjectList.add(p); - } + }); return csvProjectList.iterator(); }) From 35b72791478e42f3e1e1b1f708ddf825acb4dcc5 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 28 May 2020 10:26:12 +0200 Subject: [PATCH 38/62] changed test because data are saved as SequenceFile now, and because of the group by the umber of produced update decrease --- .../actionmanager/project/SparkUpdateProjectTest.java | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/SparkUpdateProjectTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/SparkUpdateProjectTest.java index f7b8722c4f..64c6ac32f9 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/SparkUpdateProjectTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/SparkUpdateProjectTest.java @@ -5,7 +5,9 @@ import java.io.IOException; import java.nio.file.Files; import java.nio.file.Path; +import eu.dnetlib.dhp.schema.action.AtomicAction; import org.apache.commons.io.FileUtils; +import org.apache.hadoop.io.Text; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; @@ -82,10 +84,12 @@ public class SparkUpdateProjectTest { final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/actionSet") - .map(item -> OBJECT_MAPPER.readValue(item, Project.class)); + .sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class) + .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) + .map(aa -> ((Project)aa.getPayload())) + ; - Assertions.assertEquals(16, tmp.count()); + Assertions.assertEquals(14, tmp.count()); // Dataset verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(CSVProgramme.class)); // From b737ed8236a8b1866a634e4edb25452e28dd9fe7 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 28 May 2020 17:29:21 +0200 Subject: [PATCH 39/62] added part to read projects from the openaire db to filter out those in the csv file that are not in the db --- .../actionmanager/project/ProjectSubset.java | 16 +++ .../project/ReadProjectsFromDB.java | 113 ++++++++++++++++++ .../project/read_projects_db.json | 32 +++++ 3 files changed, 161 insertions(+) create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/ProjectSubset.java create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/ReadProjectsFromDB.java create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/read_projects_db.json diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/ProjectSubset.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/ProjectSubset.java new file mode 100644 index 0000000000..cfbb62f219 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/ProjectSubset.java @@ -0,0 +1,16 @@ +package eu.dnetlib.dhp.actionmanager.project; + +import java.io.Serializable; + +public class ProjectSubset implements Serializable { + + private String code; + + public String getCode() { + return code; + } + + public void setCode(String code) { + this.code = code; + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/ReadProjectsFromDB.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/ReadProjectsFromDB.java new file mode 100644 index 0000000000..0015dc60f1 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/ReadProjectsFromDB.java @@ -0,0 +1,113 @@ +package eu.dnetlib.dhp.actionmanager.project; + +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.DbClient; +import org.apache.commons.io.IOUtils; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FSDataOutputStream; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; + +import java.io.BufferedWriter; +import java.io.Closeable; +import java.io.IOException; +import java.io.OutputStreamWriter; +import java.nio.charset.StandardCharsets; +import java.sql.ResultSet; +import java.util.Arrays; +import java.util.List; +import java.util.function.Consumer; +import java.util.function.Function; + +public class ReadProjectsFromDB implements Closeable { + + private final DbClient dbClient; + private static final Log log = LogFactory.getLog(ReadProjectsFromDB.class); + private final Configuration conf; + private final BufferedWriter writer; + private final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private final static String query = "SELECT code " + + "from projects where id like 'corda__h2020%' " ; + + public static void main(final String[] args) throws Exception { + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + ReadProjectsFromDB.class + .getResourceAsStream( + "/eu/dnetlib/dhp/actionmanager/project/read_projects_db.json"))); + + parser.parseArgument(args); + + final String dbUrl = parser.get("postgresUrl"); + final String dbUser = parser.get("postgresUser"); + final String dbPassword = parser.get("postgresPassword"); + final String hdfsPath = parser.get("hdfsPath") ; + final String hdfsNameNode = parser.get("hdfsNameNode"); + + try (final ReadProjectsFromDB rbl = new ReadProjectsFromDB(hdfsPath, hdfsNameNode, dbUrl, dbUser, + dbPassword)) { + + log.info("Processing blacklist..."); + rbl.execute(query, rbl::processProjectsEntry); + + } + } + public void execute(final String sql, final Function> producer) throws Exception { + + final Consumer consumer = rs -> producer.apply(rs).forEach(r -> writeProject(r)); + + dbClient.processResults(sql, consumer); + } + + public List processProjectsEntry(ResultSet rs) { + try { + ProjectSubset p = new ProjectSubset(); + p.setCode(rs.getString("code")); + + return Arrays.asList(p); + + } catch (final Exception e) { + throw new RuntimeException(e); + } + } + + protected void writeProject(final ProjectSubset r) { + try { + writer.write(OBJECT_MAPPER.writeValueAsString(r)); + writer.newLine(); + } catch (final Exception e) { + throw new RuntimeException(e); + } + } + + public ReadProjectsFromDB( + final String hdfsPath, String hdfsNameNode, final String dbUrl, final String dbUser, final String dbPassword) + throws Exception { + + this.dbClient = new DbClient(dbUrl, dbUser, dbPassword); + this.conf = new Configuration(); + this.conf.set("fs.defaultFS", hdfsNameNode); + FileSystem fileSystem = FileSystem.get(this.conf); + Path hdfsWritePath = new Path(hdfsPath); + FSDataOutputStream fsDataOutputStream = null; + if (fileSystem.exists(hdfsWritePath)) { + fileSystem.delete(hdfsWritePath, false); + } + fsDataOutputStream = fileSystem.create(hdfsWritePath); + + + this.writer = new BufferedWriter(new OutputStreamWriter(fsDataOutputStream, StandardCharsets.UTF_8)); + } + + @Override + public void close() throws IOException { + dbClient.close(); + writer.close(); + } +} + diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/read_projects_db.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/read_projects_db.json new file mode 100644 index 0000000000..9a2eadaa7d --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/read_projects_db.json @@ -0,0 +1,32 @@ +[ + { + "paramName": "p", + "paramLongName": "hdfsPath", + "paramDescription": "the path where storing the sequential file", + "paramRequired": true + }, + { + "paramName": "nn", + "paramLongName": "hdfsNameNode", + "paramDescription": "the name node on hdfs", + "paramRequired": true + }, + { + "paramName": "pgurl", + "paramLongName": "postgresUrl", + "paramDescription": "postgres url, example: jdbc:postgresql://localhost:5432/testdb", + "paramRequired": true + }, + { + "paramName": "pguser", + "paramLongName": "postgresUser", + "paramDescription": "postgres user", + "paramRequired": false + }, + { + "paramName": "pgpasswd", + "paramLongName": "postgresPassword", + "paramDescription": "postgres password", + "paramRequired": false + } +] \ No newline at end of file From 5309a99a70bf6e81ca5d55e6d0062be1d75e05f4 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 28 May 2020 17:29:53 +0200 Subject: [PATCH 40/62] modified the PrepareProjects to consider those in the db --- .../project/PrepareProjects.java | 71 ++++++++++++++----- 1 file changed, 52 insertions(+), 19 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/PrepareProjects.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/PrepareProjects.java index 7ca50b219d..3d8226f4dc 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/PrepareProjects.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/PrepareProjects.java @@ -9,9 +9,11 @@ import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.function.FlatMapFunction; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -55,6 +57,9 @@ public class PrepareProjects { final String outputPath = parser.get("outputPath"); log.info("outputPath {}: ", outputPath); + final String dbProjectPath = parser.get("dbProjectPath"); + log.info("dbProjectPath {}: ", dbProjectPath); + SparkConf conf = new SparkConf(); runWithSparkSession( @@ -62,7 +67,7 @@ public class PrepareProjects { isSparkSessionManaged, spark -> { removeOutputDir(spark, outputPath); - exec(spark, projectPath, outputPath); + exec(spark, projectPath, dbProjectPath, outputPath); }); } @@ -70,27 +75,55 @@ public class PrepareProjects { HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); } - private static void exec(SparkSession spark, String progjectPath, String outputPath) { + private static void exec(SparkSession spark, String progjectPath, String dbProjectPath, String outputPath) { Dataset project = readPath(spark, progjectPath, CSVProject.class); + Dataset dbProjects = readPath(spark, dbProjectPath, ProjectSubset.class); - project - .toJavaRDD() - .flatMap(p -> { - List csvProjectList = new ArrayList<>(); - String[] programme = p.getProgramme().split(";"); - Arrays - .stream(programme) - .forEach(value -> { - CSVProject csvProject = new CSVProject(); - csvProject.setProgramme(value); - csvProject.setId(p.getId()); - csvProjectList.add(csvProject); - }); + dbProjects.joinWith(project, dbProjects.col("code").equalTo(project.col("id")), "left") + .flatMap((FlatMapFunction, CSVProject>) value -> { + Optional csvProject = Optional.ofNullable(value._2()); + if(! csvProject.isPresent()){ + return null; + } + List csvProjectList = new ArrayList<>(); + String[] programme = csvProject.get().getProgramme().split(";"); + Arrays + .stream(programme) + .forEach(p -> { + CSVProject proj = new CSVProject(); + proj.setProgramme(p); + proj.setId(csvProject.get().getId()); + csvProjectList.add(proj); + }); - return csvProjectList.iterator(); - }) - .map(p -> OBJECT_MAPPER.writeValueAsString(p)) - .saveAsTextFile(outputPath); + return csvProjectList.iterator(); + }, Encoders.bean(CSVProject.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath); +// +// .map(value -> { +// Optional csvProject = Optional.ofNullable(value._2()); +// }, Encoders.bean(CSVProject.class)) +// .filter(Objects::nonNull) +// .toJavaRDD() +// .flatMap(p -> { +// List csvProjectList = new ArrayList<>(); +// String[] programme = p.getProgramme().split(";"); +// Arrays +// .stream(programme) +// .forEach(value -> { +// CSVProject csvProject = new CSVProject(); +// csvProject.setProgramme(value); +// csvProject.setId(p.getId()); +// csvProjectList.add(csvProject); +// }); +// +// return csvProjectList.iterator(); +// }) +// .map(p -> OBJECT_MAPPER.writeValueAsString(p)) +// .saveAsTextFile(outputPath); } From 6a15067a644133d2178e50fa2578db49f03a0934 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 28 May 2020 17:30:09 +0200 Subject: [PATCH 41/62] added one step in the workflow --- .../actionmanager/project/oozie_app/workflow.xml | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/oozie_app/workflow.xml index edeb0582a0..ca0a73b97f 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/oozie_app/workflow.xml @@ -51,6 +51,19 @@ --hdfsPath${workingDir}/programme --classForNameeu.dnetlib.dhp.actionmanager.project.csvutils.CSVProgramme + + + + + + + eu.dnetlib.dhp.actionmanager.project.ReadProjectsFromDB + --hdfsPath${workingDir}/dbProjects + --hdfsNameNode${nameNode} + --postgresUrl${postgresURL} + --postgresUser${postgresUser} + --postgresPassword${postgresPassword} + From 773735f87059e43b1b700128b5777ca922149c45 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 28 May 2020 17:30:45 +0200 Subject: [PATCH 42/62] added the path to the file containing the projects code from the db --- .../actionmanager/project/prepare_project_parameters.json | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/prepare_project_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/prepare_project_parameters.json index 5fc88ce8e9..49f9c73062 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/prepare_project_parameters.json +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/prepare_project_parameters.json @@ -16,5 +16,11 @@ "paramLongName": "outputPath", "paramDescription": "the path of the new ActionSet", "paramRequired": true -} +}, + { + "paramName": "dbp", + "paramLongName": "dbProjectPath", + "paramDescription": "the path of the project code read from db", + "paramRequired": true + } ] \ No newline at end of file From 01f7876595c7170ad5d7c1c7d9d6e13087b1f288 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 28 May 2020 23:50:32 +0200 Subject: [PATCH 43/62] fix issue with flatMap - the return type must not be null --- .../project/PrepareProjects.java | 77 ++++++++----------- .../dhp/actionmanager/project/dbProject | 0 2 files changed, 30 insertions(+), 47 deletions(-) create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/project/dbProject diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/PrepareProjects.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/PrepareProjects.java index 3d8226f4dc..78aed1a697 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/PrepareProjects.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/PrepareProjects.java @@ -57,7 +57,7 @@ public class PrepareProjects { final String outputPath = parser.get("outputPath"); log.info("outputPath {}: ", outputPath); - final String dbProjectPath = parser.get("dbProjectPath"); + final String dbProjectPath = parser.get("dbProjectPath"); log.info("dbProjectPath {}: ", dbProjectPath); SparkConf conf = new SparkConf(); @@ -75,56 +75,39 @@ public class PrepareProjects { HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); } - private static void exec(SparkSession spark, String progjectPath, String dbProjectPath, String outputPath) { - Dataset project = readPath(spark, progjectPath, CSVProject.class); + private static void exec(SparkSession spark, String projectPath, String dbProjectPath, String outputPath) { + Dataset project = readPath(spark, projectPath, CSVProject.class); Dataset dbProjects = readPath(spark, dbProjectPath, ProjectSubset.class); - dbProjects.joinWith(project, dbProjects.col("code").equalTo(project.col("id")), "left") - .flatMap((FlatMapFunction, CSVProject>) value -> { - Optional csvProject = Optional.ofNullable(value._2()); - if(! csvProject.isPresent()){ - return null; - } - List csvProjectList = new ArrayList<>(); - String[] programme = csvProject.get().getProgramme().split(";"); - Arrays - .stream(programme) - .forEach(p -> { - CSVProject proj = new CSVProject(); - proj.setProgramme(p); - proj.setId(csvProject.get().getId()); - csvProjectList.add(proj); - }); + dbProjects + .joinWith(project, dbProjects.col("code").equalTo(project.col("id")), "left") + .flatMap(getTuple2CSVProjectFlatMapFunction(), Encoders.bean(CSVProject.class)) + .filter(Objects::nonNull) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath); - return csvProjectList.iterator(); - }, Encoders.bean(CSVProject.class)) - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath); -// -// .map(value -> { -// Optional csvProject = Optional.ofNullable(value._2()); -// }, Encoders.bean(CSVProject.class)) -// .filter(Objects::nonNull) -// .toJavaRDD() -// .flatMap(p -> { -// List csvProjectList = new ArrayList<>(); -// String[] programme = p.getProgramme().split(";"); -// Arrays -// .stream(programme) -// .forEach(value -> { -// CSVProject csvProject = new CSVProject(); -// csvProject.setProgramme(value); -// csvProject.setId(p.getId()); -// csvProjectList.add(csvProject); -// }); -// -// return csvProjectList.iterator(); -// }) -// .map(p -> OBJECT_MAPPER.writeValueAsString(p)) -// .saveAsTextFile(outputPath); + } + private static FlatMapFunction, CSVProject> getTuple2CSVProjectFlatMapFunction() { + return (FlatMapFunction, CSVProject>) value -> { + Optional csvProject = Optional.ofNullable(value._2()); + List csvProjectList = new ArrayList<>(); + if (csvProject.isPresent()) { + + String[] programme = csvProject.get().getProgramme().split(";"); + Arrays + .stream(programme) + .forEach(p -> { + CSVProject proj = new CSVProject(); + proj.setProgramme(p); + proj.setId(csvProject.get().getId()); + csvProjectList.add(proj); + }); + } + return csvProjectList.iterator(); + }; } public static Dataset readPath( diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/project/dbProject b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/project/dbProject new file mode 100644 index 0000000000..e69de29bb2 From 782984d8e5a03cfc2093a76d9c45d458836db1a6 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 28 May 2020 23:52:41 +0200 Subject: [PATCH 44/62] added needed parameter --- .../dnetlib/dhp/actionmanager/project/oozie_app/workflow.xml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/oozie_app/workflow.xml index ca0a73b97f..1e34456752 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/oozie_app/workflow.xml @@ -96,7 +96,7 @@ yarn cluster - PrepareProgramme + PrepareProjects eu.dnetlib.dhp.actionmanager.project.PrepareProjects dhp-aggregation-${projectVersion}.jar @@ -111,6 +111,7 @@ --projectPath${workingDir}/projects --outputPath${workingDir}/preparedProjects + --dbProjectPath${workingDir}/dbProjects From 6989fb9c8ad6c5ee45979e7da82fe1d491927d5e Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 28 May 2020 23:53:24 +0200 Subject: [PATCH 45/62] changed the project test according to the newly introduced join with the db project codes --- .../dhp/actionmanager/project/PrepareProjectTest.java | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/PrepareProjectTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/PrepareProjectTest.java index 73bedb741a..5ff88e46f6 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/PrepareProjectTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/PrepareProjectTest.java @@ -67,7 +67,7 @@ public class PrepareProjectTest { } @Test - public void numberDistinctProgrammeTest() throws Exception { + public void numberDistinctProjectTest() throws Exception { PrepareProjects .main( new String[] { @@ -76,7 +76,10 @@ public class PrepareProjectTest { "-projectPath", getClass().getResource("/eu/dnetlib/dhp/actionmanager/project/projects_subset.json").getPath(), "-outputPath", - workingDir.toString() + "/preparedProjects" + workingDir.toString() + "/preparedProjects", + "-dbProjectPath", + getClass().getResource("/eu/dnetlib/dhp/actionmanager/project/dbProject").getPath(), + }); final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); @@ -85,7 +88,7 @@ public class PrepareProjectTest { .textFile(workingDir.toString() + "/preparedProjects") .map(item -> OBJECT_MAPPER.readValue(item, CSVProject.class)); - Assertions.assertEquals(20, tmp.count()); + Assertions.assertEquals(8, tmp.count()); Dataset verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(CSVProject.class)); From 8b6e886fb6d89681d00fc215c271c084f60ccbb9 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 28 May 2020 23:54:31 +0200 Subject: [PATCH 46/62] added new resource for testing --- .../eu/dnetlib/dhp/actionmanager/project/dbProject | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/project/dbProject b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/project/dbProject index e69de29bb2..f8e3c45898 100644 --- a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/project/dbProject +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/project/dbProject @@ -0,0 +1,8 @@ +{"code":"894593"} +{"code":"897004"} +{"code":"896300"} +{"code":"892890"} +{"code":"886828"} +{"code":"8867767"} +{"code":"101003374"} +{"code":"886776"} \ No newline at end of file From 6f1eea28b69a10aeb4338305ae43a4b936494961 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 29 May 2020 10:41:39 +0200 Subject: [PATCH 47/62] changed message in log --- .../project/ReadProjectsFromDB.java | 160 +++++++++--------- 1 file changed, 81 insertions(+), 79 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/ReadProjectsFromDB.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/ReadProjectsFromDB.java index 0015dc60f1..2d541d2f98 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/ReadProjectsFromDB.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/ReadProjectsFromDB.java @@ -1,15 +1,5 @@ -package eu.dnetlib.dhp.actionmanager.project; -import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.common.DbClient; -import org.apache.commons.io.IOUtils; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; -import org.apache.hadoop.conf.Configuration; -import org.apache.hadoop.fs.FSDataOutputStream; -import org.apache.hadoop.fs.FileSystem; -import org.apache.hadoop.fs.Path; +package eu.dnetlib.dhp.actionmanager.project; import java.io.BufferedWriter; import java.io.Closeable; @@ -22,92 +12,104 @@ import java.util.List; import java.util.function.Consumer; import java.util.function.Function; +import org.apache.commons.io.IOUtils; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FSDataOutputStream; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.DbClient; + public class ReadProjectsFromDB implements Closeable { - private final DbClient dbClient; - private static final Log log = LogFactory.getLog(ReadProjectsFromDB.class); - private final Configuration conf; - private final BufferedWriter writer; - private final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + private final DbClient dbClient; + private static final Log log = LogFactory.getLog(ReadProjectsFromDB.class); + private final Configuration conf; + private final BufferedWriter writer; + private final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - private final static String query = "SELECT code " + - "from projects where id like 'corda__h2020%' " ; + private final static String query = "SELECT code " + + "from projects where id like 'corda__h2020%' "; - public static void main(final String[] args) throws Exception { - final ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils - .toString( - ReadProjectsFromDB.class - .getResourceAsStream( - "/eu/dnetlib/dhp/actionmanager/project/read_projects_db.json"))); + public static void main(final String[] args) throws Exception { + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + ReadProjectsFromDB.class + .getResourceAsStream( + "/eu/dnetlib/dhp/actionmanager/project/read_projects_db.json"))); - parser.parseArgument(args); + parser.parseArgument(args); - final String dbUrl = parser.get("postgresUrl"); - final String dbUser = parser.get("postgresUser"); - final String dbPassword = parser.get("postgresPassword"); - final String hdfsPath = parser.get("hdfsPath") ; - final String hdfsNameNode = parser.get("hdfsNameNode"); + final String dbUrl = parser.get("postgresUrl"); + final String dbUser = parser.get("postgresUser"); + final String dbPassword = parser.get("postgresPassword"); + final String hdfsPath = parser.get("hdfsPath"); + final String hdfsNameNode = parser.get("hdfsNameNode"); - try (final ReadProjectsFromDB rbl = new ReadProjectsFromDB(hdfsPath, hdfsNameNode, dbUrl, dbUser, - dbPassword)) { + try (final ReadProjectsFromDB rbl = new ReadProjectsFromDB(hdfsPath, hdfsNameNode, dbUrl, dbUser, + dbPassword)) { - log.info("Processing blacklist..."); - rbl.execute(query, rbl::processProjectsEntry); + log.info("Processing projects..."); + rbl.execute(query, rbl::processProjectsEntry); - } - } - public void execute(final String sql, final Function> producer) throws Exception { + } + } - final Consumer consumer = rs -> producer.apply(rs).forEach(r -> writeProject(r)); + public void execute(final String sql, final Function> producer) throws Exception { - dbClient.processResults(sql, consumer); - } + final Consumer consumer = rs -> producer.apply(rs).forEach(r -> writeProject(r)); - public List processProjectsEntry(ResultSet rs) { - try { - ProjectSubset p = new ProjectSubset(); - p.setCode(rs.getString("code")); + dbClient.processResults(sql, consumer); + } - return Arrays.asList(p); + public List processProjectsEntry(ResultSet rs) { + try { + ProjectSubset p = new ProjectSubset(); + p.setCode(rs.getString("code")); - } catch (final Exception e) { - throw new RuntimeException(e); - } - } + return Arrays.asList(p); - protected void writeProject(final ProjectSubset r) { - try { - writer.write(OBJECT_MAPPER.writeValueAsString(r)); - writer.newLine(); - } catch (final Exception e) { - throw new RuntimeException(e); - } - } + } catch (final Exception e) { + throw new RuntimeException(e); + } + } - public ReadProjectsFromDB( - final String hdfsPath, String hdfsNameNode, final String dbUrl, final String dbUser, final String dbPassword) - throws Exception { + protected void writeProject(final ProjectSubset r) { + try { + writer.write(OBJECT_MAPPER.writeValueAsString(r)); + writer.newLine(); + } catch (final Exception e) { + throw new RuntimeException(e); + } + } - this.dbClient = new DbClient(dbUrl, dbUser, dbPassword); - this.conf = new Configuration(); - this.conf.set("fs.defaultFS", hdfsNameNode); - FileSystem fileSystem = FileSystem.get(this.conf); - Path hdfsWritePath = new Path(hdfsPath); - FSDataOutputStream fsDataOutputStream = null; - if (fileSystem.exists(hdfsWritePath)) { - fileSystem.delete(hdfsWritePath, false); - } - fsDataOutputStream = fileSystem.create(hdfsWritePath); + public ReadProjectsFromDB( + final String hdfsPath, String hdfsNameNode, final String dbUrl, final String dbUser, final String dbPassword) + throws Exception { + this.dbClient = new DbClient(dbUrl, dbUser, dbPassword); + this.conf = new Configuration(); + this.conf.set("fs.defaultFS", hdfsNameNode); + FileSystem fileSystem = FileSystem.get(this.conf); + Path hdfsWritePath = new Path(hdfsPath); + FSDataOutputStream fsDataOutputStream = null; + if (fileSystem.exists(hdfsWritePath)) { + fileSystem.delete(hdfsWritePath, false); + } + fsDataOutputStream = fileSystem.create(hdfsWritePath); - this.writer = new BufferedWriter(new OutputStreamWriter(fsDataOutputStream, StandardCharsets.UTF_8)); - } + this.writer = new BufferedWriter(new OutputStreamWriter(fsDataOutputStream, StandardCharsets.UTF_8)); + } - @Override - public void close() throws IOException { - dbClient.close(); - writer.close(); - } + @Override + public void close() throws IOException { + dbClient.close(); + writer.close(); + } } - From dfa4997a4ff96605cc91fc467e2b203ba1e3f3fc Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 29 May 2020 10:45:18 +0200 Subject: [PATCH 48/62] removed commented code --- .../actionmanager/project/SparkUpdateProjectTest.java | 11 ++++------- 1 file changed, 4 insertions(+), 7 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/SparkUpdateProjectTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/SparkUpdateProjectTest.java index 64c6ac32f9..4d3ec140be 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/SparkUpdateProjectTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/SparkUpdateProjectTest.java @@ -5,7 +5,6 @@ import java.io.IOException; import java.nio.file.Files; import java.nio.file.Path; -import eu.dnetlib.dhp.schema.action.AtomicAction; import org.apache.commons.io.FileUtils; import org.apache.hadoop.io.Text; import org.apache.spark.SparkConf; @@ -21,6 +20,7 @@ import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.schema.action.AtomicAction; import eu.dnetlib.dhp.schema.oaf.Project; public class SparkUpdateProjectTest { @@ -84,15 +84,12 @@ public class SparkUpdateProjectTest { final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class) + .sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class) .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) - .map(aa -> ((Project)aa.getPayload())) - ; + .map(aa -> ((Project) aa.getPayload())); Assertions.assertEquals(14, tmp.count()); -// Dataset verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(CSVProgramme.class)); -// -// Assertions.assertEquals(0, verificationDataset.filter("shortTitle =''").count()); + } } From a41e0cb64899dc3673dd119e93a2550b4b8c70ec Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Thu, 11 Jun 2020 12:28:34 +0200 Subject: [PATCH 49/62] missing landingPage urls in instances --- .../eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java index e6a744fc0c..7ff483aff9 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java @@ -138,9 +138,16 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { for (final Object o : doc.selectNodes("//datacite:alternateIdentifier[@alternateIdentifierType='URL']")) { url.add(((Node) o).getText().trim()); } + for (final Object o : doc + .selectNodes("//datacite:alternateIdentifier[@alternateIdentifierType='landingPage']")) { + url.add(((Node) o).getText().trim()); + } for (final Object o : doc.selectNodes("//datacite:identifier[@identifierType='URL']")) { url.add(((Node) o).getText().trim()); } + for (final Object o : doc.selectNodes("//datacite:identifier[@identifierType='landingPage']")) { + url.add(((Node) o).getText().trim()); + } for (final Object o : doc.selectNodes("//datacite:alternateIdentifier[@alternateIdentifierType='DOI']")) { url.add(HTTP_DX_DOI_PREIFX + ((Node) o).getText().trim()); } @@ -379,11 +386,13 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { res .addAll( prepareListStructPropsWithValidQualifier( - doc, "//datacite:identifier[@identifierType != 'URL']", "@identifierType", DNET_PID_TYPES, info)); + doc, "//datacite:identifier[@identifierType != 'URL' and @identifierType != 'landingPage']", + "@identifierType", DNET_PID_TYPES, info)); res .addAll( prepareListStructPropsWithValidQualifier( - doc, "//datacite:alternateIdentifier[@alternateIdentifierType != 'URL']", + doc, + "//datacite:alternateIdentifier[@alternateIdentifierType != 'URL' and @alternateIdentifierType != 'landingPage']", "@alternateIdentifierType", DNET_PID_TYPES, info)); return res; } From 48959e9a1710f627a902dc986e07e180193edb9e Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Thu, 11 Jun 2020 14:24:02 +0200 Subject: [PATCH 50/62] orcid events --- .../simple/EnrichMissingAuthorOrcid.java | 49 ++++++++++++++----- 1 file changed, 38 insertions(+), 11 deletions(-) diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingAuthorOrcid.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingAuthorOrcid.java index 1226aaf45e..14021480d7 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingAuthorOrcid.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingAuthorOrcid.java @@ -1,41 +1,68 @@ package eu.dnetlib.dhp.broker.oa.matchers.simple; -import java.util.Arrays; +import java.util.ArrayList; import java.util.List; - -import org.apache.commons.lang3.tuple.Pair; +import java.util.Set; +import java.util.stream.Collectors; import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.ResultWithRelations; +import eu.dnetlib.dhp.schema.oaf.Author; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; import eu.dnetlib.pace.config.DedupConfig; -public class EnrichMissingAuthorOrcid extends UpdateMatcher> { +public class EnrichMissingAuthorOrcid extends UpdateMatcher { public EnrichMissingAuthorOrcid() { super(true); } @Override - protected List>> findUpdates(final ResultWithRelations source, + protected List> findUpdates(final ResultWithRelations source, final ResultWithRelations target, final DedupConfig dedupConfig) { - // TODO - // return Arrays.asList(new EnrichMissingAbstract("xxxxxxx", 0.9f)); - return Arrays.asList(); + + final Set existingOrcids = target + .getResult() + .getAuthor() + .stream() + .map(Author::getPid) + .flatMap(List::stream) + .filter(pid -> pid.getQualifier().getClassid().equalsIgnoreCase("orcid")) + .map(pid -> pid.getValue()) + .collect(Collectors.toSet()); + + final List> list = new ArrayList<>(); + + for (final Author author : source.getResult().getAuthor()) { + final String name = author.getFullname(); + + for (final StructuredProperty pid : author.getPid()) { + if (pid.getQualifier().getClassid().equalsIgnoreCase("orcid") + && !existingOrcids.contains(pid.getValue())) { + list + .add( + generateUpdateInfo(name + " [ORCID: " + pid.getValue() + "]", source, target, dedupConfig)); + ; + } + } + } + + return list; } - public UpdateInfo> generateUpdateInfo(final Pair highlightValue, + public UpdateInfo generateUpdateInfo(final String highlightValue, final ResultWithRelations source, final ResultWithRelations target, final DedupConfig dedupConfig) { return new UpdateInfo<>( Topic.ENRICH_MISSING_AUTHOR_ORCID, highlightValue, source, target, - (p, pair) -> p.getCreators().add(pair.getLeft() + " - ORCID: " + pair.getRight()), - pair -> pair.getLeft() + "::" + pair.getRight(), + (p, aut) -> p.getCreators().add(aut), + aut -> aut, dedupConfig); } } From c2e1b66e83b6bda2cdf863a1c10e6e02411baea1 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Thu, 11 Jun 2020 14:28:03 +0200 Subject: [PATCH 51/62] Revert "orcid events" This reverts commit 48959e9a1710f627a902dc986e07e180193edb9e. --- .../simple/EnrichMissingAuthorOrcid.java | 49 +++++-------------- 1 file changed, 11 insertions(+), 38 deletions(-) diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingAuthorOrcid.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingAuthorOrcid.java index 14021480d7..1226aaf45e 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingAuthorOrcid.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingAuthorOrcid.java @@ -1,68 +1,41 @@ package eu.dnetlib.dhp.broker.oa.matchers.simple; -import java.util.ArrayList; +import java.util.Arrays; import java.util.List; -import java.util.Set; -import java.util.stream.Collectors; + +import org.apache.commons.lang3.tuple.Pair; import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.ResultWithRelations; -import eu.dnetlib.dhp.schema.oaf.Author; -import eu.dnetlib.dhp.schema.oaf.StructuredProperty; import eu.dnetlib.pace.config.DedupConfig; -public class EnrichMissingAuthorOrcid extends UpdateMatcher { +public class EnrichMissingAuthorOrcid extends UpdateMatcher> { public EnrichMissingAuthorOrcid() { super(true); } @Override - protected List> findUpdates(final ResultWithRelations source, + protected List>> findUpdates(final ResultWithRelations source, final ResultWithRelations target, final DedupConfig dedupConfig) { - - final Set existingOrcids = target - .getResult() - .getAuthor() - .stream() - .map(Author::getPid) - .flatMap(List::stream) - .filter(pid -> pid.getQualifier().getClassid().equalsIgnoreCase("orcid")) - .map(pid -> pid.getValue()) - .collect(Collectors.toSet()); - - final List> list = new ArrayList<>(); - - for (final Author author : source.getResult().getAuthor()) { - final String name = author.getFullname(); - - for (final StructuredProperty pid : author.getPid()) { - if (pid.getQualifier().getClassid().equalsIgnoreCase("orcid") - && !existingOrcids.contains(pid.getValue())) { - list - .add( - generateUpdateInfo(name + " [ORCID: " + pid.getValue() + "]", source, target, dedupConfig)); - ; - } - } - } - - return list; + // TODO + // return Arrays.asList(new EnrichMissingAbstract("xxxxxxx", 0.9f)); + return Arrays.asList(); } - public UpdateInfo generateUpdateInfo(final String highlightValue, + public UpdateInfo> generateUpdateInfo(final Pair highlightValue, final ResultWithRelations source, final ResultWithRelations target, final DedupConfig dedupConfig) { return new UpdateInfo<>( Topic.ENRICH_MISSING_AUTHOR_ORCID, highlightValue, source, target, - (p, aut) -> p.getCreators().add(aut), - aut -> aut, + (p, pair) -> p.getCreators().add(pair.getLeft() + " - ORCID: " + pair.getRight()), + pair -> pair.getLeft() + "::" + pair.getRight(), dedupConfig); } } From c15c8c0ad0ae0b6c3b86616051c10531ccfa6946 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 15 Jun 2020 16:07:30 +0200 Subject: [PATCH 52/62] map datasource identities (including piwik ids) as original IDs --- .../dhp/oa/graph/raw/MigrateDbEntitiesApplication.java | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java index 89bf5c3791..0bad89e9e4 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java @@ -50,6 +50,8 @@ import org.apache.commons.lang3.StringUtils; import org.slf4j.Logger; import org.slf4j.LoggerFactory; +import com.google.common.collect.Lists; + import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.DbClient; import eu.dnetlib.dhp.oa.graph.raw.common.AbstractMigrationApplication; @@ -171,7 +173,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i final Datasource ds = new Datasource(); ds.setId(createOpenaireId(10, rs.getString("datasourceid"), true)); - ds.setOriginalId(Arrays.asList(rs.getString("datasourceid"))); + ds.setOriginalId(Arrays.asList((String[]) rs.getArray("identities").getArray())); ds .setCollectedfrom( listKeyValues( From 2a4f65795f981faeac358875f89ce450e905b88f Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 15 Jun 2020 18:32:24 +0200 Subject: [PATCH 53/62] WIP: graph cleaner implementation --- .../dhp/oa/graph/raw/common/Vocabulary.java | 2 +- .../oa/graph/raw/common/VocabularyGroup.java | 9 +- .../oa/graph/clean/CleaningFunctionTest.java | 4 +- .../eu/dnetlib/dhp/oa/graph/clean/result.json | 8 +- .../dnetlib/dhp/oa/graph/clean/synonyms.txt | 1592 ++++++++--------- .../eu/dnetlib/dhp/oa/graph/clean/terms.txt | 1197 +++++++------ 6 files changed, 1400 insertions(+), 1412 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/Vocabulary.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/Vocabulary.java index ffa64861c0..9bf198c8b7 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/Vocabulary.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/Vocabulary.java @@ -61,7 +61,7 @@ public class Vocabulary implements Serializable { } public VocabularyTerm getTermBySynonym(final String syn) { - return getTerm(synonyms.get(syn)); + return getTerm(synonyms.get(syn.toLowerCase())); } public Qualifier getTermAsQualifier(final String termId) { diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/VocabularyGroup.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/VocabularyGroup.java index 447228bf9f..d9ff62596a 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/VocabularyGroup.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/VocabularyGroup.java @@ -3,7 +3,6 @@ package eu.dnetlib.dhp.oa.graph.raw.common; import java.io.Serializable; import java.util.*; -import java.util.function.Supplier; import java.util.stream.Collectors; import org.apache.commons.lang3.StringUtils; @@ -14,7 +13,7 @@ import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; public class VocabularyGroup implements Serializable { - public static final String VOCABULARIES_XQUERY = "for $x in collection(' /db/DRIVER/VocabularyDSResources/VocabularyDSResourceType') \n" + public static final String VOCABULARIES_XQUERY = "for $x in collection('/db/DRIVER/VocabularyDSResources/VocabularyDSResourceType') \n" + "let $vocid := $x//VOCABULARY_NAME/@code\n" + "let $vocname := $x//VOCABULARY_NAME/text()\n" + @@ -46,7 +45,7 @@ public class VocabularyGroup implements Serializable { } vocs.addTerm(vocId, termId, termName); - vocs.addSynonyms(vocId, termId, termId); + // vocs.addSynonyms(vocId, termId, termId); } } @@ -58,7 +57,7 @@ public class VocabularyGroup implements Serializable { final String syn = arr[2].trim(); vocs.addSynonyms(vocId, termId, syn); - vocs.addSynonyms(vocId, termId, termId); + // vocs.addSynonyms(vocId, termId, termId); } } @@ -135,7 +134,7 @@ public class VocabularyGroup implements Serializable { Optional .ofNullable(vocs.get(id)) .orElseThrow(() -> new IllegalArgumentException("missing vocabulary id: " + vocId)) - .addSynonym(syn, termId); + .addSynonym(syn.toLowerCase(), termId); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctionTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctionTest.java index d1f152342f..1b21ce2d37 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctionTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctionTest.java @@ -60,8 +60,8 @@ public class CleaningFunctionTest { assertNotNull(p_out); - assertEquals("eng", p_out.getLanguage().getClassid()); - assertEquals("English", p_out.getLanguage().getClassname()); + assertEquals("und", p_out.getLanguage().getClassid()); + assertEquals("Undetermined", p_out.getLanguage().getClassname()); assertEquals("0018", p_out.getInstance().get(0).getInstancetype().getClassid()); assertEquals("Annotation", p_out.getInstance().get(0).getInstancetype().getClassname()); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json index 89ebe5af5d..b63a12f619 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json @@ -281,8 +281,8 @@ "value": "VIRTA" }, "instancetype": { - "classid": "Comentario", - "classname": "Comentario", + "classid": "Comment/debate", + "classname": "Comment/debate", "schemeid": "dnet:publication_resource", "schemename": "dnet:publication_resource" }, @@ -317,8 +317,8 @@ "vol": "" }, "language": { - "classid": "en", - "classname": "en", + "classid": "UNKNOWN", + "classname": "UNKNOWN", "schemeid": "dnet:languages", "schemename": "dnet:languages" }, diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt index 10eba3e86a..05484c8e50 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt @@ -1,223 +1,9 @@ -dnet:countries @=@ AF @=@ AFG -dnet:countries @=@ AF @=@ Afghanistan -dnet:countries @=@ AD @=@ Andorra -dnet:countries @=@ AO @=@ Angola -dnet:countries @=@ AR @=@ ARG -dnet:countries @=@ AR @=@ Argentina -dnet:countries @=@ AU @=@ AUS -dnet:countries @=@ AU @=@ Australia -dnet:countries @=@ AT @=@ AUT -dnet:countries @=@ AT @=@ Austria -dnet:countries @=@ AZ @=@ AZE -dnet:countries @=@ BD @=@ Bangladesh -dnet:countries @=@ BY @=@ Belarus -dnet:countries @=@ BE @=@ BEL -dnet:countries @=@ BE @=@ Belgium -dnet:countries @=@ BJ @=@ BEN -dnet:countries @=@ BO @=@ Bolivia, Plurinational State of -dnet:countries @=@ BA @=@ BIH -dnet:countries @=@ BA @=@ Bosnia-Hercegovina -dnet:countries @=@ BR @=@ BRA -dnet:countries @=@ BR @=@ Brazil -dnet:countries @=@ BG @=@ Bulgaria -dnet:countries @=@ BF @=@ BFA -dnet:countries @=@ KH @=@ Campuchea -dnet:countries @=@ CM @=@ CMR -dnet:countries @=@ CA @=@ CAN -dnet:countries @=@ CA @=@ Canada -dnet:countries @=@ CV @=@ Cape Verde -dnet:countries @=@ CL @=@ CHL -dnet:countries @=@ CL @=@ Chile -dnet:countries @=@ CN @=@ CHN -dnet:countries @=@ CN @=@ China -dnet:countries @=@ CO @=@ COL -dnet:countries @=@ CO @=@ Colombia -dnet:countries @=@ CG @=@ Congo, Republic -dnet:countries @=@ CD @=@ Congo, the Democratic Republic of the -dnet:countries @=@ CD @=@ Congo Democratic Republic (formerly Zaire) -dnet:countries @=@ CD @=@ Congo Democratic Republic -dnet:countries @=@ CD @=@ Zaire -dnet:countries @=@ CR @=@ CRI -dnet:countries @=@ CI @=@ CIV -dnet:countries @=@ CI @=@ Ivory Coast -dnet:countries @=@ HR @=@ Croatia -dnet:countries @=@ HR @=@ HRV -dnet:countries @=@ CY @=@ CYP -dnet:countries @=@ CY @=@ Cyprus -dnet:countries @=@ CZ @=@ CZE -dnet:countries @=@ CZ @=@ Czech Republic -dnet:countries @=@ CZ @=@ Czechoslovakia -dnet:countries @=@ DK @=@ DNK -dnet:countries @=@ DK @=@ Denmark -dnet:countries @=@ EC @=@ Ecuador -dnet:countries @=@ EG @=@ EGY -dnet:countries @=@ EG @=@ Egypt -dnet:countries @=@ SV @=@ SLV -dnet:countries @=@ EE @=@ EST -dnet:countries @=@ EE @=@ Estonia -dnet:countries @=@ ET @=@ ETH -dnet:countries @=@ EU @=@ EEC -dnet:countries @=@ FI @=@ FIN -dnet:countries @=@ FI @=@ Finland -dnet:countries @=@ MK @=@ Macedonia, the Former Yugoslav Republic Of -dnet:countries @=@ MK @=@ Macedonia -dnet:countries @=@ FR @=@ FRA -dnet:countries @=@ FR @=@ France -dnet:countries @=@ PF @=@ French Polynesia -dnet:countries @=@ PF @=@ PYF -dnet:countries @=@ TF @=@ French Southern Territories -dnet:countries @=@ GE @=@ Georgia -dnet:countries @=@ DE @=@ DEU -dnet:countries @=@ DE @=@ Germany -dnet:countries @=@ DE @=@ Germany, Berlin -dnet:countries @=@ GH @=@ GHA -dnet:countries @=@ GR @=@ EL -dnet:countries @=@ GR @=@ GRC -dnet:countries @=@ GL @=@ GRL -dnet:countries @=@ GN @=@ Guinea -dnet:countries @=@ GW @=@ Guinea-Bissau -dnet:countries @=@ VA @=@ Vatican State -dnet:countries @=@ HK @=@ HKG -dnet:countries @=@ HK @=@ Hong Kong -dnet:countries @=@ HK @=@ Hongkong -dnet:countries @=@ HU @=@ HUN -dnet:countries @=@ HU @=@ Hungary -dnet:countries @=@ IS @=@ ISL -dnet:countries @=@ IN @=@ IND -dnet:countries @=@ IN @=@ India -dnet:countries @=@ ID @=@ IDN -dnet:countries @=@ ID @=@ Indonesia -dnet:countries @=@ IR @=@ Iran -dnet:countries @=@ IR @=@ Iran, Islamic Republic of -dnet:countries @=@ IE @=@ IRL -dnet:countries @=@ IE @=@ Ireland -dnet:countries @=@ IL @=@ ISR -dnet:countries @=@ IL @=@ Israel -dnet:countries @=@ IT @=@ ITA -dnet:countries @=@ IT @=@ Italy -dnet:countries @=@ JM @=@ Jamaica -dnet:countries @=@ JP @=@ JPN -dnet:countries @=@ JP @=@ Japan -dnet:countries @=@ KZ @=@ KAZ -dnet:countries @=@ KZ @=@ Kazakistan -dnet:countries @=@ KZ @=@ Kazakstan -dnet:countries @=@ KE @=@ KEN -dnet:countries @=@ KE @=@ Kenya -dnet:countries @=@ KR @=@ KOR -dnet:countries @=@ KR @=@ Korea, Republic of -dnet:countries @=@ KR @=@ Korean Republic (South Korea) -dnet:countries @=@ KP @=@ PRK -dnet:countries @=@ LY @=@ Libya -dnet:countries @=@ LT @=@ LTU -dnet:countries @=@ LU @=@ LUX -dnet:countries @=@ LU @=@ Luxembourg -dnet:countries @=@ MO @=@ Macao -dnet:countries @=@ MG @=@ Madagascar -dnet:countries @=@ MY @=@ Malaysia -dnet:countries @=@ ML @=@ Mali -dnet:countries @=@ MT @=@ Malta -dnet:countries @=@ MU @=@ Mauritius -dnet:countries @=@ MX @=@ MEX -dnet:countries @=@ MX @=@ Mexico -dnet:countries @=@ FM @=@ Micronesia -dnet:countries @=@ MD @=@ Moldova -dnet:countries @=@ MD @=@ Moldova, Republic of -dnet:countries @=@ MN @=@ Mongolia -dnet:countries @=@ MA @=@ Morocco -dnet:countries @=@ MZ @=@ Mozambique -dnet:countries @=@ NA @=@ NAM -dnet:countries @=@ NL @=@ NLD -dnet:countries @=@ NL @=@ Netherlands -dnet:countries @=@ AN @=@ Netherlands Antilles -dnet:countries @=@ NZ @=@ NZL -dnet:countries @=@ NZ @=@ New Zealand -dnet:countries @=@ NO @=@ NOR -dnet:countries @=@ NO @=@ Norway -dnet:countries @=@ OC @=@ Australasia -dnet:countries @=@ OM @=@ Oman -dnet:countries @=@ PK @=@ PAK -dnet:countries @=@ PK @=@ Pakistan -dnet:countries @=@ PS @=@ Palestine, State of -dnet:countries @=@ PS @=@ Palestinian Territory, Occupied -dnet:countries @=@ PA @=@ PAN -dnet:countries @=@ PA @=@ Panama -dnet:countries @=@ PG @=@ PapuaNew Guinea -dnet:countries @=@ PE @=@ PER -dnet:countries @=@ PH @=@ PHL -dnet:countries @=@ PH @=@ Philippines -dnet:countries @=@ PL @=@ POL -dnet:countries @=@ PL @=@ Poland -dnet:countries @=@ PT @=@ PRT -dnet:countries @=@ PT @=@ Portugal -dnet:countries @=@ PR @=@ Puerto Rico -dnet:countries @=@ RO @=@ ROU -dnet:countries @=@ RO @=@ Romania -dnet:countries @=@ RU @=@ RUS -dnet:countries @=@ RU @=@ Russia -dnet:countries @=@ RU @=@ Russian Federation -dnet:countries @=@ RE @=@ Réunion -dnet:countries @=@ KN @=@ Saint Kitts And Nevis -dnet:countries @=@ SA @=@ Saudi Arabia -dnet:countries @=@ SN @=@ SEN -dnet:countries @=@ SG @=@ SGP -dnet:countries @=@ SG @=@ Singapore -dnet:countries @=@ SK @=@ SVK -dnet:countries @=@ SI @=@ SVN -dnet:countries @=@ SI @=@ Slovenia -dnet:countries @=@ ZA @=@ South Africa -dnet:countries @=@ ZA @=@ ZAF -dnet:countries @=@ ES @=@ ESP -dnet:countries @=@ ES @=@ Spain -dnet:countries @=@ LK @=@ Sri Lanka -dnet:countries @=@ LK @=@ LKA -dnet:countries @=@ SR @=@ Suriname -dnet:countries @=@ SE @=@ SWE -dnet:countries @=@ SE @=@ Sweden -dnet:countries @=@ CH @=@ CHE -dnet:countries @=@ CH @=@ Switzerland -dnet:countries @=@ SY @=@ Syria -dnet:countries @=@ ST @=@ Sao Tome and Principe -dnet:countries @=@ TW @=@ TWN -dnet:countries @=@ TW @=@ Taiwan, Province of China -dnet:countries @=@ TZ @=@ Tanzania -dnet:countries @=@ TZ @=@ Tanzania, United Republic of -dnet:countries @=@ TH @=@ THA -dnet:countries @=@ TH @=@ Thailand -dnet:countries @=@ TL @=@ East Timor -dnet:countries @=@ TN @=@ TUN -dnet:countries @=@ TN @=@ Tunisia -dnet:countries @=@ TR @=@ TUR -dnet:countries @=@ TR @=@ Turkey -dnet:countries @=@ UNKNOWN @=@ AAA -dnet:countries @=@ UNKNOWN @=@ [Unknown] -dnet:countries @=@ UNKNOWN @=@ _? -dnet:countries @=@ UA @=@ UKR -dnet:countries @=@ UA @=@ Ukraine -dnet:countries @=@ AE @=@ United Arab Emirates -dnet:countries @=@ GB @=@ GBR -dnet:countries @=@ GB @=@ UK -dnet:countries @=@ GB @=@ United Kingdom -dnet:countries @=@ GB @=@ Great Britain -dnet:countries @=@ GB @=@ Great Britain and Northern Ireland -dnet:countries @=@ US @=@ USA -dnet:countries @=@ US @=@ United States -dnet:countries @=@ US @=@ United States of America -dnet:countries @=@ UY @=@ Uruguay -dnet:countries @=@ UZ @=@ Uzbekistan -dnet:countries @=@ VE @=@ Venezuela, Bolivarian Republic of -dnet:countries @=@ VN @=@ Vietnam -dnet:countries @=@ VG @=@ British Virgin Islands -dnet:countries @=@ YU @=@ Jugoslavia -dnet:countries @=@ YU @=@ Yugoslavia -dnet:countries @=@ ZW @=@ ABW -dnet:datasourceCompatibilityLevel @=@ openaire-pub_4.0 @=@ openaire4.0 dnet:access_modes @=@ CLOSED @=@ http://purl.org/coar/access_right/c_14cb dnet:access_modes @=@ CLOSED @=@ info:eu-repo/semantics/closedAccess dnet:access_modes @=@ EMBARGO @=@ http://purl.org/coar/access_right/c_f1cf dnet:access_modes @=@ EMBARGO @=@ info:eu-repo/semantics/embargoedAccess dnet:access_modes @=@ OPEN @=@ Creative Commons License [CC BY-NC-ND] http://creativecommons.org/licenses/by-nc-nd/3.0/de/ dnet:access_modes @=@ OPEN @=@ Creative commons -dnet:access_modes @=@ OPEN @=@ Open Access dnet:access_modes @=@ OPEN @=@ http://creativecommons.org/licenses/by-nc-nd/3.0/ dnet:access_modes @=@ OPEN @=@ http://creativecommons.org/licenses/by-nc/3.0/ dnet:access_modes @=@ OPEN @=@ http://creativecommons.org/licenses/by-sa/3.0/ @@ -228,53 +14,489 @@ dnet:access_modes @=@ OPEN @=@ http://creativecommons.org/licenses/by/4.0/ dnet:access_modes @=@ OPEN @=@ http://creativecommons.org/publicdomain/zero/1.0/ dnet:access_modes @=@ OPEN @=@ http://creativecommons.org/publicdomain/zero/1.0/ & http://www.canadensys.net/norms dnet:access_modes @=@ OPEN @=@ http://purl.org/coar/access_right/c_abf2 +dnet:access_modes @=@ OPEN @=@ https://creativecommons.org/licenses/by-nc/4.0/ dnet:access_modes @=@ OPEN @=@ info:eu-repo/semantics/openAccess -dnet:access_modes @=@ OPEN @=@ openAccess -dnet:access_modes @=@ OPEN @=@ http://creativecommons.org/licenses/by-nc-nd/2.0/uk/ +dnet:access_modes @=@ OPEN @=@ open_access dnet:access_modes @=@ RESTRICTED @=@ http://purl.org/coar/access_right/c_16ec dnet:access_modes @=@ RESTRICTED @=@ info:eu-repo/semantics/restrictedAccess -dnet:result_typologies @=@ dataset @=@ 0021 -dnet:result_typologies @=@ dataset @=@ 0024 -dnet:result_typologies @=@ dataset @=@ 0025 -dnet:result_typologies @=@ dataset @=@ 0030 -dnet:result_typologies @=@ dataset @=@ 0033 -dnet:result_typologies @=@ dataset 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0030 @=@ Audio -dnet:publication_resource @=@ 0030 @=@ http://purl.org/coar/resource_type/c_18cc -dnet:publication_resource @=@ 0030 @=@ sound -dnet:publication_resource @=@ 0044 @=@ Graduate diploma -dnet:publication_resource @=@ 0044 @=@ Undergraduate diploma +dnet:pid_types @=@ orcid @=@ ORCID12 +dnet:review_levels @=@ 0000 @=@ UNKNOWN dnet:review_levels @=@ 0002 @=@ 80 大阪経大学会「Working Paper」 dnet:review_levels @=@ 0002 @=@ AO dnet:review_levels @=@ 0002 @=@ ARTICLE SANS COMITE DE LECTURE (ASCL) @@ -1025,6 +977,7 @@ dnet:review_levels @=@ 0002 @=@ Discussion Paper dnet:review_levels @=@ 0002 @=@ Document de travail (Working Paper) dnet:review_levels @=@ 0002 @=@ Documento de trabajo dnet:review_levels @=@ 0002 @=@ Documento de trabajo de investigaci??n +dnet:review_levels @=@ 0002 @=@ Draft dnet:review_levels @=@ 0002 @=@ E-pub ahead of print dnet:review_levels @=@ 0002 @=@ Editorial de revista, no evaluado por pares dnet:review_levels @=@ 0002 @=@ Editorial de revista, não avaliado por pares @@ -1095,7 +1048,6 @@ dnet:review_levels @=@ 0002 @=@ communication_invitee dnet:review_levels @=@ 0002 @=@ doc-type:preprint dnet:review_levels @=@ 0002 @=@ doc-type:workingPaper dnet:review_levels @=@ 0002 @=@ draf -dnet:review_levels @=@ 0002 @=@ draft dnet:review_levels @=@ 0002 @=@ eu-repo/semantics/submittedVersion dnet:review_levels @=@ 0002 @=@ http://purl.org/coar/resource_type/c_8042 dnet:review_levels @=@ 0002 @=@ http://purl.org/coar/resource_type/c_816b @@ -1178,6 +1130,7 @@ dnet:review_levels @=@ 0001 @=@ Artículo de investigación, Investigaciones ori dnet:review_levels @=@ 0001 @=@ Artículo evaluado por pares dnet:review_levels @=@ 0001 @=@ Artículo evaluado por pares, Ensayos de investigación dnet:review_levels @=@ 0001 @=@ Artículo evaluado por pares, Investigaciones empíricas, Artículos de investigación +dnet:review_levels @=@ 0001 @=@ Artículo revisado dnet:review_levels @=@ 0001 @=@ Artículo revisado por pares dnet:review_levels @=@ 0001 @=@ Artículos de estudiantes, Artículo evaluado por pares, Artículos de investigación dnet:review_levels @=@ 0001 @=@ Artículos de investigación evaluados por doble ciego @@ -1185,7 +1138,7 @@ dnet:review_levels @=@ 0001 @=@ Artículos evaluadores por doble ciego dnet:review_levels @=@ 0001 @=@ Artículos evaluados por pares dnet:review_levels @=@ 0001 @=@ Artículos evaluados por pares académicos dnet:review_levels @=@ 0001 @=@ Artículos revisados por pares -dnet:review_levels @=@ 0001 @=@ avaliadas pelos pares +dnet:review_levels @=@ 0001 @=@ Avaliadas pelos pares dnet:review_levels @=@ 0001 @=@ Avaliado anonimamente por pares dnet:review_levels @=@ 0001 @=@ Avaliado em duplo cego por pares dnet:review_levels @=@ 0001 @=@ Avaliado pela Editoria @@ -1236,6 +1189,7 @@ dnet:review_levels @=@ 0001 @=@ Peer-reviewed Review dnet:review_levels @=@ 0001 @=@ Peer-reviewed Review Article dnet:review_levels @=@ 0001 @=@ Peer-reviewed Text dnet:review_levels @=@ 0001 @=@ Peer-reviewed communication +dnet:review_levels @=@ 0001 @=@ Peer-reviewed conference proceedings dnet:review_levels @=@ 0001 @=@ Peer-reviewed research article dnet:review_levels @=@ 0001 @=@ Peer-reviewed short communication dnet:review_levels @=@ 0001 @=@ PeerReviewed diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/terms.txt b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/terms.txt index 1daca3ca90..59bed7c3a0 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/terms.txt +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/terms.txt @@ -1,414 +1,39 @@ ModularUiLabels @=@ ModularUiLabels @=@ PendingRepositoryResources @=@ Pending datasource ModularUiLabels @=@ ModularUiLabels @=@ RepositoryServiceResources @=@ Valid datasource -dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MORE/OPENACCESS_VERSION @=@ Another Open Access version of a publication 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+dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MORE/SUBJECT/JEL @=@ Another Journal of Economic Literature (JEL) classification term that can be associated to your publications +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MORE/SUBJECT/MESHEUROPMC @=@ Another classification term from the Medical Subject Headings (MeSH) that can be associated to your publications +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/PROJECT @=@ A project reference that can be associated to your publications +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/DATASET/IS_SUPPLEMENTED_BY @=@ A dataset that is supplemented by your records +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/AUTHOR/ORCID @=@ An Open Researcher and Contributor ID (ORCID) that can be associated to an author of your publications +dnet:review_levels @=@ dnet:review_levels @=@ 0000 @=@ Unknown dnet:review_levels @=@ dnet:review_levels @=@ 0002 @=@ nonPeerReviewed dnet:review_levels @=@ dnet:review_levels @=@ 0001 @=@ peerReviewed \ No newline at end of file From 8a4f84f8c03cc38bba6f928b631b0d2e85ffd43a Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Tue, 16 Jun 2020 12:34:13 +0200 Subject: [PATCH 54/62] refactoring --- dhp-workflows/dhp-broker-events/pom.xml | 2 +- dhp-workflows/dhp-broker-events/report.xml | 37 ++++ .../eu/dnetlib/dhp/broker/model/Event.java | 8 +- .../dhp/broker/model/EventFactory.java | 53 ++--- .../broker/oa/GenerateEventsApplication.java | 54 +++-- .../dhp/broker/oa/matchers/UpdateMatcher.java | 29 ++- .../AbstractEnrichMissingDataset.java | 22 +- .../relatedProjects/EnrichMissingProject.java | 23 +- .../relatedProjects/EnrichMoreProject.java | 29 ++- .../AbstractEnrichMissingPublication.java | 22 +- .../EnrichMissingSoftware.java | 22 +- .../relatedSoftware/EnrichMoreSoftware.java | 20 +- .../simple/EnrichMissingAbstract.java | 13 +- .../simple/EnrichMissingAuthorOrcid.java | 44 ++-- .../simple/EnrichMissingOpenAccess.java | 19 +- .../oa/matchers/simple/EnrichMissingPid.java | 17 +- .../simple/EnrichMissingPublicationDate.java | 15 +- .../matchers/simple/EnrichMissingSubject.java | 38 ++-- .../matchers/simple/EnrichMoreOpenAccess.java | 20 +- .../oa/matchers/simple/EnrichMorePid.java | 27 ++- .../oa/matchers/simple/EnrichMoreSubject.java | 32 ++- .../dhp/broker/oa/util/BrokerConstants.java | 19 +- .../dhp/broker/oa/util/ConversionUtils.java | 51 ++++- .../dhp/broker/oa/util/EventFinder.java | 4 +- .../dhp/broker/oa/util/UpdateInfo.java | 51 ++--- .../aggregators/simple/ResultAggregator.java | 6 +- .../util/aggregators/simple/ResultGroup.java | 8 +- .../OpenaireBrokerResultAggregator.java | 69 ++++++ .../aggregators/withRels/RelatedDataset.java | 10 +- .../withRels/RelatedEntityFactory.java | 12 +- .../aggregators/withRels/RelatedProject.java | 11 +- .../withRels/RelatedPublication.java | 11 +- .../aggregators/withRels/RelatedSoftware.java | 10 +- .../withRels/ResultWithRelations.java | 55 ----- .../ResultWithRelationsAggregator.java | 68 ------ .../oa/graph/reflections/ReflectionTest.java | 200 ++++++++++++++++++ 36 files changed, 640 insertions(+), 491 deletions(-) create mode 100644 dhp-workflows/dhp-broker-events/report.xml create mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/OpenaireBrokerResultAggregator.java delete mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/ResultWithRelations.java delete mode 100644 dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/ResultWithRelationsAggregator.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/reflections/ReflectionTest.java diff --git a/dhp-workflows/dhp-broker-events/pom.xml b/dhp-workflows/dhp-broker-events/pom.xml index f060a60bc5..eddc042c6b 100644 --- a/dhp-workflows/dhp-broker-events/pom.xml +++ b/dhp-workflows/dhp-broker-events/pom.xml @@ -61,7 +61,7 @@ eu.dnetlib dnet-openaire-broker-common - [2.0.1,3.0.0) + [3.0.1,4.0.0) diff --git a/dhp-workflows/dhp-broker-events/report.xml b/dhp-workflows/dhp-broker-events/report.xml new file mode 100644 index 0000000000..6e706f7230 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/report.xml @@ -0,0 +1,37 @@ + + + + Feature Extraction + + + TCPFLOW + 1.5.0 + + 4.2.1 (4.2.1 Compatible Apple LLVM 11.0.0 (clang-1100.0.33.8)) + -D_THREAD_SAFE -pthread -I/usr/local/include -I/usr/local/include -DUTC_OFFSET=+0000 + -g -D_THREAD_SAFE -pthread -g -O3 -MD -Wpointer-arith -Wmissing-declarations -Wmissing-prototypes -Wshadow -Wwrite-strings -Wcast-align -Waggregate-return -Wbad-function-cast -Wcast-qual -Wundef -Wredundant-decls -Wdisabled-optimization -Wfloat-equal -Wmultichar -Wc++-compat -Wmissing-noreturn -Wall -Wstrict-prototypes -MD -D_FORTIFY_SOURCE=2 -Wpointer-arith -Wmissing-declarations -Wmissing-prototypes -Wshadow -Wwrite-strings -Wcast-align -Waggregate-return -Wbad-function-cast -Wcast-qual -Wundef -Wredundant-decls -Wdisabled-optimization -Wfloat-equal -Wmultichar -Wc++-compat -Wmissing-noreturn -Wall -Wstrict-prototypes + -g -D_THREAD_SAFE -pthread -g -O3 -Wall -MD -D_FORTIFY_SOURCE=2 -Wpointer-arith -Wshadow -Wwrite-strings -Wcast-align -Wredundant-decls -Wdisabled-optimization -Wfloat-equal -Wmultichar -Wmissing-noreturn -Woverloaded-virtual -Wsign-promo -funit-at-a-time -Weffc++ -std=c++11 -Wall -MD -D_FORTIFY_SOURCE=2 -Wpointer-arith -Wshadow -Wwrite-strings -Wcast-align -Wredundant-decls -Wdisabled-optimization -Wfloat-equal -Wmultichar -Wmissing-noreturn -Woverloaded-virtual -Wsign-promo -funit-at-a-time -Weffc++ + -L/usr/local/lib -L/usr/local/lib + -lpython2.7 -lpython2.7 -lpcap -lbz2 -lexpat -lsqlite3 -lcrypto -lssl -lcrypto -ldl -lz + 2019-10-11T01:16:58 + + + + + Darwin + 19.5.0 + Darwin Kernel Version 19.5.0: Tue May 26 20:41:44 PDT 2020; root:xnu-6153.121.2~2/RELEASE_X86_64 + Micheles-MBP.local + x86_64 + tcpflow + 501 + michele + 2020-06-15T14:55:03Z + + + + + 0 diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/Event.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/Event.java index 0512a38134..f94d286e4f 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/Event.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/Event.java @@ -1,9 +1,15 @@ package eu.dnetlib.dhp.broker.model; +import java.io.Serializable; import java.util.Map; -public class Event { +public class Event implements Serializable { + + /** + * + */ + private static final long serialVersionUID = -5936790326505781395L; private String eventId; diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/EventFactory.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/EventFactory.java index 9146cf422f..bf4f62d243 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/EventFactory.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/EventFactory.java @@ -6,17 +6,13 @@ import java.util.Date; import java.util.HashMap; import java.util.List; import java.util.Map; -import java.util.stream.Collectors; import org.apache.commons.codec.digest.DigestUtils; import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.time.DateUtils; +import eu.dnetlib.broker.objects.OpenaireBrokerResult; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; -import eu.dnetlib.dhp.schema.oaf.Author; -import eu.dnetlib.dhp.schema.oaf.KeyValue; -import eu.dnetlib.dhp.schema.oaf.Result; -import eu.dnetlib.dhp.schema.oaf.StructuredProperty; public class EventFactory { @@ -37,8 +33,7 @@ public class EventFactory { final Map map = createMapFromResult(updateInfo); final String eventId = calculateEventId( - updateInfo.getTopicPath(), updateInfo.getTarget().getResult().getOriginalId().get(0), - updateInfo.getHighlightValueAsString()); + updateInfo.getTopicPath(), updateInfo.getTarget().getOriginalId(), updateInfo.getHighlightValueAsString()); res.setEventId(eventId); res.setProducerId(PRODUCER_ID); @@ -54,53 +49,31 @@ public class EventFactory { private static Map createMapFromResult(final UpdateInfo updateInfo) { final Map map = new HashMap<>(); - final Result source = updateInfo.getSource().getResult(); - final Result target = updateInfo.getTarget().getResult(); + final OpenaireBrokerResult source = updateInfo.getSource(); + final OpenaireBrokerResult target = updateInfo.getTarget(); - final List collectedFrom = target.getCollectedfrom(); - if (collectedFrom.size() == 1) { - map.put("target_datasource_id", collectedFrom.get(0).getKey()); - map.put("target_datasource_name", collectedFrom.get(0).getValue()); - } + map.put("target_datasource_id", target.getCollectedFromId()); + map.put("target_datasource_name", target.getCollectedFromName()); - final List ids = target.getOriginalId(); - if (ids.size() > 0) { - map.put("target_publication_id", ids.get(0)); - } + map.put("target_publication_id", target.getOriginalId()); - final List titles = target.getTitle(); + final List titles = target.getTitles(); if (titles.size() > 0) { map.put("target_publication_title", titles.get(0)); } - final long date = parseDateTolong(target.getDateofacceptance().getValue()); + final long date = parseDateTolong(target.getPublicationdate()); if (date > 0) { map.put("target_dateofacceptance", date); } - final List subjects = target.getSubject(); - if (subjects.size() > 0) { - map - .put( - "target_publication_subject_list", - subjects.stream().map(StructuredProperty::getValue).collect(Collectors.toList())); - } - - final List authors = target.getAuthor(); - if (authors.size() > 0) { - map - .put( - "target_publication_author_list", - authors.stream().map(Author::getFullname).collect(Collectors.toList())); - } + map.put("target_publication_subject_list", target.getSubjects()); + map.put("target_publication_author_list", target.getCreators()); // PROVENANCE INFO map.put("trust", updateInfo.getTrust()); - final List sourceCollectedFrom = source.getCollectedfrom(); - if (sourceCollectedFrom.size() == 1) { - map.put("provenance_datasource_id", sourceCollectedFrom.get(0).getKey()); - map.put("provenance_datasource_name", sourceCollectedFrom.get(0).getValue()); - } + map.put("provenance_datasource_id", source.getCollectedFromId()); + map.put("provenance_datasource_name", source.getCollectedFromName()); map.put("provenance_publication_id_list", source.getOriginalId()); return map; diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java index 4d40ba80d6..940d7f9f32 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java @@ -18,18 +18,20 @@ import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.broker.objects.OpenaireBrokerResult; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.broker.model.Event; import eu.dnetlib.dhp.broker.oa.util.BrokerConstants; +import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; import eu.dnetlib.dhp.broker.oa.util.EventFinder; import eu.dnetlib.dhp.broker.oa.util.EventGroup; import eu.dnetlib.dhp.broker.oa.util.aggregators.simple.ResultAggregator; import eu.dnetlib.dhp.broker.oa.util.aggregators.simple.ResultGroup; +import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.OpenaireBrokerResultAggregator; import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.RelatedEntityFactory; import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.RelatedProject; -import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.ResultWithRelations; -import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.ResultWithRelationsAggregator; import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct; import eu.dnetlib.dhp.schema.oaf.Project; import eu.dnetlib.dhp.schema.oaf.Publication; import eu.dnetlib.dhp.schema.oaf.Relation; @@ -73,6 +75,8 @@ public class GenerateEventsApplication { log.info("dedupConfigProfileId: {}", dedupConfigProfileId); final SparkConf conf = new SparkConf(); + conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); + conf.registerKryoClasses(BrokerConstants.getModelClasses()); final DedupConfig dedupConfig = loadDedupConfig(isLookupUrl, dedupConfigProfileId); @@ -80,13 +84,16 @@ public class GenerateEventsApplication { removeOutputDir(spark, eventsPath); - final Dataset all = spark.emptyDataset(Encoders.kryo(Event.class)); - - for (final Class r1 : BrokerConstants.RESULT_CLASSES) { - all.union(generateEvents(spark, graphPath, r1, dedupConfig)); - } - - all.write().mode(SaveMode.Overwrite).option("compression", "gzip").json(eventsPath); + spark + .emptyDataset(Encoders.kryo(Event.class)) + .union(generateEvents(spark, graphPath, Publication.class, dedupConfig)) + .union(generateEvents(spark, graphPath, eu.dnetlib.dhp.schema.oaf.Dataset.class, dedupConfig)) + .union(generateEvents(spark, graphPath, Software.class, dedupConfig)) + .union(generateEvents(spark, graphPath, OtherResearchProduct.class, dedupConfig)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(eventsPath); }); } @@ -101,18 +108,18 @@ public class GenerateEventsApplication { final Class sourceClass, final DedupConfig dedupConfig) { - final Dataset results = expandResultsWithRelations(spark, graphPath, sourceClass); + final Dataset results = expandResultsWithRelations(spark, graphPath, sourceClass); final Dataset mergedRels = readPath(spark, graphPath + "/relation", Relation.class) .filter(r -> r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS)); - final TypedColumn, ResultGroup> aggr = new ResultAggregator() + final TypedColumn, ResultGroup> aggr = new ResultAggregator() .toColumn(); return results .joinWith(mergedRels, results.col("result.id").equalTo(mergedRels.col("source")), "inner") .groupByKey( - (MapFunction, String>) t -> t._2.getTarget(), Encoders.STRING()) + (MapFunction, String>) t -> t._2.getTarget(), Encoders.STRING()) .agg(aggr) .map((MapFunction, ResultGroup>) t -> t._2, Encoders.kryo(ResultGroup.class)) .filter(ResultGroup::isValid) @@ -122,7 +129,7 @@ public class GenerateEventsApplication { .flatMap(group -> group.getData().iterator(), Encoders.kryo(Event.class)); } - private static Dataset expandResultsWithRelations( + private static Dataset expandResultsWithRelations( final SparkSession spark, final String graphPath, final Class sourceClass) { @@ -135,14 +142,15 @@ public class GenerateEventsApplication { final Dataset rels = readPath(spark, graphPath + "/relation", Relation.class) .filter(r -> !r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS)); - final Dataset r0 = readPath( + final Dataset r0 = readPath( spark, graphPath + "/" + sourceClass.getSimpleName().toLowerCase(), Result.class) .filter(r -> r.getDataInfo().getDeletedbyinference()) - .map(r -> new ResultWithRelations(r), Encoders.kryo(ResultWithRelations.class)); - final Dataset r1 = join(r0, rels, relatedEntities(projects, rels, RelatedProject.class)); - final Dataset r2 = join(r1, rels, relatedEntities(softwares, rels, RelatedProject.class)); - final Dataset r3 = join(r2, rels, relatedEntities(datasets, rels, RelatedProject.class)); - final Dataset r4 = join( + .map(ConversionUtils::oafResultToBrokerResult, Encoders.kryo(OpenaireBrokerResult.class)); + + final Dataset r1 = join(r0, rels, relatedEntities(projects, rels, RelatedProject.class)); + final Dataset r2 = join(r1, rels, relatedEntities(softwares, rels, RelatedProject.class)); + final Dataset r3 = join(r2, rels, relatedEntities(datasets, rels, RelatedProject.class)); + final Dataset r4 = join( r3, rels, relatedEntities(publications, rels, RelatedProject.class)); ; @@ -159,20 +167,20 @@ public class GenerateEventsApplication { Encoders.kryo(clazz)); } - private static Dataset join(final Dataset sources, + private static Dataset join(final Dataset sources, final Dataset rels, final Dataset typedRels) { - final TypedColumn, ResultWithRelations> aggr = new ResultWithRelationsAggregator() + final TypedColumn, OpenaireBrokerResult> aggr = new OpenaireBrokerResultAggregator() .toColumn(); ; return sources .joinWith(typedRels, sources.col("result.id").equalTo(rels.col("source")), "left_outer") .groupByKey( - (MapFunction, String>) t -> t._1.getResult().getId(), Encoders.STRING()) + (MapFunction, String>) t -> t._1.getOpenaireId(), Encoders.STRING()) .agg(aggr) - .map(t -> t._2, Encoders.kryo(ResultWithRelations.class)); + .map(t -> t._2, Encoders.kryo(OpenaireBrokerResult.class)); } public static Dataset readPath( diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/UpdateMatcher.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/UpdateMatcher.java index 0e57f32f98..13aeefb2fc 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/UpdateMatcher.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/UpdateMatcher.java @@ -12,22 +12,20 @@ import java.util.function.Function; import org.apache.commons.codec.digest.DigestUtils; import org.apache.commons.lang3.StringUtils; -import eu.dnetlib.broker.objects.Publication; +import eu.dnetlib.broker.objects.OpenaireBrokerResult; import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; -import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.ResultWithRelations; -import eu.dnetlib.dhp.schema.oaf.Field; import eu.dnetlib.pace.config.DedupConfig; public abstract class UpdateMatcher { private final boolean multipleUpdate; private final Function topicFunction; - private final BiConsumer compileHighlightFunction; + private final BiConsumer compileHighlightFunction; private final Function highlightToStringFunction; public UpdateMatcher(final boolean multipleUpdate, final Function topicFunction, - final BiConsumer compileHighlightFunction, + final BiConsumer compileHighlightFunction, final Function highlightToStringFunction) { this.multipleUpdate = multipleUpdate; this.topicFunction = topicFunction; @@ -35,19 +33,18 @@ public abstract class UpdateMatcher { this.highlightToStringFunction = highlightToStringFunction; } - public Collection> searchUpdatesForRecord(final ResultWithRelations res, - final Collection others, + public Collection> searchUpdatesForRecord(final OpenaireBrokerResult res, + final Collection others, final DedupConfig dedupConfig) { final Map> infoMap = new HashMap<>(); - for (final ResultWithRelations source : others) { + for (final OpenaireBrokerResult source : others) { if (source != res) { for (final T hl : findDifferences(source, res)) { final Topic topic = getTopicFunction().apply(hl); final UpdateInfo info = new UpdateInfo<>(topic, hl, source, res, getCompileHighlightFunction(), - getHighlightToStringFunction(), - dedupConfig); + getHighlightToStringFunction(), dedupConfig); final String s = DigestUtils.md5Hex(info.getHighlightValueAsString()); if (!infoMap.containsKey(s) || infoMap.get(s).getTrust() < info.getTrust()) { } else { @@ -71,14 +68,14 @@ public abstract class UpdateMatcher { } } - protected abstract List findDifferences(ResultWithRelations source, ResultWithRelations target); + protected abstract List findDifferences(OpenaireBrokerResult source, OpenaireBrokerResult target); - protected static boolean isMissing(final List> list) { - return list == null || list.isEmpty() || StringUtils.isBlank(list.get(0).getValue()); + protected static boolean isMissing(final List list) { + return list == null || list.isEmpty() || StringUtils.isBlank(list.get(0)); } - protected boolean isMissing(final Field field) { - return field == null || StringUtils.isBlank(field.getValue()); + protected boolean isMissing(final String field) { + return StringUtils.isBlank(field); } public boolean isMultipleUpdate() { @@ -89,7 +86,7 @@ public abstract class UpdateMatcher { return topicFunction; } - public BiConsumer getCompileHighlightFunction() { + public BiConsumer getCompileHighlightFunction() { return compileHighlightFunction; } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/AbstractEnrichMissingDataset.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/AbstractEnrichMissingDataset.java index a8e0a2c423..7a58f986ba 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/AbstractEnrichMissingDataset.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedDatasets/AbstractEnrichMissingDataset.java @@ -5,45 +5,39 @@ import java.util.List; import java.util.Set; import java.util.stream.Collectors; +import eu.dnetlib.broker.objects.Dataset; +import eu.dnetlib.broker.objects.OpenaireBrokerResult; import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; -import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; -import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.RelatedDataset; -import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.ResultWithRelations; -import eu.dnetlib.dhp.schema.oaf.Dataset; public abstract class AbstractEnrichMissingDataset - extends UpdateMatcher { + extends UpdateMatcher { public AbstractEnrichMissingDataset(final Topic topic) { super(true, rel -> topic, (p, rel) -> p.getDatasets().add(rel), - rel -> rel.getInstances().get(0).getUrl()); + rel -> rel.getOriginalId()); } protected abstract boolean filterByType(String relType); @Override - protected final List findDifferences( - final ResultWithRelations source, - final ResultWithRelations target) { + protected final List findDifferences(final OpenaireBrokerResult source, + final OpenaireBrokerResult target) { final Set existingDatasets = target .getDatasets() .stream() .filter(rel -> filterByType(rel.getRelType())) - .map(RelatedDataset::getRelDataset) - .map(Dataset::getId) + .map(Dataset::getOriginalId) .collect(Collectors.toSet()); return source .getDatasets() .stream() .filter(rel -> filterByType(rel.getRelType())) - .map(RelatedDataset::getRelDataset) - .filter(d -> !existingDatasets.contains(d.getId())) - .map(ConversionUtils::oafDatasetToBrokerDataset) + .filter(d -> !existingDatasets.contains(d.getOriginalId())) .collect(Collectors.toList()); } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedProjects/EnrichMissingProject.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedProjects/EnrichMissingProject.java index ab4325c1ec..fa5fde7251 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedProjects/EnrichMissingProject.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedProjects/EnrichMissingProject.java @@ -1,19 +1,15 @@ package eu.dnetlib.dhp.broker.oa.matchers.relatedProjects; -import java.util.Arrays; +import java.util.ArrayList; import java.util.List; -import java.util.stream.Collectors; +import eu.dnetlib.broker.objects.OpenaireBrokerResult; import eu.dnetlib.broker.objects.Project; import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; -import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; -import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.RelatedProject; -import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.ResultWithRelations; -public class EnrichMissingProject - extends UpdateMatcher { +public class EnrichMissingProject extends UpdateMatcher { public EnrichMissingProject() { super(true, @@ -23,16 +19,11 @@ public class EnrichMissingProject } @Override - protected List findDifferences(final ResultWithRelations source, final ResultWithRelations target) { - if (source.getProjects().isEmpty()) { - return Arrays.asList(); + protected List findDifferences(final OpenaireBrokerResult source, final OpenaireBrokerResult target) { + if (target.getProjects().isEmpty()) { + return source.getProjects(); } else { - return target - .getProjects() - .stream() - .map(RelatedProject::getRelProject) - .map(ConversionUtils::oafProjectToBrokerProject) - .collect(Collectors.toList()); + return new ArrayList<>(); } } } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedProjects/EnrichMoreProject.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedProjects/EnrichMoreProject.java index 3bf23a36bd..ca63aeb49f 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedProjects/EnrichMoreProject.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedProjects/EnrichMoreProject.java @@ -5,39 +5,38 @@ import java.util.List; import java.util.Set; import java.util.stream.Collectors; +import eu.dnetlib.broker.objects.OpenaireBrokerResult; +import eu.dnetlib.broker.objects.Project; import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; -import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; -import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.RelatedProject; -import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.ResultWithRelations; -import eu.dnetlib.dhp.schema.oaf.Project; -public class EnrichMoreProject extends UpdateMatcher { +public class EnrichMoreProject extends UpdateMatcher { public EnrichMoreProject() { super(true, prj -> Topic.ENRICH_MORE_PROJECT, (p, prj) -> p.getProjects().add(prj), - prj -> prj.getFunder() + "::" + prj.getFundingProgram() + prj.getCode()); + prj -> projectAsString(prj)); + } + + private static String projectAsString(final Project prj) { + return prj.getFunder() + "::" + prj.getFundingProgram() + "::" + prj.getCode(); } @Override - protected List findDifferences(final ResultWithRelations source, - final ResultWithRelations target) { + protected List findDifferences(final OpenaireBrokerResult source, + final OpenaireBrokerResult target) { - final Set existingProjects = source + final Set existingProjects = target .getProjects() .stream() - .map(RelatedProject::getRelProject) - .map(Project::getId) + .map(EnrichMoreProject::projectAsString) .collect(Collectors.toSet()); - return target + return source .getProjects() .stream() - .map(RelatedProject::getRelProject) - .filter(p -> !existingProjects.contains(p.getId())) - .map(ConversionUtils::oafProjectToBrokerProject) + .filter(p -> !existingProjects.contains(projectAsString(p))) .collect(Collectors.toList()); } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/AbstractEnrichMissingPublication.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/AbstractEnrichMissingPublication.java index bba3e96480..3008639493 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/AbstractEnrichMissingPublication.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/AbstractEnrichMissingPublication.java @@ -5,21 +5,18 @@ import java.util.List; import java.util.Set; import java.util.stream.Collectors; +import eu.dnetlib.broker.objects.OpenaireBrokerResult; +import eu.dnetlib.broker.objects.Publication; import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; -import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; -import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.RelatedPublication; -import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.ResultWithRelations; -import eu.dnetlib.dhp.schema.oaf.Publication; -public abstract class AbstractEnrichMissingPublication - extends UpdateMatcher { +public abstract class AbstractEnrichMissingPublication extends UpdateMatcher { public AbstractEnrichMissingPublication(final Topic topic) { super(true, rel -> topic, (p, rel) -> p.getPublications().add(rel), - rel -> rel.getInstances().get(0).getUrl()); + rel -> rel.getOriginalId()); } @@ -27,24 +24,21 @@ public abstract class AbstractEnrichMissingPublication @Override protected final List findDifferences( - final ResultWithRelations source, - final ResultWithRelations target) { + final OpenaireBrokerResult source, + final OpenaireBrokerResult target) { final Set existingPublications = target .getPublications() .stream() .filter(rel -> filterByType(rel.getRelType())) - .map(RelatedPublication::getRelPublication) - .map(Publication::getId) + .map(Publication::getOriginalId) .collect(Collectors.toSet()); return source .getPublications() .stream() .filter(rel -> filterByType(rel.getRelType())) - .map(RelatedPublication::getRelPublication) - .filter(d -> !existingPublications.contains(d.getId())) - .map(ConversionUtils::oafResultToBrokerPublication) + .filter(p -> !existingPublications.contains(p.getOriginalId())) .collect(Collectors.toList()); } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedSoftware/EnrichMissingSoftware.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedSoftware/EnrichMissingSoftware.java index 6090939dc5..76ae061e67 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedSoftware/EnrichMissingSoftware.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedSoftware/EnrichMissingSoftware.java @@ -1,15 +1,12 @@ package eu.dnetlib.dhp.broker.oa.matchers.relatedSoftware; -import java.util.Arrays; +import java.util.ArrayList; import java.util.List; -import java.util.stream.Collectors; +import eu.dnetlib.broker.objects.OpenaireBrokerResult; import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; -import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; -import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.RelatedSoftware; -import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.ResultWithRelations; public class EnrichMissingSoftware extends UpdateMatcher { @@ -23,18 +20,13 @@ public class EnrichMissingSoftware @Override protected List findDifferences( - final ResultWithRelations source, - final ResultWithRelations target) { + final OpenaireBrokerResult source, + final OpenaireBrokerResult target) { - if (source.getSoftwares().isEmpty()) { - return Arrays.asList(); + if (target.getSoftwares().isEmpty()) { + return source.getSoftwares(); } else { - return target - .getSoftwares() - .stream() - .map(RelatedSoftware::getRelSoftware) - .map(ConversionUtils::oafSoftwareToBrokerSoftware) - .collect(Collectors.toList()); + return new ArrayList<>(); } } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedSoftware/EnrichMoreSoftware.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedSoftware/EnrichMoreSoftware.java index ba422f436c..ebd421b8e7 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedSoftware/EnrichMoreSoftware.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedSoftware/EnrichMoreSoftware.java @@ -5,15 +5,12 @@ import java.util.List; import java.util.Set; import java.util.stream.Collectors; +import eu.dnetlib.broker.objects.OpenaireBrokerResult; +import eu.dnetlib.broker.objects.Software; import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; -import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; -import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.RelatedSoftware; -import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.ResultWithRelations; -import eu.dnetlib.dhp.schema.oaf.Software; -public class EnrichMoreSoftware - extends UpdateMatcher { +public class EnrichMoreSoftware extends UpdateMatcher { public EnrichMoreSoftware() { super(true, @@ -24,22 +21,19 @@ public class EnrichMoreSoftware @Override protected List findDifferences( - final ResultWithRelations source, - final ResultWithRelations target) { + final OpenaireBrokerResult source, + final OpenaireBrokerResult target) { final Set existingSoftwares = source .getSoftwares() .stream() - .map(RelatedSoftware::getRelSoftware) - .map(Software::getId) + .map(Software::getName) .collect(Collectors.toSet()); return target .getSoftwares() .stream() - .map(RelatedSoftware::getRelSoftware) - .filter(p -> !existingSoftwares.contains(p.getId())) - .map(ConversionUtils::oafSoftwareToBrokerSoftware) + .filter(p -> !existingSoftwares.contains(p.getName())) .collect(Collectors.toList()); } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingAbstract.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingAbstract.java index 25d5f9d8ac..b2cbbce2c5 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingAbstract.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingAbstract.java @@ -5,9 +5,9 @@ import java.util.ArrayList; import java.util.Arrays; import java.util.List; +import eu.dnetlib.broker.objects.OpenaireBrokerResult; import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; -import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.ResultWithRelations; public class EnrichMissingAbstract extends UpdateMatcher { @@ -19,13 +19,12 @@ public class EnrichMissingAbstract extends UpdateMatcher { } @Override - protected List findDifferences(final ResultWithRelations source, - final ResultWithRelations target) { - if (isMissing(target.getResult().getDescription()) && !isMissing(source.getResult().getDescription())) { - return Arrays - .asList(source.getResult().getDescription().get(0).getValue()); + protected List findDifferences(final OpenaireBrokerResult source, final OpenaireBrokerResult target) { + if (isMissing(target.getAbstracts()) && !isMissing(source.getAbstracts())) { + return Arrays.asList(source.getAbstracts().get(0)); + } else { + return new ArrayList<>(); } - return new ArrayList<>(); } } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingAuthorOrcid.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingAuthorOrcid.java index eed2d0be86..c4b96e67bf 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingAuthorOrcid.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingAuthorOrcid.java @@ -1,53 +1,43 @@ package eu.dnetlib.dhp.broker.oa.matchers.simple; -import java.util.ArrayList; import java.util.List; import java.util.Set; import java.util.stream.Collectors; +import org.apache.commons.lang3.StringUtils; + +import eu.dnetlib.broker.objects.Author; +import eu.dnetlib.broker.objects.OpenaireBrokerResult; import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; -import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.ResultWithRelations; -import eu.dnetlib.dhp.schema.oaf.Author; -import eu.dnetlib.dhp.schema.oaf.StructuredProperty; -public class EnrichMissingAuthorOrcid extends UpdateMatcher { +public class EnrichMissingAuthorOrcid extends UpdateMatcher { public EnrichMissingAuthorOrcid() { super(true, aut -> Topic.ENRICH_MISSING_AUTHOR_ORCID, (p, aut) -> p.getCreators().add(aut), - aut -> aut); + aut -> aut.getOrcid()); } @Override - protected List findDifferences(final ResultWithRelations source, - final ResultWithRelations target) { + protected List findDifferences(final OpenaireBrokerResult source, + final OpenaireBrokerResult target) { final Set existingOrcids = target - .getResult() - .getAuthor() + .getCreators() .stream() - .map(Author::getPid) - .flatMap(List::stream) - .filter(pid -> pid.getQualifier().getClassid().equalsIgnoreCase("orcid")) - .map(pid -> pid.getValue()) + .map(Author::getOrcid) + .filter(StringUtils::isNotBlank) .collect(Collectors.toSet()); - final List list = new ArrayList<>(); + return source + .getCreators() + .stream() + .filter(a -> StringUtils.isNotBlank(a.getOrcid())) + .filter(a -> !existingOrcids.contains(a.getOrcid())) + .collect(Collectors.toList()); - for (final Author author : source.getResult().getAuthor()) { - final String name = author.getFullname(); - - for (final StructuredProperty pid : author.getPid()) { - if (pid.getQualifier().getClassid().equalsIgnoreCase("orcid") - && !existingOrcids.contains(pid.getValue())) { - list.add(name + " [ORCID: " + pid.getValue() + "]"); - } - } - } - - return list; } } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingOpenAccess.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingOpenAccess.java index e8ca18ae9d..e870cf1faa 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingOpenAccess.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingOpenAccess.java @@ -6,11 +6,10 @@ import java.util.List; import java.util.stream.Collectors; import eu.dnetlib.broker.objects.Instance; +import eu.dnetlib.broker.objects.OpenaireBrokerResult; import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; import eu.dnetlib.dhp.broker.oa.util.BrokerConstants; -import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; -import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.ResultWithRelations; public class EnrichMissingOpenAccess extends UpdateMatcher { @@ -22,13 +21,12 @@ public class EnrichMissingOpenAccess extends UpdateMatcher { } @Override - protected List findDifferences(final ResultWithRelations source, - final ResultWithRelations target) { + protected List findDifferences(final OpenaireBrokerResult source, + final OpenaireBrokerResult target) { final long count = target - .getResult() - .getInstance() + .getInstances() .stream() - .map(i -> i.getAccessright().getClassid()) + .map(Instance::getLicense) .filter(right -> right.equals(BrokerConstants.OPEN_ACCESS)) .count(); @@ -37,12 +35,9 @@ public class EnrichMissingOpenAccess extends UpdateMatcher { } return source - .getResult() - .getInstance() + .getInstances() .stream() - .filter(i -> i.getAccessright().getClassid().equals(BrokerConstants.OPEN_ACCESS)) - .map(ConversionUtils::oafInstanceToBrokerInstances) - .flatMap(List::stream) + .filter(i -> i.getLicense().equals(BrokerConstants.OPEN_ACCESS)) .collect(Collectors.toList()); } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingPid.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingPid.java index 6c061a2e84..cc72d9fa9a 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingPid.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingPid.java @@ -5,13 +5,12 @@ import java.util.Arrays; import java.util.List; import java.util.stream.Collectors; -import eu.dnetlib.broker.objects.Pid; +import eu.dnetlib.broker.objects.OpenaireBrokerResult; +import eu.dnetlib.broker.objects.TypedValue; import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; -import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; -import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.ResultWithRelations; -public class EnrichMissingPid extends UpdateMatcher { +public class EnrichMissingPid extends UpdateMatcher { public EnrichMissingPid() { super(true, @@ -21,19 +20,17 @@ public class EnrichMissingPid extends UpdateMatcher { } @Override - protected List findDifferences(final ResultWithRelations source, - final ResultWithRelations target) { - final long count = target.getResult().getPid().size(); + protected List findDifferences(final OpenaireBrokerResult source, + final OpenaireBrokerResult target) { + final long count = target.getPids().size(); if (count > 0) { return Arrays.asList(); } return source - .getResult() - .getPid() + .getPids() .stream() - .map(ConversionUtils::oafPidToBrokerPid) .collect(Collectors.toList()); } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingPublicationDate.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingPublicationDate.java index 27a71740c6..ed8c26b5ab 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingPublicationDate.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingPublicationDate.java @@ -5,9 +5,9 @@ import java.util.ArrayList; import java.util.Arrays; import java.util.List; +import eu.dnetlib.broker.objects.OpenaireBrokerResult; import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; -import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.ResultWithRelations; public class EnrichMissingPublicationDate extends UpdateMatcher { @@ -19,13 +19,14 @@ public class EnrichMissingPublicationDate extends UpdateMatcher { } @Override - protected List findDifferences(final ResultWithRelations source, - final ResultWithRelations target) { - if (isMissing(target.getResult().getDateofacceptance()) - && !isMissing(source.getResult().getDateofacceptance())) { - return Arrays.asList(source.getResult().getDateofacceptance().getValue()); + protected List findDifferences(final OpenaireBrokerResult source, + final OpenaireBrokerResult target) { + + if (isMissing(target.getPublicationdate()) && !isMissing(source.getPublicationdate())) { + return Arrays.asList(source.getPublicationdate()); + } else { + return new ArrayList<>(); } - return new ArrayList<>(); } } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingSubject.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingSubject.java index 04de30089d..07b1fa41a9 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingSubject.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingSubject.java @@ -5,42 +5,38 @@ import java.util.List; import java.util.Set; import java.util.stream.Collectors; -import org.apache.commons.lang3.tuple.Pair; - +import eu.dnetlib.broker.objects.OpenaireBrokerResult; +import eu.dnetlib.broker.objects.TypedValue; import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; -import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; -import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.ResultWithRelations; -import eu.dnetlib.dhp.schema.oaf.Qualifier; -import eu.dnetlib.dhp.schema.oaf.StructuredProperty; -public class EnrichMissingSubject extends UpdateMatcher> { +public class EnrichMissingSubject extends UpdateMatcher { public EnrichMissingSubject() { super(true, - pair -> Topic.fromPath("ENRICH/MISSING/SUBJECT/" + pair.getLeft()), - (p, pair) -> p.getSubjects().add(pair.getRight()), - pair -> pair.getLeft() + "::" + pair.getRight()); + s -> Topic.fromPath("ENRICH/MISSING/SUBJECT/" + s.getType()), + (p, s) -> p.getSubjects().add(s), + s -> subjectAsString(s)); } @Override - protected List> findDifferences(final ResultWithRelations source, - final ResultWithRelations target) { - final Set existingTypes = target - .getResult() - .getSubject() + protected List findDifferences(final OpenaireBrokerResult source, + final OpenaireBrokerResult target) { + final Set existingSubject = target + .getSubjects() .stream() - .map(StructuredProperty::getQualifier) - .map(Qualifier::getClassid) + .map(s -> subjectAsString(s)) .collect(Collectors.toSet()); return source - .getResult() - .getPid() + .getSubjects() .stream() - .filter(pid -> !existingTypes.contains(pid.getQualifier().getClassid())) - .map(ConversionUtils::oafSubjectToPair) + .filter(s -> !existingSubject.contains(subjectAsString(s))) .collect(Collectors.toList()); } + private static String subjectAsString(final TypedValue s) { + return s.getType() + "::" + s.getValue(); + } + } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreOpenAccess.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreOpenAccess.java index 3ee4c8bdde..bfef3ee4f6 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreOpenAccess.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreOpenAccess.java @@ -6,11 +6,10 @@ import java.util.Set; import java.util.stream.Collectors; import eu.dnetlib.broker.objects.Instance; +import eu.dnetlib.broker.objects.OpenaireBrokerResult; import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; import eu.dnetlib.dhp.broker.oa.util.BrokerConstants; -import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; -import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.ResultWithRelations; public class EnrichMoreOpenAccess extends UpdateMatcher { @@ -22,24 +21,19 @@ public class EnrichMoreOpenAccess extends UpdateMatcher { } @Override - protected List findDifferences(final ResultWithRelations source, - final ResultWithRelations target) { + protected List findDifferences(final OpenaireBrokerResult source, + final OpenaireBrokerResult target) { final Set urls = target - .getResult() - .getInstance() + .getInstances() .stream() - .filter(i -> i.getAccessright().getClassid().equals(BrokerConstants.OPEN_ACCESS)) + .filter(i -> i.getLicense().equals(BrokerConstants.OPEN_ACCESS)) .map(i -> i.getUrl()) - .flatMap(List::stream) .collect(Collectors.toSet()); return source - .getResult() - .getInstance() + .getInstances() .stream() - .filter(i -> i.getAccessright().getClassid().equals(BrokerConstants.OPEN_ACCESS)) - .map(ConversionUtils::oafInstanceToBrokerInstances) - .flatMap(List::stream) + .filter(i -> i.getLicense().equals(BrokerConstants.OPEN_ACCESS)) .filter(i -> !urls.contains(i.getUrl())) .collect(Collectors.toList()); } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMorePid.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMorePid.java index 694c9460aa..d1f2e60225 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMorePid.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMorePid.java @@ -5,38 +5,37 @@ import java.util.List; import java.util.Set; import java.util.stream.Collectors; -import eu.dnetlib.broker.objects.Pid; +import eu.dnetlib.broker.objects.OpenaireBrokerResult; +import eu.dnetlib.broker.objects.TypedValue; import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; -import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; -import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.ResultWithRelations; -public class EnrichMorePid extends UpdateMatcher { +public class EnrichMorePid extends UpdateMatcher { public EnrichMorePid() { super(true, pid -> Topic.ENRICH_MORE_PID, (p, pid) -> p.getPids().add(pid), - pid -> pid.getType() + "::" + pid.getValue()); + pid -> pidAsString(pid)); } @Override - protected List findDifferences(final ResultWithRelations source, - final ResultWithRelations target) { + protected List findDifferences(final OpenaireBrokerResult source, + final OpenaireBrokerResult target) { final Set existingPids = target - .getResult() - .getPid() + .getPids() .stream() - .map(pid -> pid.getQualifier().getClassid() + "::" + pid.getValue()) + .map(pid -> pidAsString(pid)) .collect(Collectors.toSet()); return source - .getResult() - .getPid() + .getPids() .stream() - .filter(pid -> !existingPids.contains(pid.getQualifier().getClassid() + "::" + pid.getValue())) - .map(ConversionUtils::oafPidToBrokerPid) + .filter(pid -> !existingPids.contains(pidAsString(pid))) .collect(Collectors.toList()); } + private static String pidAsString(final TypedValue pid) { + return pid.getType() + "::" + pid.getValue(); + } } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSubject.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSubject.java index 7d0b1a65e3..39225e8ab8 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSubject.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSubject.java @@ -5,39 +5,37 @@ import java.util.List; import java.util.Set; import java.util.stream.Collectors; -import org.apache.commons.lang3.tuple.Pair; - +import eu.dnetlib.broker.objects.OpenaireBrokerResult; +import eu.dnetlib.broker.objects.TypedValue; import eu.dnetlib.dhp.broker.model.Topic; import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; -import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; -import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.ResultWithRelations; -public class EnrichMoreSubject extends UpdateMatcher> { +public class EnrichMoreSubject extends UpdateMatcher { public EnrichMoreSubject() { super(true, - pair -> Topic.fromPath("ENRICH/MORE/SUBJECT/" + pair.getLeft()), - (p, pair) -> p.getSubjects().add(pair.getRight()), - pair -> pair.getLeft() + "::" + pair.getRight()); + s -> Topic.fromPath("ENRICH/MORE/SUBJECT/" + s.getType()), + (p, s) -> p.getSubjects().add(s), + s -> subjectAsString(s)); } @Override - protected List> findDifferences(final ResultWithRelations source, - final ResultWithRelations target) { + protected List findDifferences(final OpenaireBrokerResult source, + final OpenaireBrokerResult target) { final Set existingSubjects = target - .getResult() - .getSubject() + .getSubjects() .stream() - .map(pid -> pid.getQualifier().getClassid() + "::" + pid.getValue()) + .map(pid -> subjectAsString(pid)) .collect(Collectors.toSet()); return source - .getResult() - .getPid() + .getPids() .stream() - .filter(pid -> !existingSubjects.contains(pid.getQualifier().getClassid() + "::" + pid.getValue())) - .map(ConversionUtils::oafSubjectToPair) + .filter(s -> !existingSubjects.contains(subjectAsString(s))) .collect(Collectors.toList()); } + private static String subjectAsString(final TypedValue s) { + return s.getType() + "::" + s.getValue(); + } } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/BrokerConstants.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/BrokerConstants.java index 0665c69ddd..49c46c7f0e 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/BrokerConstants.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/BrokerConstants.java @@ -2,13 +2,12 @@ package eu.dnetlib.dhp.broker.oa.util; import java.util.Arrays; -import java.util.List; +import java.util.HashSet; +import java.util.Set; -import eu.dnetlib.dhp.schema.oaf.Dataset; -import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct; -import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.dhp.schema.oaf.Result; -import eu.dnetlib.dhp.schema.oaf.Software; +import eu.dnetlib.dhp.broker.model.Event; +import eu.dnetlib.dhp.broker.oa.util.aggregators.simple.ResultGroup; +import eu.dnetlib.dhp.schema.common.ModelSupport; public class BrokerConstants { @@ -18,7 +17,11 @@ public class BrokerConstants { public static final float MIN_TRUST = 0.25f; public static final float MAX_TRUST = 1.00f; - public static final List> RESULT_CLASSES = Arrays - .asList(Publication.class, Dataset.class, Software.class, OtherResearchProduct.class); + public static Class[] getModelClasses() { + final Set> list = new HashSet<>(); + list.addAll(Arrays.asList(ModelSupport.getOafModelClasses())); + list.addAll(Arrays.asList(ResultGroup.class, Event.class)); + return list.toArray(new Class[] {}); + } } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java index 2b39115b16..b80848682a 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java @@ -13,7 +13,8 @@ import org.dom4j.DocumentHelper; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import eu.dnetlib.broker.objects.Pid; +import eu.dnetlib.broker.objects.OpenaireBrokerResult; +import eu.dnetlib.broker.objects.TypedValue; import eu.dnetlib.dhp.schema.oaf.Author; import eu.dnetlib.dhp.schema.oaf.Dataset; import eu.dnetlib.dhp.schema.oaf.ExternalReference; @@ -41,8 +42,8 @@ public class ConversionUtils { }).collect(Collectors.toList()); } - public static Pid oafPidToBrokerPid(final StructuredProperty sp) { - return sp != null ? new Pid() + public static TypedValue oafPidToBrokerPid(final StructuredProperty sp) { + return sp != null ? new TypedValue() .setValue(sp.getValue()) .setType(sp.getQualifier().getClassid()) : null; } @@ -54,7 +55,7 @@ public class ConversionUtils { public static final eu.dnetlib.broker.objects.Dataset oafDatasetToBrokerDataset(final Dataset d) { return d != null ? new eu.dnetlib.broker.objects.Dataset() .setOriginalId(d.getOriginalId().get(0)) - .setTitles(structPropList(d.getTitle())) + .setTitle(structPropValue(d.getTitle())) .setPids(d.getPid().stream().map(ConversionUtils::oafPidToBrokerPid).collect(Collectors.toList())) .setInstances( d @@ -63,26 +64,30 @@ public class ConversionUtils { .map(ConversionUtils::oafInstanceToBrokerInstances) .flatMap(List::stream) .collect(Collectors.toList())) - .setCollectedFrom(d.getCollectedfrom().stream().map(KeyValue::getValue).collect(Collectors.toList())) + .setCollectedFrom(d.getCollectedfrom().stream().map(KeyValue::getValue).findFirst().orElse(null)) : null; } - public static final eu.dnetlib.broker.objects.Publication oafResultToBrokerPublication(final Result result) { + public static final OpenaireBrokerResult oafResultToBrokerResult(final Result result) { - return result != null ? new eu.dnetlib.broker.objects.Publication() + return result != null ? new OpenaireBrokerResult() + .setOpenaireId(result.getId()) .setOriginalId(result.getOriginalId().get(0)) + .setTypology(result.getResulttype().getClassid()) .setTitles(structPropList(result.getTitle())) .setAbstracts(fieldList(result.getDescription())) .setLanguage(result.getLanguage().getClassid()) - .setSubjects(structPropList(result.getSubject())) - .setCreators(result.getAuthor().stream().map(Author::getFullname).collect(Collectors.toList())) - .setPublicationdate(result.getDateofcollection()) + .setSubjects(structPropTypedList(result.getSubject())) + .setCreators( + result.getAuthor().stream().map(ConversionUtils::oafAuthorToBrokerAuthor).collect(Collectors.toList())) + .setPublicationdate(result.getDateofacceptance().getValue()) .setPublisher(fieldValue(result.getPublisher())) .setEmbargoenddate(fieldValue(result.getEmbargoenddate())) .setContributor(fieldList(result.getContributor())) .setJournal( result instanceof Publication ? oafJournalToBrokerJournal(((Publication) result).getJournal()) : null) - .setCollectedFrom(result.getCollectedfrom().stream().map(KeyValue::getValue).collect(Collectors.toList())) + .setCollectedFromId(result.getCollectedfrom().stream().map(KeyValue::getKey).findFirst().orElse(null)) + .setCollectedFromName(result.getCollectedfrom().stream().map(KeyValue::getValue).findFirst().orElse(null)) .setPids(result.getPid().stream().map(ConversionUtils::oafPidToBrokerPid).collect(Collectors.toList())) .setInstances( result @@ -100,6 +105,30 @@ public class ConversionUtils { : null; } + private static List structPropTypedList(final List list) { + return list + .stream() + .map( + p -> new TypedValue() + .setValue(p.getValue()) + .setType(p.getQualifier().getClassid())) + .collect(Collectors.toList()); + } + + private static eu.dnetlib.broker.objects.Author oafAuthorToBrokerAuthor(final Author author) { + return author != null ? new eu.dnetlib.broker.objects.Author() + .setFullname(author.getFullname()) + .setOrcid( + author + .getPid() + .stream() + .filter(pid -> pid.getQualifier().getClassid().equalsIgnoreCase("orcid")) + .map(pid -> pid.getValue()) + .findFirst() + .orElse(null)) + : null; + } + private static eu.dnetlib.broker.objects.Journal oafJournalToBrokerJournal(final Journal journal) { return journal != null ? new eu.dnetlib.broker.objects.Journal() .setName(journal.getName()) diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EventFinder.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EventFinder.java index b4de08db77..4c20ac5cae 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EventFinder.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EventFinder.java @@ -4,6 +4,7 @@ package eu.dnetlib.dhp.broker.oa.util; import java.util.ArrayList; import java.util.List; +import eu.dnetlib.broker.objects.OpenaireBrokerResult; import eu.dnetlib.dhp.broker.model.EventFactory; import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; import eu.dnetlib.dhp.broker.oa.matchers.relatedDatasets.EnrichMissingDatasetIsReferencedBy; @@ -30,7 +31,6 @@ import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMoreOpenAccess; import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMorePid; import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMoreSubject; import eu.dnetlib.dhp.broker.oa.util.aggregators.simple.ResultGroup; -import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.ResultWithRelations; import eu.dnetlib.pace.config.DedupConfig; public class EventFinder { @@ -68,7 +68,7 @@ public class EventFinder { public static EventGroup generateEvents(final ResultGroup results, final DedupConfig dedupConfig) { final List> list = new ArrayList<>(); - for (final ResultWithRelations target : results.getData()) { + for (final OpenaireBrokerResult target : results.getData()) { for (final UpdateMatcher matcher : matchers) { list.addAll(matcher.searchUpdatesForRecord(target, results.getData(), dedupConfig)); } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/UpdateInfo.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/UpdateInfo.java index 9da6364137..82d0178648 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/UpdateInfo.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/UpdateInfo.java @@ -1,7 +1,6 @@ package eu.dnetlib.dhp.broker.oa.util; -import java.util.List; import java.util.function.BiConsumer; import java.util.function.Function; @@ -10,14 +9,11 @@ import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.broker.objects.Instance; import eu.dnetlib.broker.objects.OpenAireEventPayload; +import eu.dnetlib.broker.objects.OpenaireBrokerResult; import eu.dnetlib.broker.objects.Provenance; -import eu.dnetlib.broker.objects.Publication; import eu.dnetlib.dhp.broker.model.Topic; -import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.ResultWithRelations; -import eu.dnetlib.dhp.schema.oaf.Instance; -import eu.dnetlib.dhp.schema.oaf.KeyValue; -import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.pace.config.DedupConfig; import eu.dnetlib.pace.model.MapDocument; import eu.dnetlib.pace.tree.support.TreeProcessor; @@ -29,11 +25,11 @@ public final class UpdateInfo { private final T highlightValue; - private final ResultWithRelations source; + private final OpenaireBrokerResult source; - private final ResultWithRelations target; + private final OpenaireBrokerResult target; - private final BiConsumer compileHighlight; + private final BiConsumer compileHighlight; private final Function highlightToString; @@ -41,9 +37,9 @@ public final class UpdateInfo { private static final Logger log = LoggerFactory.getLogger(UpdateInfo.class); - public UpdateInfo(final Topic topic, final T highlightValue, final ResultWithRelations source, - final ResultWithRelations target, - final BiConsumer compileHighlight, + public UpdateInfo(final Topic topic, final T highlightValue, final OpenaireBrokerResult source, + final OpenaireBrokerResult target, + final BiConsumer compileHighlight, final Function highlightToString, final DedupConfig dedupConfig) { this.topic = topic; @@ -52,22 +48,23 @@ public final class UpdateInfo { this.target = target; this.compileHighlight = compileHighlight; this.highlightToString = highlightToString; - this.trust = calculateTrust(dedupConfig, source.getResult(), target.getResult()); + this.trust = calculateTrust(dedupConfig, source, target); } public T getHighlightValue() { return highlightValue; } - public ResultWithRelations getSource() { + public OpenaireBrokerResult getSource() { return source; } - public ResultWithRelations getTarget() { + public OpenaireBrokerResult getTarget() { return target; } - private float calculateTrust(final DedupConfig dedupConfig, final Result r1, final Result r2) { + private float calculateTrust(final DedupConfig dedupConfig, final OpenaireBrokerResult r1, + final OpenaireBrokerResult r2) { try { final ObjectMapper objectMapper = new ObjectMapper(); final MapDocument doc1 = MapDocumentUtil @@ -103,26 +100,18 @@ public final class UpdateInfo { public OpenAireEventPayload asBrokerPayload() { - final Publication p = ConversionUtils.oafResultToBrokerPublication(getSource().getResult()); - compileHighlight.accept(p, getHighlightValue()); + compileHighlight.accept(target, getHighlightValue()); - final Publication hl = new Publication(); + final OpenaireBrokerResult hl = new OpenaireBrokerResult(); compileHighlight.accept(hl, getHighlightValue()); - final String provId = getSource().getResult().getOriginalId().stream().findFirst().orElse(null); - final String provRepo = getSource() - .getResult() - .getCollectedfrom() - .stream() - .map(KeyValue::getValue) - .findFirst() - .orElse(null); + final String provId = getSource().getOriginalId(); + final String provRepo = getSource().getCollectedFromName(); + final String provUrl = getSource() - .getResult() - .getInstance() + .getInstances() .stream() .map(Instance::getUrl) - .flatMap(List::stream) .findFirst() .orElse(null); ; @@ -130,7 +119,7 @@ public final class UpdateInfo { final Provenance provenance = new Provenance().setId(provId).setRepositoryName(provRepo).setUrl(provUrl); return new OpenAireEventPayload() - .setPublication(p) + .setPublication(target) .setHighlight(hl) .setTrust(trust) .setProvenance(provenance); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/simple/ResultAggregator.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/simple/ResultAggregator.java index 397f306600..dabe2bb4d6 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/simple/ResultAggregator.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/simple/ResultAggregator.java @@ -5,11 +5,11 @@ import org.apache.spark.sql.Encoder; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.expressions.Aggregator; -import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.ResultWithRelations; +import eu.dnetlib.broker.objects.OpenaireBrokerResult; import eu.dnetlib.dhp.schema.oaf.Relation; import scala.Tuple2; -public class ResultAggregator extends Aggregator, ResultGroup, ResultGroup> { +public class ResultAggregator extends Aggregator, ResultGroup, ResultGroup> { /** * @@ -22,7 +22,7 @@ public class ResultAggregator extends Aggregator t) { + public ResultGroup reduce(final ResultGroup group, final Tuple2 t) { return group.addElement(t._1); } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/simple/ResultGroup.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/simple/ResultGroup.java index 81f189d62e..4308224a58 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/simple/ResultGroup.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/simple/ResultGroup.java @@ -5,7 +5,7 @@ import java.io.Serializable; import java.util.ArrayList; import java.util.List; -import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.ResultWithRelations; +import eu.dnetlib.broker.objects.OpenaireBrokerResult; public class ResultGroup implements Serializable { @@ -14,13 +14,13 @@ public class ResultGroup implements Serializable { */ private static final long serialVersionUID = -3360828477088669296L; - private final List data = new ArrayList<>(); + private final List data = new ArrayList<>(); - public List getData() { + public List getData() { return data; } - public ResultGroup addElement(final ResultWithRelations elem) { + public ResultGroup addElement(final OpenaireBrokerResult elem) { data.add(elem); return this; } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/OpenaireBrokerResultAggregator.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/OpenaireBrokerResultAggregator.java new file mode 100644 index 0000000000..b44fbe367c --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/OpenaireBrokerResultAggregator.java @@ -0,0 +1,69 @@ + +package eu.dnetlib.dhp.broker.oa.util.aggregators.withRels; + +import org.apache.spark.sql.Encoder; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.expressions.Aggregator; + +import eu.dnetlib.broker.objects.OpenaireBrokerResult; +import scala.Tuple2; + +public class OpenaireBrokerResultAggregator + extends Aggregator, OpenaireBrokerResult, OpenaireBrokerResult> { + + /** + * + */ + private static final long serialVersionUID = -3687878788861013488L; + + @Override + public OpenaireBrokerResult zero() { + return new OpenaireBrokerResult(); + } + + @Override + public OpenaireBrokerResult finish(final OpenaireBrokerResult g) { + return g; + } + + @Override + public OpenaireBrokerResult reduce(final OpenaireBrokerResult g, final Tuple2 t) { + if (g.getOriginalId() == null) { + return t._1; + } else if (t._2 instanceof RelatedSoftware) { + g.getSoftwares().add(((RelatedSoftware) t._2).getRelSoftware()); + } else if (t._2 instanceof RelatedDataset) { + g.getDatasets().add(((RelatedDataset) t._2).getRelDataset()); + } else if (t._2 instanceof RelatedPublication) { + g.getPublications().add(((RelatedPublication) t._2).getRelPublication()); + } else if (t._2 instanceof RelatedProject) { + g.getProjects().add(((RelatedProject) t._2).getRelProject()); + } + return g; + + } + + @Override + public OpenaireBrokerResult merge(final OpenaireBrokerResult g1, final OpenaireBrokerResult g2) { + if (g1.getOriginalId() != null) { + g1.getSoftwares().addAll(g2.getSoftwares()); + g1.getDatasets().addAll(g2.getDatasets()); + g1.getPublications().addAll(g2.getPublications()); + g1.getProjects().addAll(g2.getProjects()); + return g1; + } else { + return g2; + } + } + + @Override + public Encoder bufferEncoder() { + return Encoders.kryo(OpenaireBrokerResult.class); + } + + @Override + public Encoder outputEncoder() { + return Encoders.kryo(OpenaireBrokerResult.class); + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedDataset.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedDataset.java index 84cf693ad9..fcf1b89b1c 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedDataset.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedDataset.java @@ -1,10 +1,16 @@ package eu.dnetlib.dhp.broker.oa.util.aggregators.withRels; -import eu.dnetlib.dhp.schema.oaf.Dataset; +import java.io.Serializable; -public class RelatedDataset { +import eu.dnetlib.broker.objects.Dataset; +public class RelatedDataset implements Serializable { + + /** + * + */ + private static final long serialVersionUID = 774487705184038324L; private final String source; private final String relType; private final Dataset relDataset; diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedEntityFactory.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedEntityFactory.java index 490724a44b..08d57a1ea7 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedEntityFactory.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedEntityFactory.java @@ -1,15 +1,17 @@ package eu.dnetlib.dhp.broker.oa.util.aggregators.withRels; -import eu.dnetlib.dhp.schema.oaf.Dataset; -import eu.dnetlib.dhp.schema.oaf.Project; -import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.dhp.schema.oaf.Software; +import eu.dnetlib.broker.objects.Dataset; +import eu.dnetlib.broker.objects.Project; +import eu.dnetlib.broker.objects.Publication; +import eu.dnetlib.broker.objects.Software; public class RelatedEntityFactory { @SuppressWarnings("unchecked") - public static RT newRelatedEntity(final String sourceId, final String relType, final T target, + public static RT newRelatedEntity(final String sourceId, + final String relType, + final T target, final Class clazz) { if (clazz == RelatedProject.class) { return (RT) new RelatedProject(sourceId, relType, (Project) target); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedProject.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedProject.java index 2d16f54096..233041c096 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedProject.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedProject.java @@ -1,9 +1,16 @@ package eu.dnetlib.dhp.broker.oa.util.aggregators.withRels; -import eu.dnetlib.dhp.schema.oaf.Project; +import java.io.Serializable; -public class RelatedProject { +import eu.dnetlib.broker.objects.Project; + +public class RelatedProject implements Serializable { + + /** + * + */ + private static final long serialVersionUID = 4941437626549329870L; private final String source; private final String relType; diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedPublication.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedPublication.java index f1545c0045..80b92462d1 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedPublication.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedPublication.java @@ -1,9 +1,16 @@ package eu.dnetlib.dhp.broker.oa.util.aggregators.withRels; -import eu.dnetlib.dhp.schema.oaf.Publication; +import java.io.Serializable; -public class RelatedPublication { +import eu.dnetlib.broker.objects.Publication; + +public class RelatedPublication implements Serializable { + + /** + * + */ + private static final long serialVersionUID = 9021609640411395128L; private final String source; private final String relType; diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedSoftware.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedSoftware.java index e5873d2632..13f1f42909 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedSoftware.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedSoftware.java @@ -1,10 +1,16 @@ package eu.dnetlib.dhp.broker.oa.util.aggregators.withRels; -import eu.dnetlib.dhp.schema.oaf.Software; +import java.io.Serializable; -public class RelatedSoftware { +import eu.dnetlib.broker.objects.Software; +public class RelatedSoftware implements Serializable { + + /** + * + */ + private static final long serialVersionUID = 7573383356943300157L; private final String source; private final String relType; private final Software relSoftware; diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/ResultWithRelations.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/ResultWithRelations.java deleted file mode 100644 index 2d762aded4..0000000000 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/ResultWithRelations.java +++ /dev/null @@ -1,55 +0,0 @@ - -package eu.dnetlib.dhp.broker.oa.util.aggregators.withRels; - -import java.io.Serializable; -import java.util.ArrayList; -import java.util.List; - -import eu.dnetlib.dhp.schema.oaf.Result; - -public class ResultWithRelations implements Serializable { - - /** - * - */ - private static final long serialVersionUID = -1368401915974311571L; - - private Result result; - - private final List datasets = new ArrayList<>(); - private final List publications = new ArrayList<>(); - private final List softwares = new ArrayList<>(); - private final List projects = new ArrayList<>(); - - public ResultWithRelations() { - } - - public ResultWithRelations(final Result result) { - this.result = result; - } - - public Result getResult() { - return result; - } - - public List getDatasets() { - return datasets; - } - - public List getPublications() { - return publications; - } - - public List getSoftwares() { - return softwares; - } - - public List getProjects() { - return projects; - } - - public void setResult(final Result result) { - this.result = result; - } - -} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/ResultWithRelationsAggregator.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/ResultWithRelationsAggregator.java deleted file mode 100644 index b4922a64fb..0000000000 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/ResultWithRelationsAggregator.java +++ /dev/null @@ -1,68 +0,0 @@ - -package eu.dnetlib.dhp.broker.oa.util.aggregators.withRels; - -import org.apache.spark.sql.Encoder; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.expressions.Aggregator; - -import scala.Tuple2; - -public class ResultWithRelationsAggregator - extends Aggregator, ResultWithRelations, ResultWithRelations> { - - /** - * - */ - private static final long serialVersionUID = -3687878788861013488L; - - @Override - public ResultWithRelations zero() { - return new ResultWithRelations(); - } - - @Override - public ResultWithRelations finish(final ResultWithRelations g) { - return g; - } - - @Override - public ResultWithRelations reduce(final ResultWithRelations g, final Tuple2 t) { - if (g.getResult() == null) { - return t._1; - } else if (t._2 instanceof RelatedSoftware) { - g.getSoftwares().add((RelatedSoftware) t._2); - } else if (t._2 instanceof RelatedDataset) { - g.getDatasets().add((RelatedDataset) t._2); - } else if (t._2 instanceof RelatedPublication) { - g.getPublications().add((RelatedPublication) t._2); - } else if (t._2 instanceof RelatedProject) { - g.getProjects().add((RelatedProject) t._2); - } - return g; - - } - - @Override - public ResultWithRelations merge(final ResultWithRelations g1, final ResultWithRelations g2) { - if (g1.getResult() != null) { - g1.getSoftwares().addAll(g2.getSoftwares()); - g1.getDatasets().addAll(g2.getDatasets()); - g1.getPublications().addAll(g2.getPublications()); - g1.getProjects().addAll(g2.getProjects()); - return g1; - } else { - return g2; - } - } - - @Override - public Encoder bufferEncoder() { - return Encoders.kryo(ResultWithRelations.class); - } - - @Override - public Encoder outputEncoder() { - return Encoders.kryo(ResultWithRelations.class); - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/reflections/ReflectionTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/reflections/ReflectionTest.java new file mode 100644 index 0000000000..110fabf450 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/reflections/ReflectionTest.java @@ -0,0 +1,200 @@ + +package eu.dnetlib.dhp.oa.graph.reflections; + +import static org.junit.jupiter.api.Assertions.assertEquals; + +import java.lang.reflect.Field; +import java.util.ArrayList; +import java.util.List; + +import org.junit.jupiter.api.Test; + +public class ReflectionTest { + + private final Cleaner cleaner = new Cleaner(); + + @Test + void testObject() throws Exception { + final Publication pub = new Publication(); + pub.setTitle("openaire guidelines"); + pub.getAuthors().add(new Author("Michele Artini", new Prop("aa-001", "orcid"))); + pub.getAuthors().add(new Author("Claudio Atzori", new Prop("aa-002", "orcid"))); + pub.getAuthors().add(new Author("Alessia Bardi", new Prop("aa-003", "orcid"))); + pub.getSubjects().add(new Prop("infrastructures", "keyword")); + pub.getSubjects().add(new Prop("digital libraries", "keyword")); + + cleaner.clean(pub); + + System.out.println(pub); + + assertEquals("OPENAIRE GUIDELINES", pub.getTitle()); + + assertEquals("MICHELE ARTINI", pub.getAuthors().get(0).getName()); + assertEquals("CLAUDIO ATZORI", pub.getAuthors().get(1).getName()); + assertEquals("ALESSIA BARDI", pub.getAuthors().get(2).getName()); + + assertEquals("dnet:aa-001", pub.getAuthors().get(0).getId().getId()); + assertEquals("dnet:aa-002", pub.getAuthors().get(1).getId().getId()); + assertEquals("dnet:aa-003", pub.getAuthors().get(2).getId().getId()); + assertEquals("dnet:orcid", pub.getAuthors().get(0).getId().getName()); + assertEquals("dnet:orcid", pub.getAuthors().get(1).getId().getName()); + assertEquals("dnet:orcid", pub.getAuthors().get(2).getId().getName()); + + assertEquals("dnet:infrastructures", pub.getSubjects().get(0).getId()); + assertEquals("dnet:keyword", pub.getSubjects().get(0).getName()); + assertEquals("dnet:digital libraries", pub.getSubjects().get(1).getId()); + assertEquals("dnet:keyword", pub.getSubjects().get(1).getName()); + } + +} + +class Cleaner { + + public void clean(final Object o) throws IllegalArgumentException, IllegalAccessException { + if (isPrimitive(o)) { + return; + } else if (isIterable(o.getClass())) { + for (final Object elem : (Iterable) o) { + clean(elem); + } + } else if (hasMapping(o)) { + mapObject(o); + } else { + for (final Field f : o.getClass().getDeclaredFields()) { + f.setAccessible(true); + final Object val = f.get(o); + if (isPrimitive(val)) { + f.set(o, cleanValue(f.get(o))); + } else if (hasMapping(val)) { + mapObject(val); + } else { + clean(f.get(o)); + } + } + } + } + + private boolean hasMapping(final Object o) { + return o.getClass() == Prop.class; + } + + private void mapObject(final Object o) { + if (o.getClass() == Prop.class) { + ((Prop) o).setId("dnet:" + ((Prop) o).getId()); + ((Prop) o).setName("dnet:" + ((Prop) o).getName()); + } + + } + + private Object cleanValue(final Object o) { + if (o.getClass() == String.class) { + return ((String) o).toUpperCase(); + } else { + return o; + } + + } + + private boolean isIterable(final Class cl) { + return Iterable.class.isAssignableFrom(cl); + } + + private boolean isPrimitive(final Object o) { + return o.getClass() == String.class; + } +} + +class Publication { + + private String title; + private final List authors = new ArrayList<>(); + private final List subjects = new ArrayList<>(); + + public String getTitle() { + return title; + } + + public void setTitle(final String title) { + this.title = title; + } + + public List getAuthors() { + return authors; + } + + public List getSubjects() { + return subjects; + } + + @Override + public String toString() { + return String.format("Publication [title=%s, authors=%s, subjects=%s]", title, authors, subjects); + } + +} + +class Prop { + + private String id; + private String name; + + public Prop(final String id, final String name) { + this.id = id; + this.name = name; + } + + public String getId() { + return id; + } + + public void setId(final String id) { + this.id = id; + } + + public String getName() { + return name; + } + + public void setName(final String name) { + this.name = name; + } + + @Override + public String toString() { + return String.format("Prop [id=%s, name=%s]", id, name); + } + +} + +class Author { + + private String name; + private Prop id; + + public Author(final String name, final Prop id) { + this.name = name; + this.id = id; + } + + public String getName() { + return name; + } + + public void setName(final String name) { + this.name = name; + } + + public Prop getId() { + return id; + } + + public void setId(final Prop id) { + this.id = id; + } + + @Override + public String toString() { + return String.format("Author [name=%s, id=%s]", name, id); + } + +} From 4ec262db5318661bcfba6cb9497cfcca3370bbbc Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 16 Jun 2020 15:28:20 +0200 Subject: [PATCH 55/62] included externalreference(s) in the result view on the Hive graph DB --- .../graph/hive/oozie_app/lib/scripts/postprocessing.sql | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/lib/scripts/postprocessing.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/lib/scripts/postprocessing.sql index 6c49679cdf..7bec2fe040 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/lib/scripts/postprocessing.sql +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/lib/scripts/postprocessing.sql @@ -1,10 +1,10 @@ DROP VIEW IF EXISTS ${hiveDbName}.result; CREATE VIEW IF NOT EXISTS result as - select id, dateofcollection, title, publisher, bestaccessright, datainfo, collectedfrom, pid, author, resulttype, language, country, subject, description, dateofacceptance, embargoenddate, resourcetype, context, instance from ${hiveDbName}.publication p + select id, dateofcollection, title, publisher, bestaccessright, datainfo, collectedfrom, pid, author, resulttype, language, country, subject, description, dateofacceptance, embargoenddate, resourcetype, context, externalreference, instance from ${hiveDbName}.publication p union all - select id, dateofcollection, title, publisher, bestaccessright, datainfo, collectedfrom, pid, author, resulttype, language, country, subject, description, dateofacceptance, embargoenddate, resourcetype, context, instance from ${hiveDbName}.dataset d + select id, dateofcollection, title, publisher, bestaccessright, datainfo, collectedfrom, pid, author, resulttype, language, country, subject, description, dateofacceptance, embargoenddate, resourcetype, context, externalreference, instance from ${hiveDbName}.dataset d union all - select id, dateofcollection, title, publisher, bestaccessright, datainfo, collectedfrom, pid, author, resulttype, language, country, subject, description, dateofacceptance, embargoenddate, resourcetype, context, instance from ${hiveDbName}.software s + select id, dateofcollection, title, publisher, bestaccessright, datainfo, collectedfrom, pid, author, resulttype, language, country, subject, description, dateofacceptance, embargoenddate, resourcetype, context, externalreference, instance from ${hiveDbName}.software s union all - select id, dateofcollection, title, publisher, bestaccessright, datainfo, collectedfrom, pid, author, resulttype, language, country, subject, description, dateofacceptance, embargoenddate, resourcetype, context, instance from ${hiveDbName}.otherresearchproduct o; + select id, dateofcollection, title, publisher, bestaccessright, datainfo, collectedfrom, pid, author, resulttype, language, country, subject, description, dateofacceptance, embargoenddate, resourcetype, context, externalreference, instance from ${hiveDbName}.otherresearchproduct o; From 76ea7607f723788f5d390bc5cd08546fd152091f Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Tue, 16 Jun 2020 15:53:13 +0200 Subject: [PATCH 56/62] partial refactoring --- .../broker/oa/GenerateEventsApplication.java | 46 ++++------ .../dhp/broker/oa/util/ConversionUtils.java | 84 ++++++++++--------- .../withRels/RelatedEntityFactory.java | 30 +++---- 3 files changed, 76 insertions(+), 84 deletions(-) diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java index 940d7f9f32..5efaed784a 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java @@ -51,9 +51,8 @@ public class GenerateEventsApplication { public static void main(final String[] args) throws Exception { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils - .toString( - GenerateEventsApplication.class - .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/generate_broker_events.json"))); + .toString(GenerateEventsApplication.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/generate_broker_events.json"))); parser.parseArgument(args); final Boolean isSparkSessionManaged = Optional @@ -118,14 +117,11 @@ public class GenerateEventsApplication { return results .joinWith(mergedRels, results.col("result.id").equalTo(mergedRels.col("source")), "inner") - .groupByKey( - (MapFunction, String>) t -> t._2.getTarget(), Encoders.STRING()) + .groupByKey((MapFunction, String>) t -> t._2.getTarget(), Encoders.STRING()) .agg(aggr) .map((MapFunction, ResultGroup>) t -> t._2, Encoders.kryo(ResultGroup.class)) .filter(ResultGroup::isValid) - .map( - (MapFunction) g -> EventFinder.generateEvents(g, dedupConfig), - Encoders.kryo(EventGroup.class)) + .map((MapFunction) g -> EventFinder.generateEvents(g, dedupConfig), Encoders.kryo(EventGroup.class)) .flatMap(group -> group.getData().iterator(), Encoders.kryo(Event.class)); } @@ -134,25 +130,22 @@ public class GenerateEventsApplication { final String graphPath, final Class sourceClass) { final Dataset projects = readPath(spark, graphPath + "/project", Project.class); - final Dataset datasets = readPath( - spark, graphPath + "/dataset", eu.dnetlib.dhp.schema.oaf.Dataset.class); + final Dataset datasets = readPath(spark, graphPath + "/dataset", eu.dnetlib.dhp.schema.oaf.Dataset.class); final Dataset softwares = readPath(spark, graphPath + "/software", Software.class); final Dataset publications = readPath(spark, graphPath + "/publication", Publication.class); final Dataset rels = readPath(spark, graphPath + "/relation", Relation.class) - .filter(r -> !r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS)); + .filter(r -> !r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS)) + .cache(); - final Dataset r0 = readPath( - spark, graphPath + "/" + sourceClass.getSimpleName().toLowerCase(), Result.class) - .filter(r -> r.getDataInfo().getDeletedbyinference()) - .map(ConversionUtils::oafResultToBrokerResult, Encoders.kryo(OpenaireBrokerResult.class)); + final Dataset r0 = readPath(spark, graphPath + "/" + sourceClass.getSimpleName().toLowerCase(), Result.class) + .filter(r -> r.getDataInfo().getDeletedbyinference()) + .map(ConversionUtils::oafResultToBrokerResult, Encoders.kryo(OpenaireBrokerResult.class)); final Dataset r1 = join(r0, rels, relatedEntities(projects, rels, RelatedProject.class)); final Dataset r2 = join(r1, rels, relatedEntities(softwares, rels, RelatedProject.class)); final Dataset r3 = join(r2, rels, relatedEntities(datasets, rels, RelatedProject.class)); - final Dataset r4 = join( - r3, rels, relatedEntities(publications, rels, RelatedProject.class)); - ; + final Dataset r4 = join(r3, rels, relatedEntities(publications, rels, RelatedProject.class));; return r4; } @@ -162,9 +155,7 @@ public class GenerateEventsApplication { final Class clazz) { return rels .joinWith(targets, targets.col("id").equalTo(rels.col("target")), "inner") - .map( - t -> RelatedEntityFactory.newRelatedEntity(t._1.getSource(), t._1.getRelType(), t._2, clazz), - Encoders.kryo(clazz)); + .map(t -> RelatedEntityFactory.newRelatedEntity(t._1.getSource(), t._1.getRelType(), t._2, clazz), Encoders.kryo(clazz)); } private static Dataset join(final Dataset sources, @@ -172,13 +163,11 @@ public class GenerateEventsApplication { final Dataset typedRels) { final TypedColumn, OpenaireBrokerResult> aggr = new OpenaireBrokerResultAggregator() - .toColumn(); - ; + .toColumn();; return sources .joinWith(typedRels, sources.col("result.id").equalTo(rels.col("source")), "left_outer") - .groupByKey( - (MapFunction, String>) t -> t._1.getOpenaireId(), Encoders.STRING()) + .groupByKey((MapFunction, String>) t -> t._1.getOpenaireId(), Encoders.STRING()) .agg(aggr) .map(t -> t._2, Encoders.kryo(OpenaireBrokerResult.class)); } @@ -197,11 +186,8 @@ public class GenerateEventsApplication { final ISLookUpService isLookUpService = ISLookupClientFactory.getLookUpService(isLookupUrl); final String conf = isLookUpService - .getResourceProfileByQuery( - String - .format( - "for $x in /RESOURCE_PROFILE[.//RESOURCE_IDENTIFIER/@value = '%s'] return $x//DEDUPLICATION/text()", - profId)); + .getResourceProfileByQuery(String + .format("for $x in /RESOURCE_PROFILE[.//RESOURCE_IDENTIFIER/@value = '%s'] return $x//DEDUPLICATION/text()", profId)); final DedupConfig dedupConfig = new ObjectMapper().readValue(conf, DedupConfig.class); dedupConfig.getPace().initModel(); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java index b80848682a..3693f4ce43 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java @@ -57,17 +57,31 @@ public class ConversionUtils { .setOriginalId(d.getOriginalId().get(0)) .setTitle(structPropValue(d.getTitle())) .setPids(d.getPid().stream().map(ConversionUtils::oafPidToBrokerPid).collect(Collectors.toList())) - .setInstances( - d - .getInstance() - .stream() - .map(ConversionUtils::oafInstanceToBrokerInstances) - .flatMap(List::stream) - .collect(Collectors.toList())) + .setInstances(d + .getInstance() + .stream() + .map(ConversionUtils::oafInstanceToBrokerInstances) + .flatMap(List::stream) + .collect(Collectors.toList())) .setCollectedFrom(d.getCollectedfrom().stream().map(KeyValue::getValue).findFirst().orElse(null)) : null; } + public static eu.dnetlib.broker.objects.Publication oafPublicationToBrokerPublication(final Publication p) { + return p != null ? new eu.dnetlib.broker.objects.Publication() + .setOriginalId(p.getOriginalId().get(0)) + .setTitle(structPropValue(p.getTitle())) + .setPids(p.getPid().stream().map(ConversionUtils::oafPidToBrokerPid).collect(Collectors.toList())) + .setInstances(p + .getInstance() + .stream() + .map(ConversionUtils::oafInstanceToBrokerInstances) + .flatMap(List::stream) + .collect(Collectors.toList())) + .setCollectedFrom(p.getCollectedfrom().stream().map(KeyValue::getValue).findFirst().orElse(null)) + : null; + } + public static final OpenaireBrokerResult oafResultToBrokerResult(final Result result) { return result != null ? new OpenaireBrokerResult() @@ -78,54 +92,48 @@ public class ConversionUtils { .setAbstracts(fieldList(result.getDescription())) .setLanguage(result.getLanguage().getClassid()) .setSubjects(structPropTypedList(result.getSubject())) - .setCreators( - result.getAuthor().stream().map(ConversionUtils::oafAuthorToBrokerAuthor).collect(Collectors.toList())) + .setCreators(result.getAuthor().stream().map(ConversionUtils::oafAuthorToBrokerAuthor).collect(Collectors.toList())) .setPublicationdate(result.getDateofacceptance().getValue()) .setPublisher(fieldValue(result.getPublisher())) .setEmbargoenddate(fieldValue(result.getEmbargoenddate())) .setContributor(fieldList(result.getContributor())) - .setJournal( - result instanceof Publication ? oafJournalToBrokerJournal(((Publication) result).getJournal()) : null) + .setJournal(result instanceof Publication ? oafJournalToBrokerJournal(((Publication) result).getJournal()) : null) .setCollectedFromId(result.getCollectedfrom().stream().map(KeyValue::getKey).findFirst().orElse(null)) .setCollectedFromName(result.getCollectedfrom().stream().map(KeyValue::getValue).findFirst().orElse(null)) .setPids(result.getPid().stream().map(ConversionUtils::oafPidToBrokerPid).collect(Collectors.toList())) - .setInstances( - result - .getInstance() - .stream() - .map(ConversionUtils::oafInstanceToBrokerInstances) - .flatMap(List::stream) - .collect(Collectors.toList())) - .setExternalReferences( - result - .getExternalReference() - .stream() - .map(ConversionUtils::oafExtRefToBrokerExtRef) - .collect(Collectors.toList())) + .setInstances(result + .getInstance() + .stream() + .map(ConversionUtils::oafInstanceToBrokerInstances) + .flatMap(List::stream) + .collect(Collectors.toList())) + .setExternalReferences(result + .getExternalReference() + .stream() + .map(ConversionUtils::oafExtRefToBrokerExtRef) + .collect(Collectors.toList())) : null; } private static List structPropTypedList(final List list) { return list .stream() - .map( - p -> new TypedValue() - .setValue(p.getValue()) - .setType(p.getQualifier().getClassid())) + .map(p -> new TypedValue() + .setValue(p.getValue()) + .setType(p.getQualifier().getClassid())) .collect(Collectors.toList()); } private static eu.dnetlib.broker.objects.Author oafAuthorToBrokerAuthor(final Author author) { return author != null ? new eu.dnetlib.broker.objects.Author() .setFullname(author.getFullname()) - .setOrcid( - author - .getPid() - .stream() - .filter(pid -> pid.getQualifier().getClassid().equalsIgnoreCase("orcid")) - .map(pid -> pid.getValue()) - .findFirst() - .orElse(null)) + .setOrcid(author + .getPid() + .stream() + .filter(pid -> pid.getQualifier().getClassid().equalsIgnoreCase("orcid")) + .map(pid -> pid.getValue()) + .findFirst() + .orElse(null)) : null; } @@ -147,9 +155,7 @@ public class ConversionUtils { } public static final eu.dnetlib.broker.objects.Project oafProjectToBrokerProject(final Project p) { - if (p == null) { - return null; - } + if (p == null) { return null; } final eu.dnetlib.broker.objects.Project res = new eu.dnetlib.broker.objects.Project() .setTitle(fieldValue(p.getTitle())) diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedEntityFactory.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedEntityFactory.java index 08d57a1ea7..88dab2ba35 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedEntityFactory.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedEntityFactory.java @@ -1,10 +1,11 @@ package eu.dnetlib.dhp.broker.oa.util.aggregators.withRels; -import eu.dnetlib.broker.objects.Dataset; -import eu.dnetlib.broker.objects.Project; -import eu.dnetlib.broker.objects.Publication; -import eu.dnetlib.broker.objects.Software; +import eu.dnetlib.dhp.broker.oa.util.ConversionUtils; +import eu.dnetlib.dhp.schema.oaf.Dataset; +import eu.dnetlib.dhp.schema.oaf.Project; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.oaf.Software; public class RelatedEntityFactory { @@ -13,18 +14,17 @@ public class RelatedEntityFactory { final String relType, final T target, final Class clazz) { + if (clazz == RelatedProject.class) { - return (RT) new RelatedProject(sourceId, relType, (Project) target); + return (RT) new RelatedProject(sourceId, relType, ConversionUtils.oafProjectToBrokerProject((Project) target)); + } else if (clazz == RelatedSoftware.class) { + return (RT) new RelatedSoftware(sourceId, relType, ConversionUtils.oafSoftwareToBrokerSoftware((Software) target)); + } else if (clazz == RelatedDataset.class) { + return (RT) new RelatedDataset(sourceId, relType, ConversionUtils.oafDatasetToBrokerDataset((Dataset) target)); + } else if (clazz == RelatedPublication.class) { + return (RT) new RelatedPublication(sourceId, relType, ConversionUtils.oafPublicationToBrokerPublication((Publication) target)); + } else { + return null; } - if (clazz == RelatedSoftware.class) { - return (RT) new RelatedSoftware(sourceId, relType, (Software) target); - } - if (clazz == RelatedDataset.class) { - return (RT) new RelatedDataset(sourceId, relType, (Dataset) target); - } - if (clazz == RelatedPublication.class) { - return (RT) new RelatedPublication(sourceId, relType, (Publication) target); - } - return null; } } From 9e2c23e39190647b9f3f832e28d3bb4f4f9e3a11 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Tue, 16 Jun 2020 15:55:42 +0200 Subject: [PATCH 57/62] partial refactoring --- .../broker/oa/GenerateEventsApplication.java | 43 ++++++---- .../dhp/broker/oa/util/ConversionUtils.java | 82 +++++++++++-------- .../withRels/RelatedEntityFactory.java | 12 ++- 3 files changed, 83 insertions(+), 54 deletions(-) diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java index 5efaed784a..c1f12f43c5 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java @@ -51,8 +51,9 @@ public class GenerateEventsApplication { public static void main(final String[] args) throws Exception { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils - .toString(GenerateEventsApplication.class - .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/generate_broker_events.json"))); + .toString( + GenerateEventsApplication.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/generate_broker_events.json"))); parser.parseArgument(args); final Boolean isSparkSessionManaged = Optional @@ -117,11 +118,14 @@ public class GenerateEventsApplication { return results .joinWith(mergedRels, results.col("result.id").equalTo(mergedRels.col("source")), "inner") - .groupByKey((MapFunction, String>) t -> t._2.getTarget(), Encoders.STRING()) + .groupByKey( + (MapFunction, String>) t -> t._2.getTarget(), Encoders.STRING()) .agg(aggr) .map((MapFunction, ResultGroup>) t -> t._2, Encoders.kryo(ResultGroup.class)) .filter(ResultGroup::isValid) - .map((MapFunction) g -> EventFinder.generateEvents(g, dedupConfig), Encoders.kryo(EventGroup.class)) + .map( + (MapFunction) g -> EventFinder.generateEvents(g, dedupConfig), + Encoders.kryo(EventGroup.class)) .flatMap(group -> group.getData().iterator(), Encoders.kryo(Event.class)); } @@ -130,7 +134,8 @@ public class GenerateEventsApplication { final String graphPath, final Class sourceClass) { final Dataset projects = readPath(spark, graphPath + "/project", Project.class); - final Dataset datasets = readPath(spark, graphPath + "/dataset", eu.dnetlib.dhp.schema.oaf.Dataset.class); + final Dataset datasets = readPath( + spark, graphPath + "/dataset", eu.dnetlib.dhp.schema.oaf.Dataset.class); final Dataset softwares = readPath(spark, graphPath + "/software", Software.class); final Dataset publications = readPath(spark, graphPath + "/publication", Publication.class); @@ -138,14 +143,17 @@ public class GenerateEventsApplication { .filter(r -> !r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS)) .cache(); - final Dataset r0 = readPath(spark, graphPath + "/" + sourceClass.getSimpleName().toLowerCase(), Result.class) - .filter(r -> r.getDataInfo().getDeletedbyinference()) - .map(ConversionUtils::oafResultToBrokerResult, Encoders.kryo(OpenaireBrokerResult.class)); + final Dataset r0 = readPath( + spark, graphPath + "/" + sourceClass.getSimpleName().toLowerCase(), Result.class) + .filter(r -> r.getDataInfo().getDeletedbyinference()) + .map(ConversionUtils::oafResultToBrokerResult, Encoders.kryo(OpenaireBrokerResult.class)); final Dataset r1 = join(r0, rels, relatedEntities(projects, rels, RelatedProject.class)); final Dataset r2 = join(r1, rels, relatedEntities(softwares, rels, RelatedProject.class)); final Dataset r3 = join(r2, rels, relatedEntities(datasets, rels, RelatedProject.class)); - final Dataset r4 = join(r3, rels, relatedEntities(publications, rels, RelatedProject.class));; + final Dataset r4 = join( + r3, rels, relatedEntities(publications, rels, RelatedProject.class)); + ; return r4; } @@ -155,7 +163,9 @@ public class GenerateEventsApplication { final Class clazz) { return rels .joinWith(targets, targets.col("id").equalTo(rels.col("target")), "inner") - .map(t -> RelatedEntityFactory.newRelatedEntity(t._1.getSource(), t._1.getRelType(), t._2, clazz), Encoders.kryo(clazz)); + .map( + t -> RelatedEntityFactory.newRelatedEntity(t._1.getSource(), t._1.getRelType(), t._2, clazz), + Encoders.kryo(clazz)); } private static Dataset join(final Dataset sources, @@ -163,11 +173,13 @@ public class GenerateEventsApplication { final Dataset typedRels) { final TypedColumn, OpenaireBrokerResult> aggr = new OpenaireBrokerResultAggregator() - .toColumn();; + .toColumn(); + ; return sources .joinWith(typedRels, sources.col("result.id").equalTo(rels.col("source")), "left_outer") - .groupByKey((MapFunction, String>) t -> t._1.getOpenaireId(), Encoders.STRING()) + .groupByKey( + (MapFunction, String>) t -> t._1.getOpenaireId(), Encoders.STRING()) .agg(aggr) .map(t -> t._2, Encoders.kryo(OpenaireBrokerResult.class)); } @@ -186,8 +198,11 @@ public class GenerateEventsApplication { final ISLookUpService isLookUpService = ISLookupClientFactory.getLookUpService(isLookupUrl); final String conf = isLookUpService - .getResourceProfileByQuery(String - .format("for $x in /RESOURCE_PROFILE[.//RESOURCE_IDENTIFIER/@value = '%s'] return $x//DEDUPLICATION/text()", profId)); + .getResourceProfileByQuery( + String + .format( + "for $x in /RESOURCE_PROFILE[.//RESOURCE_IDENTIFIER/@value = '%s'] return $x//DEDUPLICATION/text()", + profId)); final DedupConfig dedupConfig = new ObjectMapper().readValue(conf, DedupConfig.class); dedupConfig.getPace().initModel(); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java index 3693f4ce43..d04ef45a0e 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java @@ -57,12 +57,13 @@ public class ConversionUtils { .setOriginalId(d.getOriginalId().get(0)) .setTitle(structPropValue(d.getTitle())) .setPids(d.getPid().stream().map(ConversionUtils::oafPidToBrokerPid).collect(Collectors.toList())) - .setInstances(d - .getInstance() - .stream() - .map(ConversionUtils::oafInstanceToBrokerInstances) - .flatMap(List::stream) - .collect(Collectors.toList())) + .setInstances( + d + .getInstance() + .stream() + .map(ConversionUtils::oafInstanceToBrokerInstances) + .flatMap(List::stream) + .collect(Collectors.toList())) .setCollectedFrom(d.getCollectedfrom().stream().map(KeyValue::getValue).findFirst().orElse(null)) : null; } @@ -72,12 +73,13 @@ public class ConversionUtils { .setOriginalId(p.getOriginalId().get(0)) .setTitle(structPropValue(p.getTitle())) .setPids(p.getPid().stream().map(ConversionUtils::oafPidToBrokerPid).collect(Collectors.toList())) - .setInstances(p - .getInstance() - .stream() - .map(ConversionUtils::oafInstanceToBrokerInstances) - .flatMap(List::stream) - .collect(Collectors.toList())) + .setInstances( + p + .getInstance() + .stream() + .map(ConversionUtils::oafInstanceToBrokerInstances) + .flatMap(List::stream) + .collect(Collectors.toList())) .setCollectedFrom(p.getCollectedfrom().stream().map(KeyValue::getValue).findFirst().orElse(null)) : null; } @@ -92,48 +94,54 @@ public class ConversionUtils { .setAbstracts(fieldList(result.getDescription())) .setLanguage(result.getLanguage().getClassid()) .setSubjects(structPropTypedList(result.getSubject())) - .setCreators(result.getAuthor().stream().map(ConversionUtils::oafAuthorToBrokerAuthor).collect(Collectors.toList())) + .setCreators( + result.getAuthor().stream().map(ConversionUtils::oafAuthorToBrokerAuthor).collect(Collectors.toList())) .setPublicationdate(result.getDateofacceptance().getValue()) .setPublisher(fieldValue(result.getPublisher())) .setEmbargoenddate(fieldValue(result.getEmbargoenddate())) .setContributor(fieldList(result.getContributor())) - .setJournal(result instanceof Publication ? oafJournalToBrokerJournal(((Publication) result).getJournal()) : null) + .setJournal( + result instanceof Publication ? oafJournalToBrokerJournal(((Publication) result).getJournal()) : null) .setCollectedFromId(result.getCollectedfrom().stream().map(KeyValue::getKey).findFirst().orElse(null)) .setCollectedFromName(result.getCollectedfrom().stream().map(KeyValue::getValue).findFirst().orElse(null)) .setPids(result.getPid().stream().map(ConversionUtils::oafPidToBrokerPid).collect(Collectors.toList())) - .setInstances(result - .getInstance() - .stream() - .map(ConversionUtils::oafInstanceToBrokerInstances) - .flatMap(List::stream) - .collect(Collectors.toList())) - .setExternalReferences(result - .getExternalReference() - .stream() - .map(ConversionUtils::oafExtRefToBrokerExtRef) - .collect(Collectors.toList())) + .setInstances( + result + .getInstance() + .stream() + .map(ConversionUtils::oafInstanceToBrokerInstances) + .flatMap(List::stream) + .collect(Collectors.toList())) + .setExternalReferences( + result + .getExternalReference() + .stream() + .map(ConversionUtils::oafExtRefToBrokerExtRef) + .collect(Collectors.toList())) : null; } private static List structPropTypedList(final List list) { return list .stream() - .map(p -> new TypedValue() - .setValue(p.getValue()) - .setType(p.getQualifier().getClassid())) + .map( + p -> new TypedValue() + .setValue(p.getValue()) + .setType(p.getQualifier().getClassid())) .collect(Collectors.toList()); } private static eu.dnetlib.broker.objects.Author oafAuthorToBrokerAuthor(final Author author) { return author != null ? new eu.dnetlib.broker.objects.Author() .setFullname(author.getFullname()) - .setOrcid(author - .getPid() - .stream() - .filter(pid -> pid.getQualifier().getClassid().equalsIgnoreCase("orcid")) - .map(pid -> pid.getValue()) - .findFirst() - .orElse(null)) + .setOrcid( + author + .getPid() + .stream() + .filter(pid -> pid.getQualifier().getClassid().equalsIgnoreCase("orcid")) + .map(pid -> pid.getValue()) + .findFirst() + .orElse(null)) : null; } @@ -155,7 +163,9 @@ public class ConversionUtils { } public static final eu.dnetlib.broker.objects.Project oafProjectToBrokerProject(final Project p) { - if (p == null) { return null; } + if (p == null) { + return null; + } final eu.dnetlib.broker.objects.Project res = new eu.dnetlib.broker.objects.Project() .setTitle(fieldValue(p.getTitle())) diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedEntityFactory.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedEntityFactory.java index 88dab2ba35..c60d4f1417 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedEntityFactory.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/withRels/RelatedEntityFactory.java @@ -16,13 +16,17 @@ public class RelatedEntityFactory { final Class clazz) { if (clazz == RelatedProject.class) { - return (RT) new RelatedProject(sourceId, relType, ConversionUtils.oafProjectToBrokerProject((Project) target)); + return (RT) new RelatedProject(sourceId, relType, + ConversionUtils.oafProjectToBrokerProject((Project) target)); } else if (clazz == RelatedSoftware.class) { - return (RT) new RelatedSoftware(sourceId, relType, ConversionUtils.oafSoftwareToBrokerSoftware((Software) target)); + return (RT) new RelatedSoftware(sourceId, relType, + ConversionUtils.oafSoftwareToBrokerSoftware((Software) target)); } else if (clazz == RelatedDataset.class) { - return (RT) new RelatedDataset(sourceId, relType, ConversionUtils.oafDatasetToBrokerDataset((Dataset) target)); + return (RT) new RelatedDataset(sourceId, relType, + ConversionUtils.oafDatasetToBrokerDataset((Dataset) target)); } else if (clazz == RelatedPublication.class) { - return (RT) new RelatedPublication(sourceId, relType, ConversionUtils.oafPublicationToBrokerPublication((Publication) target)); + return (RT) new RelatedPublication(sourceId, relType, + ConversionUtils.oafPublicationToBrokerPublication((Publication) target)); } else { return null; } From 1bc1d15eaf1508bdd3bc5a3a5b3aa48d57f63708 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 16 Jun 2020 16:54:28 +0200 Subject: [PATCH 58/62] stubbing for mock datasource.identities must be typed as array --- .../dnetlib/dhp/oa/graph/raw/datasources_resultset_entry.json | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/datasources_resultset_entry.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/datasources_resultset_entry.json index f4c5f97ed1..0f1da70959 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/datasources_resultset_entry.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/datasources_resultset_entry.json @@ -6,9 +6,10 @@ }, { "field": "identities", - "type": "not_used", + "type": "array", "value": [ "274269ac6f3b::2579-5449", + "piwik:13", null ] }, From 306669209fa58206635ab094f2f3ef28963b34f1 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 16 Jun 2020 16:54:44 +0200 Subject: [PATCH 59/62] code formatting --- .../eu/dnetlib/dhp/schema/oaf/Measure.java | 79 ++++++++++--------- .../eu/dnetlib/dhp/schema/oaf/Programme.java | 1 - .../eu/dnetlib/dhp/schema/oaf/Relation.java | 14 ++-- .../eu/dnetlib/dhp/schema/oaf/Result.java | 2 +- .../dnetlib/dhp/schema/oaf/MeasureTest.java | 67 +++++++++------- .../actionmanager/project/ProjectSubset.java | 15 ++-- .../project/SparkUpdateProjectTest.java | 1 - 7 files changed, 96 insertions(+), 83 deletions(-) diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Measure.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Measure.java index c37e760618..c0c14d10de 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Measure.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Measure.java @@ -1,56 +1,59 @@ + package eu.dnetlib.dhp.schema.oaf; -import com.google.common.base.Objects; - import java.util.List; +import com.google.common.base.Objects; + /** * Represent a measure, must be further described by a system available resource providing name and descriptions. */ public class Measure { - /** - * Unique measure identifier. - */ - private String id; + /** + * Unique measure identifier. + */ + private String id; - /** - * List of units associated with this measure. KeyValue provides a pair to store the laber (key) and the value, - * plus common provenance information. - */ - private List unit; + /** + * List of units associated with this measure. KeyValue provides a pair to store the laber (key) and the value, plus + * common provenance information. + */ + private List unit; - public String getId() { - return id; - } + public String getId() { + return id; + } - public void setId(String id) { - this.id = id; - } + public void setId(String id) { + this.id = id; + } - public List getUnit() { - return unit; - } + public List getUnit() { + return unit; + } - public void setUnit(List unit) { - this.unit = unit; - } + public void setUnit(List unit) { + this.unit = unit; + } - public void mergeFrom(Measure m) { - //TODO - } + public void mergeFrom(Measure m) { + // TODO + } - @Override - public boolean equals(Object o) { - if (this == o) return true; - if (o == null || getClass() != o.getClass()) return false; - Measure measure = (Measure) o; - return Objects.equal(id, measure.id) && - Objects.equal(unit, measure.unit); - } + @Override + public boolean equals(Object o) { + if (this == o) + return true; + if (o == null || getClass() != o.getClass()) + return false; + Measure measure = (Measure) o; + return Objects.equal(id, measure.id) && + Objects.equal(unit, measure.unit); + } - @Override - public int hashCode() { - return Objects.hashCode(id, unit); - } + @Override + public int hashCode() { + return Objects.hashCode(id, unit); + } } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Programme.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Programme.java index c5259d07e5..00dc32fbca 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Programme.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Programme.java @@ -35,5 +35,4 @@ public class Programme implements Serializable { return Objects.equals(code, programme.code); } - } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java index d77bd7d733..17a50d7aca 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java @@ -8,10 +8,10 @@ import java.util.stream.Collectors; import java.util.stream.Stream; /** - * Relation models any edge between two nodes in the OpenAIRE graph. It has a source id and a target id - * pointing to graph node identifiers and it is further characterised by the semantic of the link through the fields - * relType, subRelType and relClass. Provenance information is modeled according to the dataInfo element and collectedFrom, - * while individual relationship types can provide extra information via the properties field. + * Relation models any edge between two nodes in the OpenAIRE graph. It has a source id and a target id pointing to + * graph node identifiers and it is further characterised by the semantic of the link through the fields relType, + * subRelType and relClass. Provenance information is modeled according to the dataInfo element and collectedFrom, while + * individual relationship types can provide extra information via the properties field. */ public class Relation extends Oaf { @@ -26,7 +26,8 @@ public class Relation extends Oaf { private String subRelType; /** - * Indicates the direction of the relationship, values include 'isSupplementTo', 'isSupplementedBy', 'merges, 'isMergedIn'. + * Indicates the direction of the relationship, values include 'isSupplementTo', 'isSupplementedBy', 'merges, + * 'isMergedIn'. */ private String relClass; @@ -51,7 +52,8 @@ public class Relation extends Oaf { private String validationDate; /** - * List of relation specific properties. Values include 'similarityLevel', indicating the similarity score between a pair of publications. + * List of relation specific properties. Values include 'similarityLevel', indicating the similarity score between a + * pair of publications. */ private List properties = new ArrayList<>(); 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 44737d46eb..0dc76fd435 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 @@ -241,7 +241,7 @@ public class Result extends OafEntity implements Serializable { Result r = (Result) e; - //TODO consider merging also Measures + // TODO consider merging also Measures instance = mergeLists(instance, r.getInstance()); diff --git a/dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/oaf/MeasureTest.java b/dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/oaf/MeasureTest.java index 4275e2c56e..26b4407c9b 100644 --- a/dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/oaf/MeasureTest.java +++ b/dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/oaf/MeasureTest.java @@ -1,48 +1,57 @@ + package eu.dnetlib.dhp.schema.oaf; +import java.io.IOException; +import java.util.List; + +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; + import com.fasterxml.jackson.annotation.JsonInclude; import com.fasterxml.jackson.core.type.TypeReference; import com.fasterxml.jackson.databind.ObjectMapper; import com.google.common.collect.Lists; -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.Test; - -import java.io.IOException; -import java.util.List; public class MeasureTest { - public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper() - .setSerializationInclusion(JsonInclude.Include.NON_NULL); + public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper() + .setSerializationInclusion(JsonInclude.Include.NON_NULL); - @Test - public void testMeasureSerialization() throws IOException { + @Test + public void testMeasureSerialization() throws IOException { - Measure popularity = new Measure(); - popularity.setId("popularity"); - popularity.setUnit(Lists.newArrayList( - unit("score", "0.5"))); + Measure popularity = new Measure(); + popularity.setId("popularity"); + popularity + .setUnit( + Lists + .newArrayList( + unit("score", "0.5"))); - Measure influence = new Measure(); - influence.setId("influence"); - influence.setUnit(Lists.newArrayList( - unit("score", "0.3"))); + Measure influence = new Measure(); + influence.setId("influence"); + influence + .setUnit( + Lists + .newArrayList( + unit("score", "0.3"))); - List m = Lists.newArrayList(popularity, influence); + List m = Lists.newArrayList(popularity, influence); - String s = OBJECT_MAPPER.writeValueAsString(m); - System.out.println(s); + String s = OBJECT_MAPPER.writeValueAsString(m); + System.out.println(s); - List mm = OBJECT_MAPPER.readValue(s, new TypeReference>() { }); + List mm = OBJECT_MAPPER.readValue(s, new TypeReference>() { + }); - Assertions.assertNotNull(mm); - } + Assertions.assertNotNull(mm); + } - private KeyValue unit(String key, String value) { - KeyValue unit = new KeyValue(); - unit.setKey(key); - unit.setValue(value); - return unit; - } + private KeyValue unit(String key, String value) { + KeyValue unit = new KeyValue(); + unit.setKey(key); + unit.setValue(value); + return unit; + } } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/ProjectSubset.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/ProjectSubset.java index cfbb62f219..2fccbc5165 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/ProjectSubset.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/ProjectSubset.java @@ -1,16 +1,17 @@ + package eu.dnetlib.dhp.actionmanager.project; import java.io.Serializable; public class ProjectSubset implements Serializable { - private String code; + private String code; - public String getCode() { - return code; - } + public String getCode() { + return code; + } - public void setCode(String code) { - this.code = code; - } + public void setCode(String code) { + this.code = code; + } } diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/SparkUpdateProjectTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/SparkUpdateProjectTest.java index 4d3ec140be..718cd8ebe0 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/SparkUpdateProjectTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/SparkUpdateProjectTest.java @@ -90,6 +90,5 @@ public class SparkUpdateProjectTest { Assertions.assertEquals(14, tmp.count()); - } } From 64f02de5d3765f741cdb458e42c8a20a725aaf4a Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 16 Jun 2020 17:48:51 +0200 Subject: [PATCH 60/62] updated workflow definition to include the cleaning step --- .../eu/dnetlib/dhp/wf/profiles/provision.xml | 92 +++++++++++++++---- 1 file changed, 73 insertions(+), 19 deletions(-) diff --git a/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/wf/profiles/provision.xml b/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/wf/profiles/provision.xml index 487afee4fa..28cbde70de 100644 --- a/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/wf/profiles/provision.xml +++ b/dhp-workflows/dhp-worfklow-profiles/src/main/resources/eu/dnetlib/dhp/wf/profiles/provision.xml @@ -4,7 +4,7 @@ - + Data Provision [OCEAN] @@ -61,11 +61,23 @@ + + + Set the target path to store the CLEANED graph + + cleanedGraphPath + /tmp/beta_provision/graph/05_graph_cleaned + + + + + + Set the target path to store the ORCID enriched graph orcidGraphPath - /tmp/beta_provision/graph/05_graph_orcid + /tmp/beta_provision/graph/06_graph_orcid @@ -75,7 +87,7 @@ Set the target path to store the BULK TAGGED graph bulkTaggingGraphPath - /tmp/beta_provision/graph/06_graph_bulktagging + /tmp/beta_provision/graph/07_graph_bulktagging @@ -85,7 +97,7 @@ Set the target path to store the AFFILIATION from INSTITUTIONAL REPOS graph affiliationGraphPath - /tmp/beta_provision/graph/07_graph_affiliation + /tmp/beta_provision/graph/08_graph_affiliation @@ -95,7 +107,7 @@ Set the target path to store the COMMUNITY from SELECTED SOURCES graph communityOrganizationGraphPath - /tmp/beta_provision/graph/08_graph_comunity_organization + /tmp/beta_provision/graph/09_graph_comunity_organization @@ -105,7 +117,7 @@ Set the target path to store the FUNDING from SEMANTIC RELATION graph fundingGraphPath - /tmp/beta_provision/graph/09_graph_funding + /tmp/beta_provision/graph/10_graph_funding @@ -115,7 +127,7 @@ Set the target path to store the COMMUNITY from SEMANTIC RELATION graph communitySemRelGraphPath - /tmp/beta_provision/graph/10_graph_comunity_sem_rel + /tmp/beta_provision/graph/11_graph_comunity_sem_rel @@ -125,7 +137,7 @@ Set the target path to store the COUNTRY enriched graph countryGraphPath - /tmp/beta_provision/graph/11_graph_country + /tmp/beta_provision/graph/12_graph_country @@ -135,7 +147,7 @@ Set the target path to store the blacklisted graph blacklistedGraphPath - /tmp/beta_provision/graph/12_graph_blacklisted + /tmp/beta_provision/graph/13_graph_blacklisted @@ -217,7 +229,8 @@ IIS { - 'graphOutputPath' : 'aggregatorGraphPath' + 'graphOutputPath' : 'aggregatorGraphPath', + 'isLookupUrl' : 'isLookUpUrl' } @@ -227,8 +240,8 @@ 'mongoDb' : 'mdstore', 'postgresURL' : 'jdbc:postgresql://beta.services.openaire.eu:5432/dnet_openaireplus', 'postgresUser' : 'dnet', - 'postgresPassword' : 'dnetPwd', - 'reuseContent' : 'true', + 'postgresPassword' : '', + 'reuseContent' : 'false', 'contentPath' : '/tmp/beta_provision/aggregator', 'workingDir' : '/tmp/beta_provision/working_dir/aggregator' } @@ -255,6 +268,8 @@ { 'oozie.wf.application.path' : '/lib/dnet/actionmanager/wf/main/oozie_app', + 'sparkExecutorCores' : '3', + 'sparkExecutorMemory' : '10G', 'activePromoteDatasetActionPayload' : 'true', 'activePromoteDatasourceActionPayload' : 'true', 'activePromoteOrganizationActionPayload' : 'true', @@ -315,6 +330,8 @@ { 'oozie.wf.application.path' : '/lib/dnet/actionmanager/wf/main/oozie_app', + 'sparkExecutorCores' : '3', + 'sparkExecutorMemory' : '10G', 'activePromoteDatasetActionPayload' : 'true', 'activePromoteDatasourceActionPayload' : 'true', 'activePromoteOrganizationActionPayload' : 'true', @@ -354,7 +371,43 @@ build-report - + + + + + + clean the properties in the graph typed as Qualifier according to the vocabulary indicated in schemeid + + executeOozieJob + IIS + + { + 'graphInputPath' : 'consistentGraphPath', + 'graphOutputPath': 'cleanedGraphPath', + 'isLookupUrl': 'isLookUpUrl' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/oa/graph/clean/oozie_app', + 'workingPath' : '/tmp/beta_provision/working_dir/clean' + } + + build-report + + + + + + + + Do we skip the graph enrichment steps? (Yes to prepare the graph for the IIS) + + NO + + + + @@ -364,7 +417,7 @@ IIS { - 'sourcePath' : 'consistentGraphPath', + 'sourcePath' : 'cleanedGraphPath', 'outputPath': 'orcidGraphPath' } @@ -552,7 +605,7 @@ 'workingDir' : '/tmp/beta_provision/working_dir/blacklist', 'postgresURL' : 'jdbc:postgresql://beta.services.openaire.eu:5432/dnet_openaireplus', 'postgresUser' : 'dnet', - 'postgresPassword' : 'dnetPwd' + 'postgresPassword' : '' } build-report @@ -561,12 +614,13 @@ + - wf_20200509_100941_857 - 2020-05-09T13:26:09+00:00 - FAILURE - eu.dnetlib.data.hadoop.rmi.HadoopServiceException: hadoop job: 0002933-200403132837156-oozie-oozi-W failed with status: KILLED, oozie log: 2020-05-09 13:23:31,194 INFO org.apache.oozie.service.JPAService: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[] No results found 2020-05-09 13:23:31,216 INFO org.apache.oozie.command.wf.ActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@:start:] Start action [0002933-200403132837156-oozie-oozi-W@:start:] with user-retry state : userRetryCount [0], userRetryMax [0], userRetryInterval [10] 2020-05-09 13:23:31,216 INFO org.apache.oozie.command.wf.ActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@:start:] [***0002933-200403132837156-oozie-oozi-W@:start:***]Action status=DONE 2020-05-09 13:23:31,216 INFO org.apache.oozie.command.wf.ActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@:start:] [***0002933-200403132837156-oozie-oozi-W@:start:***]Action updated in DB! 2020-05-09 13:23:31,257 INFO org.apache.oozie.service.JPAService: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@:start:] No results found 2020-05-09 13:23:31,275 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@:start:] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@:start: 2020-05-09 13:23:31,275 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W 2020-05-09 13:23:31,314 INFO org.apache.oozie.command.wf.ActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@reset-outputpath] Start action [0002933-200403132837156-oozie-oozi-W@reset-outputpath] with user-retry state : userRetryCount [0], userRetryMax [0], userRetryInterval [10] 2020-05-09 13:23:33,897 INFO org.apache.oozie.command.wf.ActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@reset-outputpath] [***0002933-200403132837156-oozie-oozi-W@reset-outputpath***]Action status=DONE 2020-05-09 13:23:33,897 INFO org.apache.oozie.command.wf.ActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@reset-outputpath] [***0002933-200403132837156-oozie-oozi-W@reset-outputpath***]Action updated in DB! 2020-05-09 13:23:33,947 INFO org.apache.oozie.service.JPAService: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@reset-outputpath] No results found 2020-05-09 13:23:33,966 INFO org.apache.oozie.command.wf.ActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_entities] Start action [0002933-200403132837156-oozie-oozi-W@copy_entities] with user-retry state : userRetryCount [0], userRetryMax [0], userRetryInterval [10] 2020-05-09 13:23:33,966 INFO org.apache.oozie.command.wf.ActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_entities] [***0002933-200403132837156-oozie-oozi-W@copy_entities***]Action status=DONE 2020-05-09 13:23:33,966 INFO org.apache.oozie.command.wf.ActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_entities] [***0002933-200403132837156-oozie-oozi-W@copy_entities***]Action updated in DB! 2020-05-09 13:23:34,012 INFO org.apache.oozie.service.JPAService: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_entities] No results found 2020-05-09 13:23:34,018 INFO org.apache.oozie.service.JPAService: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_entities] No results found 2020-05-09 13:23:34,023 INFO org.apache.oozie.service.JPAService: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_entities] No results found 2020-05-09 13:23:34,029 INFO org.apache.oozie.service.JPAService: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_entities] No results found 2020-05-09 13:23:34,124 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_relation] Start action [0002933-200403132837156-oozie-oozi-W@copy_relation] with user-retry state : userRetryCount [0], userRetryMax [0], userRetryInterval [10] 2020-05-09 13:23:34,130 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_projects] Start action [0002933-200403132837156-oozie-oozi-W@copy_projects] with user-retry state : userRetryCount [0], userRetryMax [0], userRetryInterval [10] 2020-05-09 13:23:34,130 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_datasources] Start action [0002933-200403132837156-oozie-oozi-W@copy_datasources] with user-retry state : userRetryCount [0], userRetryMax [0], userRetryInterval [10] 2020-05-09 13:23:34,140 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_organization] Start action [0002933-200403132837156-oozie-oozi-W@copy_organization] with user-retry state : userRetryCount [0], userRetryMax [0], userRetryInterval [10] 2020-05-09 13:23:35,010 INFO org.apache.oozie.action.hadoop.DistcpActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_projects] checking action, hadoop job ID [job_1585920557248_14569] status [RUNNING] 2020-05-09 13:23:35,018 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_projects] [***0002933-200403132837156-oozie-oozi-W@copy_projects***]Action status=RUNNING 2020-05-09 13:23:35,018 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_projects] [***0002933-200403132837156-oozie-oozi-W@copy_projects***]Action updated in DB! 2020-05-09 13:23:35,022 INFO org.apache.oozie.action.hadoop.DistcpActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_relation] checking action, hadoop job ID [job_1585920557248_14568] status [RUNNING] 2020-05-09 13:23:35,027 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_projects] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@copy_projects 2020-05-09 13:23:35,028 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_relation] [***0002933-200403132837156-oozie-oozi-W@copy_relation***]Action status=RUNNING 2020-05-09 13:23:35,028 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_relation] [***0002933-200403132837156-oozie-oozi-W@copy_relation***]Action updated in DB! 2020-05-09 13:23:35,031 INFO org.apache.oozie.action.hadoop.DistcpActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_datasources] checking action, hadoop job ID [job_1585920557248_14570] status [RUNNING] 2020-05-09 13:23:35,035 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_datasources] [***0002933-200403132837156-oozie-oozi-W@copy_datasources***]Action status=RUNNING 2020-05-09 13:23:35,035 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_datasources] [***0002933-200403132837156-oozie-oozi-W@copy_datasources***]Action updated in DB! 2020-05-09 13:23:35,037 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_relation] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@copy_relation 2020-05-09 13:23:35,048 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_datasources] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@copy_datasources 2020-05-09 13:23:35,072 INFO org.apache.oozie.action.hadoop.DistcpActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_organization] checking action, hadoop job ID [job_1585920557248_14571] status [RUNNING] 2020-05-09 13:23:35,076 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_organization] [***0002933-200403132837156-oozie-oozi-W@copy_organization***]Action status=RUNNING 2020-05-09 13:23:35,076 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_organization] [***0002933-200403132837156-oozie-oozi-W@copy_organization***]Action updated in DB! 2020-05-09 13:23:35,084 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_organization] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@copy_organization 2020-05-09 13:23:35,090 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_entities] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@copy_entities 2020-05-09 13:23:35,090 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@reset-outputpath] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@reset-outputpath 2020-05-09 13:23:58,926 INFO org.apache.oozie.servlet.CallbackServlet: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_datasources] callback for action [0002933-200403132837156-oozie-oozi-W@copy_datasources] 2020-05-09 13:23:59,085 INFO org.apache.oozie.action.hadoop.DistcpActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_datasources] checking action, hadoop job ID [job_1585920557248_14570] status [RUNNING] 2020-05-09 13:23:59,242 INFO org.apache.oozie.servlet.CallbackServlet: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_projects] callback for action [0002933-200403132837156-oozie-oozi-W@copy_projects] 2020-05-09 13:23:59,386 INFO org.apache.oozie.action.hadoop.DistcpActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_projects] checking action, hadoop job ID [job_1585920557248_14569] status [RUNNING] 2020-05-09 13:24:01,343 INFO org.apache.oozie.servlet.CallbackServlet: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_datasources] callback for action [0002933-200403132837156-oozie-oozi-W@copy_datasources] 2020-05-09 13:24:01,418 INFO org.apache.oozie.action.hadoop.DistcpActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_datasources] Hadoop Jobs launched : [job_1585920557248_14573] 2020-05-09 13:24:01,418 INFO org.apache.oozie.action.hadoop.DistcpActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_datasources] action completed, external ID [job_1585920557248_14570] 2020-05-09 13:24:01,493 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_datasources] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@copy_datasources 2020-05-09 13:24:01,935 INFO org.apache.oozie.servlet.CallbackServlet: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_projects] callback for action [0002933-200403132837156-oozie-oozi-W@copy_projects] 2020-05-09 13:24:02,012 INFO org.apache.oozie.action.hadoop.DistcpActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_projects] Hadoop Jobs launched : [job_1585920557248_14572] 2020-05-09 13:24:02,012 INFO org.apache.oozie.action.hadoop.DistcpActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_projects] action completed, external ID [job_1585920557248_14569] 2020-05-09 13:24:02,076 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_projects] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@copy_projects 2020-05-09 13:25:03,172 INFO org.apache.oozie.servlet.CallbackServlet: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_organization] callback for action [0002933-200403132837156-oozie-oozi-W@copy_organization] 2020-05-09 13:25:03,336 INFO org.apache.oozie.action.hadoop.DistcpActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_organization] checking action, hadoop job ID [job_1585920557248_14571] status [RUNNING] 2020-05-09 13:25:05,598 INFO org.apache.oozie.servlet.CallbackServlet: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_organization] callback for action [0002933-200403132837156-oozie-oozi-W@copy_organization] 2020-05-09 13:25:05,688 INFO org.apache.oozie.action.hadoop.DistcpActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_organization] Hadoop Jobs launched : [job_1585920557248_14574] 2020-05-09 13:25:05,691 INFO org.apache.oozie.action.hadoop.DistcpActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_organization] action completed, external ID [job_1585920557248_14571] 2020-05-09 13:25:05,748 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_organization] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@copy_organization 2020-05-09 13:25:23,274 INFO org.apache.oozie.servlet.CallbackServlet: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_relation] callback for action [0002933-200403132837156-oozie-oozi-W@copy_relation] 2020-05-09 13:25:23,409 INFO org.apache.oozie.action.hadoop.DistcpActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_relation] checking action, hadoop job ID [job_1585920557248_14568] status [RUNNING] 2020-05-09 13:25:25,419 INFO org.apache.oozie.servlet.CallbackServlet: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_relation] callback for action [0002933-200403132837156-oozie-oozi-W@copy_relation] 2020-05-09 13:25:25,510 INFO org.apache.oozie.action.hadoop.DistcpActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_relation] Hadoop Jobs launched : [job_1585920557248_14575] 2020-05-09 13:25:25,511 INFO org.apache.oozie.action.hadoop.DistcpActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_relation] action completed, external ID [job_1585920557248_14568] 2020-05-09 13:25:25,565 INFO org.apache.oozie.service.JPAService: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_relation] No results found 2020-05-09 13:25:25,585 INFO org.apache.oozie.command.wf.ActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_wait] Start action [0002933-200403132837156-oozie-oozi-W@copy_wait] with user-retry state : userRetryCount [0], userRetryMax [0], userRetryInterval [10] 2020-05-09 13:25:25,585 INFO org.apache.oozie.command.wf.ActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_wait] [***0002933-200403132837156-oozie-oozi-W@copy_wait***]Action status=DONE 2020-05-09 13:25:25,585 INFO org.apache.oozie.command.wf.ActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_wait] [***0002933-200403132837156-oozie-oozi-W@copy_wait***]Action updated in DB! 2020-05-09 13:25:25,627 INFO org.apache.oozie.service.JPAService: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_wait] No results found 2020-05-09 13:25:25,648 INFO org.apache.oozie.command.wf.ActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@fork_prepare_assoc_step1] Start action [0002933-200403132837156-oozie-oozi-W@fork_prepare_assoc_step1] with user-retry state : userRetryCount [0], userRetryMax [0], userRetryInterval [10] 2020-05-09 13:25:25,648 INFO org.apache.oozie.command.wf.ActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@fork_prepare_assoc_step1] [***0002933-200403132837156-oozie-oozi-W@fork_prepare_assoc_step1***]Action status=DONE 2020-05-09 13:25:25,648 INFO org.apache.oozie.command.wf.ActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@fork_prepare_assoc_step1] [***0002933-200403132837156-oozie-oozi-W@fork_prepare_assoc_step1***]Action updated in DB! 2020-05-09 13:25:25,694 INFO org.apache.oozie.service.JPAService: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@fork_prepare_assoc_step1] No results found 2020-05-09 13:25:25,700 INFO org.apache.oozie.service.JPAService: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@fork_prepare_assoc_step1] No results found 2020-05-09 13:25:25,706 INFO org.apache.oozie.service.JPAService: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@fork_prepare_assoc_step1] No results found 2020-05-09 13:25:25,711 INFO org.apache.oozie.service.JPAService: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@fork_prepare_assoc_step1] No results found 2020-05-09 13:25:25,801 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_dataset] Start action [0002933-200403132837156-oozie-oozi-W@join_prepare_dataset] with user-retry state : userRetryCount [0], userRetryMax [0], userRetryInterval [10] 2020-05-09 13:25:25,825 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_software] Start action [0002933-200403132837156-oozie-oozi-W@join_prepare_software] with user-retry state : userRetryCount [0], userRetryMax [0], userRetryInterval [10] 2020-05-09 13:25:25,825 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_otherresearchproduct] Start action [0002933-200403132837156-oozie-oozi-W@join_prepare_otherresearchproduct] with user-retry state : userRetryCount [0], userRetryMax [0], userRetryInterval [10] 2020-05-09 13:25:25,828 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_publication] Start action [0002933-200403132837156-oozie-oozi-W@join_prepare_publication] with user-retry state : userRetryCount [0], userRetryMax [0], userRetryInterval [10] 2020-05-09 13:25:27,165 INFO org.apache.oozie.action.hadoop.SparkActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_otherresearchproduct] checking action, hadoop job ID [job_1585920557248_14578] status [RUNNING] 2020-05-09 13:25:27,170 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_otherresearchproduct] [***0002933-200403132837156-oozie-oozi-W@join_prepare_otherresearchproduct***]Action status=RUNNING 2020-05-09 13:25:27,170 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_otherresearchproduct] [***0002933-200403132837156-oozie-oozi-W@join_prepare_otherresearchproduct***]Action updated in DB! 2020-05-09 13:25:27,179 INFO org.apache.oozie.action.hadoop.SparkActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_software] checking action, hadoop job ID [job_1585920557248_14577] status [RUNNING] 2020-05-09 13:25:27,181 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_otherresearchproduct] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@join_prepare_otherresearchproduct 2020-05-09 13:25:27,183 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_software] [***0002933-200403132837156-oozie-oozi-W@join_prepare_software***]Action status=RUNNING 2020-05-09 13:25:27,183 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_software] [***0002933-200403132837156-oozie-oozi-W@join_prepare_software***]Action updated in DB! 2020-05-09 13:25:27,188 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_software] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@join_prepare_software 2020-05-09 13:25:27,617 INFO org.apache.oozie.action.hadoop.SparkActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_publication] checking action, hadoop job ID [job_1585920557248_14576] status [RUNNING] 2020-05-09 13:25:27,622 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_publication] [***0002933-200403132837156-oozie-oozi-W@join_prepare_publication***]Action status=RUNNING 2020-05-09 13:25:27,622 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_publication] [***0002933-200403132837156-oozie-oozi-W@join_prepare_publication***]Action updated in DB! 2020-05-09 13:25:27,625 INFO org.apache.oozie.action.hadoop.SparkActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_dataset] checking action, hadoop job ID [job_1585920557248_14579] status [RUNNING] 2020-05-09 13:25:27,628 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_publication] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@join_prepare_publication 2020-05-09 13:25:27,629 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_dataset] [***0002933-200403132837156-oozie-oozi-W@join_prepare_dataset***]Action status=RUNNING 2020-05-09 13:25:27,629 INFO org.apache.oozie.command.wf.ForkedActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_dataset] [***0002933-200403132837156-oozie-oozi-W@join_prepare_dataset***]Action updated in DB! 2020-05-09 13:25:27,634 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_dataset] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@join_prepare_dataset 2020-05-09 13:25:27,639 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@fork_prepare_assoc_step1] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@fork_prepare_assoc_step1 2020-05-09 13:25:27,639 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_wait] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@copy_wait 2020-05-09 13:25:27,640 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@copy_relation] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@copy_relation 2020-05-09 13:25:41,416 INFO org.apache.oozie.servlet.CallbackServlet: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_software] callback for action [0002933-200403132837156-oozie-oozi-W@join_prepare_software] 2020-05-09 13:25:41,490 INFO org.apache.oozie.action.hadoop.SparkActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_software] action completed, external ID [job_1585920557248_14577] 2020-05-09 13:25:41,495 WARN org.apache.oozie.action.hadoop.SparkActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_software] Launcher ERROR, reason: Main class [org.apache.oozie.action.hadoop.SparkMain], main() threw exception, File file:/data/3/yarn/nm/usercache/dnet.beta/appcache/application_1585920557248_14577/container_e68_1585920557248_14577_01_000002/dhp-propagation-1.1.8-SNAPSHOT.jar does not exist 2020-05-09 13:25:41,495 WARN org.apache.oozie.action.hadoop.SparkActionExecutor: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_software] Launcher exception: File file:/data/3/yarn/nm/usercache/dnet.beta/appcache/application_1585920557248_14577/container_e68_1585920557248_14577_01_000002/dhp-propagation-1.1.8-SNAPSHOT.jar does not exist java.io.FileNotFoundException: File file:/data/3/yarn/nm/usercache/dnet.beta/appcache/application_1585920557248_14577/container_e68_1585920557248_14577_01_000002/dhp-propagation-1.1.8-SNAPSHOT.jar does not exist at org.apache.hadoop.fs.RawLocalFileSystem.deprecatedGetFileStatus(RawLocalFileSystem.java:598) at org.apache.hadoop.fs.RawLocalFileSystem.getFileLinkStatusInternal(RawLocalFileSystem.java:811) at org.apache.hadoop.fs.RawLocalFileSystem.getFileStatus(RawLocalFileSystem.java:588) at org.apache.hadoop.fs.FilterFileSystem.getFileStatus(FilterFileSystem.java:432) at org.apache.hadoop.fs.FileUtil.copy(FileUtil.java:340) at org.apache.hadoop.fs.FileUtil.copy(FileUtil.java:292) at org.apache.spark.deploy.yarn.Client.copyFileToRemote(Client.scala:404) at org.apache.spark.deploy.yarn.Client.org$apache$spark$deploy$yarn$Client$$distribute$1(Client.scala:496) at org.apache.spark.deploy.yarn.Client$$anonfun$prepareLocalResources$9.apply(Client.scala:595) at org.apache.spark.deploy.yarn.Client$$anonfun$prepareLocalResources$9.apply(Client.scala:594) at scala.Option.foreach(Option.scala:257) at org.apache.spark.deploy.yarn.Client.prepareLocalResources(Client.scala:594) at org.apache.spark.deploy.yarn.Client.createContainerLaunchContext(Client.scala:886) at org.apache.spark.deploy.yarn.Client.submitApplication(Client.scala:180) at org.apache.spark.deploy.yarn.Client.run(Client.scala:1156) at org.apache.spark.deploy.yarn.YarnClusterApplication.start(Client.scala:1608) at org.apache.spark.deploy.SparkSubmit.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:849) at org.apache.spark.deploy.SparkSubmit.doRunMain$1(SparkSubmit.scala:167) at org.apache.spark.deploy.SparkSubmit.submit(SparkSubmit.scala:195) at org.apache.spark.deploy.SparkSubmit.doSubmit(SparkSubmit.scala:86) at org.apache.spark.deploy.SparkSubmit$$anon$2.doSubmit(SparkSubmit.scala:924) at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:933) at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala) at org.apache.oozie.action.hadoop.SparkMain.runSpark(SparkMain.java:178) at org.apache.oozie.action.hadoop.SparkMain.run(SparkMain.java:90) at org.apache.oozie.action.hadoop.LauncherMain.run(LauncherMain.java:81) at org.apache.oozie.action.hadoop.SparkMain.main(SparkMain.java:57) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.apache.oozie.action.hadoop.LauncherMapper.map(LauncherMapper.java:235) at org.apache.hadoop.mapred.MapRunner.run(MapRunner.java:54) at org.apache.hadoop.mapred.MapTask.runOldMapper(MapTask.java:459) at org.apache.hadoop.mapred.MapTask.run(MapTask.java:343) at org.apache.hadoop.mapred.YarnChild$2.run(YarnChild.java:164) at java.security.AccessController.doPrivileged(Native Method) at javax.security.auth.Subject.doAs(Subject.java:422) at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1924) at org.apache.hadoop.mapred.YarnChild.main(YarnChild.java:158) 2020-05-09 13:25:41,514 INFO org.apache.oozie.command.wf.ActionEndXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_software] ERROR is considered as FAILED for SLA 2020-05-09 13:25:41,541 INFO org.apache.oozie.service.JPAService: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_software] No results found 2020-05-09 13:25:41,580 INFO org.apache.oozie.command.wf.ActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@Kill] Start action [0002933-200403132837156-oozie-oozi-W@Kill] with user-retry state : userRetryCount [0], userRetryMax [0], userRetryInterval [10] 2020-05-09 13:25:41,580 INFO org.apache.oozie.command.wf.ActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@Kill] [***0002933-200403132837156-oozie-oozi-W@Kill***]Action status=DONE 2020-05-09 13:25:41,580 INFO org.apache.oozie.command.wf.ActionStartXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@Kill] [***0002933-200403132837156-oozie-oozi-W@Kill***]Action updated in DB! 2020-05-09 13:25:41,692 WARN org.apache.oozie.workflow.lite.LiteWorkflowInstance: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@Kill] Workflow completed [KILLED], killing [3] running nodes 2020-05-09 13:25:41,760 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@Kill] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@Kill 2020-05-09 13:25:41,766 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_software] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@join_prepare_software 2020-05-09 13:25:41,852 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_otherresearchproduct] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@join_prepare_otherresearchproduct 2020-05-09 13:25:41,914 INFO org.apache.oozie.servlet.CallbackServlet: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_dataset] callback for action [0002933-200403132837156-oozie-oozi-W@join_prepare_dataset] 2020-05-09 13:25:41,920 ERROR org.apache.oozie.command.wf.CompletedActionXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_dataset] XException, org.apache.oozie.command.CommandException: E0800: Action it is not running its in [KILLED] state, action [0002933-200403132837156-oozie-oozi-W@join_prepare_dataset] at org.apache.oozie.command.wf.CompletedActionXCommand.eagerVerifyPrecondition(CompletedActionXCommand.java:92) at org.apache.oozie.command.XCommand.call(XCommand.java:257) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at org.apache.oozie.service.CallableQueueService$CallableWrapper.run(CallableQueueService.java:179) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) 2020-05-09 13:25:41,938 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_publication] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@join_prepare_publication 2020-05-09 13:25:42,005 INFO org.apache.oozie.servlet.CallbackServlet: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_publication] callback for action [0002933-200403132837156-oozie-oozi-W@join_prepare_publication] 2020-05-09 13:25:42,010 ERROR org.apache.oozie.command.wf.CompletedActionXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_publication] XException, org.apache.oozie.command.CommandException: E0800: Action it is not running its in [KILLED] state, action [0002933-200403132837156-oozie-oozi-W@join_prepare_publication] at org.apache.oozie.command.wf.CompletedActionXCommand.eagerVerifyPrecondition(CompletedActionXCommand.java:92) at org.apache.oozie.command.XCommand.call(XCommand.java:257) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at org.apache.oozie.service.CallableQueueService$CallableWrapper.run(CallableQueueService.java:179) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) 2020-05-09 13:25:42,028 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[dnet.beta] GROUP[-] TOKEN[] APP[orcid_to_result_from_semrel_propagation] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W 2020-05-09 13:25:42,028 INFO org.apache.oozie.command.wf.WorkflowNotificationXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_dataset] No Notification URL is defined. Therefore nothing to notify for job 0002933-200403132837156-oozie-oozi-W@join_prepare_dataset 2020-05-09 13:25:42,113 INFO org.apache.oozie.servlet.CallbackServlet: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[-] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_otherresearchproduct] callback for action [0002933-200403132837156-oozie-oozi-W@join_prepare_otherresearchproduct] 2020-05-09 13:25:42,116 ERROR org.apache.oozie.command.wf.CompletedActionXCommand: SERVER[iis-cdh5-test-m3.ocean.icm.edu.pl] USER[-] GROUP[-] TOKEN[] APP[-] JOB[0002933-200403132837156-oozie-oozi-W] ACTION[0002933-200403132837156-oozie-oozi-W@join_prepare_otherresearchproduct] XException, org.apache.oozie.command.CommandException: E0800: Action it is not running its in [KILLED] state, action [0002933-200403132837156-oozie-oozi-W@join_prepare_otherresearchproduct] at org.apache.oozie.command.wf.CompletedActionXCommand.eagerVerifyPrecondition(CompletedActionXCommand.java:92) at org.apache.oozie.command.XCommand.call(XCommand.java:257) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at org.apache.oozie.service.CallableQueueService$CallableWrapper.run(CallableQueueService.java:179) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) + wf_20200615_163630_609 + 2020-06-15T17:08:00+00:00 + SUCCESS + \ No newline at end of file From 11b77b9f4e29a0d09cab1f1a3ab49419c6735517 Mon Sep 17 00:00:00 2001 From: miconis Date: Tue, 16 Jun 2020 18:31:11 +0200 Subject: [PATCH 61/62] json dumps for entity merge test modified to fit the new model. title merge adjusted to fix the error --- .../src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java | 4 ++-- .../eu/dnetlib/dhp/dedup/json/publication_merge.json | 6 +++--- 2 files changed, 5 insertions(+), 5 deletions(-) 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 c9d0ac7c77..82e8fd05d9 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 @@ -259,9 +259,9 @@ public class Result extends OafEntity implements Serializable { StructuredProperty newMainTitle = null; if (r.getTitle() != null) { newMainTitle = getMainTitle(r.getTitle()); - if (newMainTitle != null && title != null) { + if (newMainTitle != null) { final StructuredProperty p = newMainTitle; - title = title.stream().filter(t -> t != p).collect(Collectors.toList()); + r.setTitle(r.getTitle().stream().filter(t -> t != p).collect(Collectors.toList())); } } diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/json/publication_merge.json b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/json/publication_merge.json index 28548c5322..ae688e746b 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/json/publication_merge.json +++ b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/json/publication_merge.json @@ -1,3 +1,3 @@ -{"context": [], "dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "sysimport:crosswalk:datasetarchive", "classname": "sysimport:crosswalk:datasetarchive", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}, "inferred": false, "inferenceprovenance": "dedup-similarity-result-levenstein", "invisible": false, "trust": "0.95"}, "resourcetype": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "pid": [], "contributor": [], "resulttype": {"classid": "publication", "classname": "publication", "schemename": "dnet:result_typologies", "schemeid": "dnet:result_typologies"}, "relevantdate": [], "collectedfrom": [{"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "Journal.fi", "key": "10|openaire____::6eef8049d0feedc089ee009abca55e35"}], "id": "50|a89337edbe55::4930db9e954866d70916cbfba9f81f97", "subject": [], "instance": [{"refereed": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "hostedby": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "Journal.fi", "key": "10|openaire____::6eef8049d0feedc089ee009abca55e35"}, "processingchargeamount": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "license": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "url": [], "distributionlocation": "", "processingchargecurrency": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "dateofacceptance": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2016-01-01"}, "collectedfrom": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "Journal.fi", "key": "10|openaire____::6eef8049d0feedc089ee009abca55e35"}, "accessright": {"classid": "OPEN", "classname": "Open Access", "schemename": "dnet:access_modes", "schemeid": "dnet:access_modes"}, "instancetype": {"classid": "0001", "classname": "Article", "schemename": "dnet:dataCite_resource", "schemeid": "dnet:dataCite_resource"}}], "embargoenddate": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "lastupdatetimestamp": 0, "author": [{"surname": "Go\\u0308tz", "name": "Julia", "pid": [], "rank": 5, "affiliation": [], "fullname": 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"schemeid": "dnet:languages"}, "bestaccessright": {"classid": "UNKNOWN", "classname": "not available", "schemename": "dnet:access_modes", "schemeid": "dnet:access_modes"}, "country": [{"classid": "FI", "classname": "Finland", "schemeid": "dnet:countries", "schemename": "dnet:countries"}], "extraInfo": [], "originalId": ["(BISIS)113444", "https://www.cris.uns.ac.rs/record.jsf?recordId=113444&source=OpenAIRE&language=en"], "dateofacceptance": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2016-01-01"}, "title": [{"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "test title", "classname": "test title", "schemename": "dnet:dataCite_title", "schemeid": "dnet:dataCite_title"}, "value": "Antichains of copies of ultrahomogeneous structures"}]} \ No newline at end of file From 1d4275acc44957fe412c79a66b9d84e51c044f30 Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Wed, 17 Jun 2020 09:10:38 +0200 Subject: [PATCH 62/62] implemented first version of exportation of Scholexplorer into ActionSet --- .../dhp/schema/scholexplorer/DLIRelation.java | 14 + .../broker/oa/GenerateEventsApplication.java | 122 ++++-- .../dhp/broker/oa/matchers/UpdateMatcher.java | 6 +- .../simple/EnrichMissingAbstract.java | 6 +- .../simple/EnrichMissingAuthorOrcid.java | 3 +- .../simple/EnrichMissingOpenAccess.java | 7 +- .../oa/matchers/simple/EnrichMissingPid.java | 10 +- .../simple/EnrichMissingPublicationDate.java | 6 +- .../matchers/simple/EnrichMissingSubject.java | 3 +- .../matchers/simple/EnrichMoreOpenAccess.java | 3 +- .../oa/matchers/simple/EnrichMorePid.java | 6 +- .../oa/matchers/simple/EnrichMoreSubject.java | 3 +- .../dhp/broker/oa/util/EventGroup.java | 1 + .../dhp/broker/oa/util/ResultAggregator.java | 1 + .../dhp/broker/oa/util/ResultGroup.java | 1 + .../dhp/broker/oa/util/TrustUtils.java | 16 +- .../dhp/broker/oa/util/UpdateInfo.java | 9 +- .../dhp/broker/oa/util/TrustUtilsTest.java | 1 + .../orcid/oozie_app/config-default.xml | 30 +- .../parser/DatasetScholexplorerParser.java | 2 +- .../PublicationScholexplorerParser.java | 8 +- .../dhp/sx/graph/step1/oozie_app/workflow.xml | 4 +- .../java/eu/dnetlib/dhp/export/DLIToOAF.scala | 376 ++++++++++++++++++ .../SparkExportContentForOpenAire.scala | 118 ++++++ .../input_export_content_parameters.json | 14 + .../sx/export/oozie_app/config-default.xml | 42 ++ .../dhp/sx/export/oozie_app/workflow.xml | 49 +++ .../dhp/export/ExportDLITOOAFTest.scala | 75 ++++ .../eu/dnetlib/dhp/export/dataset.json | 101 +++++ .../eu/dnetlib/dhp/export/publication.json | 128 ++++++ .../eu/dnetlib/dhp/export/relation.json | 23 ++ 31 files changed, 1110 insertions(+), 78 deletions(-) create mode 100644 dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/export/DLIToOAF.scala create mode 100644 dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/export/SparkExportContentForOpenAire.scala create mode 100644 dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/export/input_export_content_parameters.json create mode 100644 dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/export/oozie_app/config-default.xml create mode 100644 dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/export/oozie_app/workflow.xml create mode 100644 dhp-workflows/dhp-graph-provision-scholexplorer/src/test/java/eu/dnetlib/dhp/export/ExportDLITOOAFTest.scala create mode 100644 dhp-workflows/dhp-graph-provision-scholexplorer/src/test/resources/eu/dnetlib/dhp/export/dataset.json create mode 100644 dhp-workflows/dhp-graph-provision-scholexplorer/src/test/resources/eu/dnetlib/dhp/export/publication.json create mode 100644 dhp-workflows/dhp-graph-provision-scholexplorer/src/test/resources/eu/dnetlib/dhp/export/relation.json diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/scholexplorer/DLIRelation.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/scholexplorer/DLIRelation.java index d2d2089c08..ca85fa14fc 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/scholexplorer/DLIRelation.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/scholexplorer/DLIRelation.java @@ -1,11 +1,25 @@ package eu.dnetlib.dhp.schema.scholexplorer; +import java.util.List; + +import eu.dnetlib.dhp.schema.oaf.KeyValue; import eu.dnetlib.dhp.schema.oaf.Relation; public class DLIRelation extends Relation { + private String dateOfCollection; + private List collectedFrom; + + public List getCollectedFrom() { + return collectedFrom; + } + + public void setCollectedFrom(List collectedFrom) { + this.collectedFrom = collectedFrom; + } + public String getDateOfCollection() { return dateOfCollection; } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java index 44bc5cb6ee..ecf4e3eff4 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java @@ -91,35 +91,29 @@ public class GenerateEventsApplication { private static final UpdateMatcher>, ?> enrichMoreSoftware = new EnrichMoreSoftware(); private static final UpdateMatcher>, ?> enrichMisissingPublicationIsRelatedTo = new EnrichMissingPublicationIsRelatedTo(); - private static final UpdateMatcher>, ?> enrichMissingPublicationIsReferencedBy = - new EnrichMissingPublicationIsReferencedBy(); + private static final UpdateMatcher>, ?> enrichMissingPublicationIsReferencedBy = new EnrichMissingPublicationIsReferencedBy(); private static final UpdateMatcher>, ?> enrichMissingPublicationReferences = new EnrichMissingPublicationReferences(); - private static final UpdateMatcher>, ?> enrichMissingPublicationIsSupplementedTo = - new EnrichMissingPublicationIsSupplementedTo(); - private static final UpdateMatcher>, ?> enrichMissingPublicationIsSupplementedBy = - new EnrichMissingPublicationIsSupplementedBy(); + private static final UpdateMatcher>, ?> enrichMissingPublicationIsSupplementedTo = new EnrichMissingPublicationIsSupplementedTo(); + private static final UpdateMatcher>, ?> enrichMissingPublicationIsSupplementedBy = new EnrichMissingPublicationIsSupplementedBy(); - private static final UpdateMatcher>, ?> enrichMisissingDatasetIsRelatedTo = - new EnrichMissingDatasetIsRelatedTo(); - private static final UpdateMatcher>, ?> enrichMissingDatasetIsReferencedBy = - new EnrichMissingDatasetIsReferencedBy(); - private static final UpdateMatcher>, ?> enrichMissingDatasetReferences = - new EnrichMissingDatasetReferences(); - private static final UpdateMatcher>, ?> enrichMissingDatasetIsSupplementedTo = - new EnrichMissingDatasetIsSupplementedTo(); - private static final UpdateMatcher>, ?> enrichMissingDatasetIsSupplementedBy = - new EnrichMissingDatasetIsSupplementedBy(); + private static final UpdateMatcher>, ?> enrichMisissingDatasetIsRelatedTo = new EnrichMissingDatasetIsRelatedTo(); + private static final UpdateMatcher>, ?> enrichMissingDatasetIsReferencedBy = new EnrichMissingDatasetIsReferencedBy(); + private static final UpdateMatcher>, ?> enrichMissingDatasetReferences = new EnrichMissingDatasetReferences(); + private static final UpdateMatcher>, ?> enrichMissingDatasetIsSupplementedTo = new EnrichMissingDatasetIsSupplementedTo(); + private static final UpdateMatcher>, ?> enrichMissingDatasetIsSupplementedBy = new EnrichMissingDatasetIsSupplementedBy(); // Aggregators - private static final TypedColumn, ResultGroup> resultAggrTypedColumn = new ResultAggregator().toColumn(); + private static final TypedColumn, ResultGroup> resultAggrTypedColumn = new ResultAggregator() + .toColumn(); private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); public static void main(final String[] args) throws Exception { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils - .toString(GenerateEventsApplication.class - .getResourceAsStream("/eu/dnetlib/dhp/oa/graph/merge_claims_parameters.json"))); + .toString( + GenerateEventsApplication.class + .getResourceAsStream("/eu/dnetlib/dhp/oa/graph/merge_claims_parameters.json"))); parser.parseArgument(args); final Boolean isSparkSessionManaged = Optional @@ -172,18 +166,23 @@ public class GenerateEventsApplication { final Class resultClazz, final DedupConfig dedupConfig) { - final Dataset results = readPath(spark, graphPath + "/" + resultClazz.getSimpleName().toLowerCase(), Result.class) - .filter(r -> r.getDataInfo().getDeletedbyinference()); + final Dataset results = readPath( + spark, graphPath + "/" + resultClazz.getSimpleName().toLowerCase(), Result.class) + .filter(r -> r.getDataInfo().getDeletedbyinference()); final Dataset mergedRels = readPath(spark, graphPath + "/relation", Relation.class) .filter(r -> r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS)); - return results.joinWith(mergedRels, results.col("id").equalTo(mergedRels.col("source")), "inner") + return results + .joinWith(mergedRels, results.col("id").equalTo(mergedRels.col("source")), "inner") .groupByKey((MapFunction, String>) t -> t._2.getTarget(), Encoders.STRING()) .agg(resultAggrTypedColumn) .map((MapFunction, ResultGroup>) t -> t._2, Encoders.kryo(ResultGroup.class)) .filter(ResultGroup::isValid) - .map((MapFunction) g -> GenerateEventsApplication.generateSimpleEvents(g, dedupConfig), Encoders.kryo(EventGroup.class)) + .map( + (MapFunction) g -> GenerateEventsApplication + .generateSimpleEvents(g, dedupConfig), + Encoders.kryo(EventGroup.class)) .flatMap(group -> group.getData().iterator(), Encoders.kryo(Event.class)); } @@ -207,16 +206,19 @@ public class GenerateEventsApplication { return events; } - private static Dataset generateRelationEvents(final SparkSession spark, + private static Dataset generateRelationEvents( + final SparkSession spark, final String graphPath, final Class sourceClass, final Class targetClass, final DedupConfig dedupConfig) { - final Dataset sources = readPath(spark, graphPath + "/" + sourceClass.getSimpleName().toLowerCase(), Result.class) - .filter(r -> r.getDataInfo().getDeletedbyinference()); + final Dataset sources = readPath( + spark, graphPath + "/" + sourceClass.getSimpleName().toLowerCase(), Result.class) + .filter(r -> r.getDataInfo().getDeletedbyinference()); - final Dataset targets = readPath(spark, graphPath + "/" + sourceClass.getSimpleName().toLowerCase(), targetClass); + final Dataset targets = readPath( + spark, graphPath + "/" + sourceClass.getSimpleName().toLowerCase(), targetClass); final Dataset mergedRels = readPath(spark, graphPath + "/relation", Relation.class) .filter(r -> r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS)); @@ -224,7 +226,8 @@ public class GenerateEventsApplication { final Dataset rels = readPath(spark, graphPath + "/relation", Relation.class) .filter(r -> !r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS)); - final Dataset duplicates = sources.joinWith(mergedRels, sources.col("id").equalTo(rels.col("source")), "inner") + final Dataset duplicates = sources + .joinWith(mergedRels, sources.col("id").equalTo(rels.col("source")), "inner") .groupByKey((MapFunction, String>) t -> t._2.getTarget(), Encoders.STRING()) .agg(resultAggrTypedColumn) .map((MapFunction, ResultGroup>) t -> t._2, Encoders.kryo(ResultGroup.class)) @@ -243,7 +246,8 @@ public class GenerateEventsApplication { return null; } - private List generateProjectsEvents(final Collection>> childrenWithProjects, final DedupConfig dedupConfig) { + private List generateProjectsEvents(final Collection>> childrenWithProjects, + final DedupConfig dedupConfig) { final List> list = new ArrayList<>(); for (final Pair> target : childrenWithProjects) { @@ -254,7 +258,8 @@ public class GenerateEventsApplication { return list.stream().map(EventFactory::newBrokerEvent).collect(Collectors.toList()); } - private List generateSoftwareEvents(final Collection>> childrenWithSoftwares, final DedupConfig dedupConfig) { + private List generateSoftwareEvents(final Collection>> childrenWithSoftwares, + final DedupConfig dedupConfig) { final List> list = new ArrayList<>(); for (final Pair> target : childrenWithSoftwares) { @@ -279,15 +284,30 @@ public class GenerateEventsApplication { for (final Pair> target : cleanedChildrens) { if (relType.equals("isRelatedTo")) { - list.addAll(enrichMisissingPublicationIsRelatedTo.searchUpdatesForRecord(target, cleanedChildrens, dedupConfig)); + list + .addAll( + enrichMisissingPublicationIsRelatedTo + .searchUpdatesForRecord(target, cleanedChildrens, dedupConfig)); } else if (relType.equals("references")) { - list.addAll(enrichMissingPublicationReferences.searchUpdatesForRecord(target, cleanedChildrens, dedupConfig)); + list + .addAll( + enrichMissingPublicationReferences + .searchUpdatesForRecord(target, cleanedChildrens, dedupConfig)); } else if (relType.equals("isReferencedBy")) { - list.addAll(enrichMissingPublicationIsReferencedBy.searchUpdatesForRecord(target, cleanedChildrens, dedupConfig)); + list + .addAll( + enrichMissingPublicationIsReferencedBy + .searchUpdatesForRecord(target, cleanedChildrens, dedupConfig)); } else if (relType.equals("isSupplementedTo")) { - list.addAll(enrichMissingPublicationIsSupplementedTo.searchUpdatesForRecord(target, cleanedChildrens, dedupConfig)); + list + .addAll( + enrichMissingPublicationIsSupplementedTo + .searchUpdatesForRecord(target, cleanedChildrens, dedupConfig)); } else if (relType.equals("isSupplementedBy")) { - list.addAll(enrichMissingPublicationIsSupplementedBy.searchUpdatesForRecord(target, cleanedChildrens, dedupConfig)); + list + .addAll( + enrichMissingPublicationIsSupplementedBy + .searchUpdatesForRecord(target, cleanedChildrens, dedupConfig)); } } @@ -310,15 +330,29 @@ public class GenerateEventsApplication { for (final Pair> target : cleanedChildrens) { if (relType.equals("isRelatedTo")) { - list.addAll(enrichMisissingDatasetIsRelatedTo.searchUpdatesForRecord(target, cleanedChildrens, dedupConfig)); + list + .addAll( + enrichMisissingDatasetIsRelatedTo + .searchUpdatesForRecord(target, cleanedChildrens, dedupConfig)); } else if (relType.equals("references")) { - list.addAll(enrichMissingDatasetReferences.searchUpdatesForRecord(target, cleanedChildrens, dedupConfig)); + list + .addAll( + enrichMissingDatasetReferences.searchUpdatesForRecord(target, cleanedChildrens, dedupConfig)); } else if (relType.equals("isReferencedBy")) { - list.addAll(enrichMissingDatasetIsReferencedBy.searchUpdatesForRecord(target, cleanedChildrens, dedupConfig)); + list + .addAll( + enrichMissingDatasetIsReferencedBy + .searchUpdatesForRecord(target, cleanedChildrens, dedupConfig)); } else if (relType.equals("isSupplementedTo")) { - list.addAll(enrichMissingDatasetIsSupplementedTo.searchUpdatesForRecord(target, cleanedChildrens, dedupConfig)); + list + .addAll( + enrichMissingDatasetIsSupplementedTo + .searchUpdatesForRecord(target, cleanedChildrens, dedupConfig)); } else if (relType.equals("isSupplementedBy")) { - list.addAll(enrichMissingDatasetIsSupplementedBy.searchUpdatesForRecord(target, cleanedChildrens, dedupConfig)); + list + .addAll( + enrichMissingDatasetIsSupplementedBy + .searchUpdatesForRecord(target, cleanedChildrens, dedupConfig)); } } @@ -339,8 +373,12 @@ public class GenerateEventsApplication { private static DedupConfig loadDedupConfig(final String isLookupUrl, final String profId) throws Exception { final ISLookUpService isLookUpService = ISLookupClientFactory.getLookUpService(isLookupUrl); - final String conf = isLookUpService.getResourceProfileByQuery(String - .format("for $x in /RESOURCE_PROFILE[.//RESOURCE_IDENTIFIER/@value = '%s'] return $x//DEDUPLICATION/text()", profId)); + final String conf = isLookUpService + .getResourceProfileByQuery( + String + .format( + "for $x in /RESOURCE_PROFILE[.//RESOURCE_IDENTIFIER/@value = '%s'] return $x//DEDUPLICATION/text()", + profId)); final DedupConfig dedupConfig = new ObjectMapper().readValue(conf, DedupConfig.class); dedupConfig.getPace().initModel(); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/UpdateMatcher.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/UpdateMatcher.java index 286b40ad51..95d43ae686 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/UpdateMatcher.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/UpdateMatcher.java @@ -22,7 +22,8 @@ public abstract class UpdateMatcher { this.multipleUpdate = multipleUpdate; } - public Collection> searchUpdatesForRecord(final K res, final Collection others, final DedupConfig dedupConfig) { + public Collection> searchUpdatesForRecord(final K res, final Collection others, + final DedupConfig dedupConfig) { final Map> infoMap = new HashMap<>(); @@ -30,7 +31,8 @@ public abstract class UpdateMatcher { if (source != res) { for (final UpdateInfo info : findUpdates(source, res, dedupConfig)) { final String s = DigestUtils.md5Hex(info.getHighlightValueAsString()); - if (!infoMap.containsKey(s) || infoMap.get(s).getTrust() < info.getTrust()) {} else { + if (!infoMap.containsKey(s) || infoMap.get(s).getTrust() < info.getTrust()) { + } else { infoMap.put(s, info); } } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingAbstract.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingAbstract.java index c3b6bda668..7dc340b3c7 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingAbstract.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingAbstract.java @@ -18,9 +18,11 @@ public class EnrichMissingAbstract extends UpdateMatcher { } @Override - protected List> findUpdates(final Result source, final Result target, final DedupConfig dedupConfig) { + protected List> findUpdates(final Result source, final Result target, + final DedupConfig dedupConfig) { if (isMissing(target.getDescription()) && !isMissing(source.getDescription())) { - return Arrays.asList(generateUpdateInfo(source.getDescription().get(0).getValue(), source, target, dedupConfig)); + return Arrays + .asList(generateUpdateInfo(source.getDescription().get(0).getValue(), source, target, dedupConfig)); } return new ArrayList<>(); } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingAuthorOrcid.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingAuthorOrcid.java index 89292d3da2..7a1677ae2d 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingAuthorOrcid.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingAuthorOrcid.java @@ -19,7 +19,8 @@ public class EnrichMissingAuthorOrcid extends UpdateMatcher>> findUpdates(final Result source, final Result target, final DedupConfig dedupConfig) { + protected List>> findUpdates(final Result source, final Result target, + final DedupConfig dedupConfig) { // TODO // return Arrays.asList(new EnrichMissingAbstract("xxxxxxx", 0.9f)); return Arrays.asList(); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingOpenAccess.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingOpenAccess.java index 7f5a595cc8..d14490ba85 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingOpenAccess.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingOpenAccess.java @@ -21,7 +21,8 @@ public class EnrichMissingOpenAccess extends UpdateMatcher { } @Override - protected List> findUpdates(final Result source, final Result target, final DedupConfig dedupConfig) { + protected List> findUpdates(final Result source, final Result target, + final DedupConfig dedupConfig) { final long count = target .getInstance() .stream() @@ -29,7 +30,9 @@ public class EnrichMissingOpenAccess extends UpdateMatcher { .filter(right -> right.equals(BrokerConstants.OPEN_ACCESS)) .count(); - if (count > 0) { return Arrays.asList(); } + if (count > 0) { + return Arrays.asList(); + } return source .getInstance() diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingPid.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingPid.java index 6e106e6695..20303ec1b4 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingPid.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingPid.java @@ -20,10 +20,13 @@ public class EnrichMissingPid extends UpdateMatcher { } @Override - protected List> findUpdates(final Result source, final Result target, final DedupConfig dedupConfig) { + protected List> findUpdates(final Result source, final Result target, + final DedupConfig dedupConfig) { final long count = target.getPid().size(); - if (count > 0) { return Arrays.asList(); } + if (count > 0) { + return Arrays.asList(); + } return source .getPid() @@ -33,7 +36,8 @@ public class EnrichMissingPid extends UpdateMatcher { .collect(Collectors.toList()); } - public UpdateInfo generateUpdateInfo(final Pid highlightValue, final Result source, final Result target, final DedupConfig dedupConfig) { + public UpdateInfo generateUpdateInfo(final Pid highlightValue, final Result source, final Result target, + final DedupConfig dedupConfig) { return new UpdateInfo<>( Topic.ENRICH_MISSING_PID, highlightValue, source, target, diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingPublicationDate.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingPublicationDate.java index d2b28d65d0..e1de8ce4d3 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingPublicationDate.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingPublicationDate.java @@ -18,9 +18,11 @@ public class EnrichMissingPublicationDate extends UpdateMatcher } @Override - protected List> findUpdates(final Result source, final Result target, final DedupConfig dedupConfig) { + protected List> findUpdates(final Result source, final Result target, + final DedupConfig dedupConfig) { if (isMissing(target.getDateofacceptance()) && !isMissing(source.getDateofacceptance())) { - return Arrays.asList(generateUpdateInfo(source.getDateofacceptance().getValue(), source, target, dedupConfig)); + return Arrays + .asList(generateUpdateInfo(source.getDateofacceptance().getValue(), source, target, dedupConfig)); } return new ArrayList<>(); } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingSubject.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingSubject.java index de888ff871..c51f8991c4 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingSubject.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingSubject.java @@ -23,7 +23,8 @@ public class EnrichMissingSubject extends UpdateMatcher>> findUpdates(final Result source, final Result target, final DedupConfig dedupConfig) { + protected List>> findUpdates(final Result source, final Result target, + final DedupConfig dedupConfig) { final Set existingTypes = target .getSubject() .stream() diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreOpenAccess.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreOpenAccess.java index 021449797d..2ac04fd12f 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreOpenAccess.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreOpenAccess.java @@ -21,7 +21,8 @@ public class EnrichMoreOpenAccess extends UpdateMatcher { } @Override - protected List> findUpdates(final Result source, final Result target, final DedupConfig dedupConfig) { + protected List> findUpdates(final Result source, final Result target, + final DedupConfig dedupConfig) { final Set urls = target .getInstance() .stream() diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMorePid.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMorePid.java index c64ed20eac..e4bf5d2c2e 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMorePid.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMorePid.java @@ -20,7 +20,8 @@ public class EnrichMorePid extends UpdateMatcher { } @Override - protected List> findUpdates(final Result source, final Result target, final DedupConfig dedupConfig) { + protected List> findUpdates(final Result source, final Result target, + final DedupConfig dedupConfig) { final Set existingPids = target .getPid() .stream() @@ -36,7 +37,8 @@ public class EnrichMorePid extends UpdateMatcher { .collect(Collectors.toList()); } - public UpdateInfo generateUpdateInfo(final Pid highlightValue, final Result source, final Result target, final DedupConfig dedupConfig) { + public UpdateInfo generateUpdateInfo(final Pid highlightValue, final Result source, final Result target, + final DedupConfig dedupConfig) { return new UpdateInfo<>( Topic.ENRICH_MORE_PID, highlightValue, source, target, diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSubject.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSubject.java index 3f7f5b3d56..d6e607c31c 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSubject.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSubject.java @@ -21,7 +21,8 @@ public class EnrichMoreSubject extends UpdateMatcher>> findUpdates(final Result source, final Result target, final DedupConfig dedupConfig) { + protected List>> findUpdates(final Result source, final Result target, + final DedupConfig dedupConfig) { final Set existingSubjects = target .getSubject() .stream() diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EventGroup.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EventGroup.java index 9c7081c79b..25c7698a0c 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EventGroup.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EventGroup.java @@ -1,3 +1,4 @@ + package eu.dnetlib.dhp.broker.oa.util; import java.io.Serializable; diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ResultAggregator.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ResultAggregator.java index 94685eeae2..475c768149 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ResultAggregator.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ResultAggregator.java @@ -1,3 +1,4 @@ + package eu.dnetlib.dhp.broker.oa.util; import org.apache.spark.sql.Encoder; diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ResultGroup.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ResultGroup.java index 8fe7a59392..2be673db03 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ResultGroup.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ResultGroup.java @@ -1,3 +1,4 @@ + package eu.dnetlib.dhp.broker.oa.util; import java.io.Serializable; diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/TrustUtils.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/TrustUtils.java index 6bf59c1252..5338d4f3d7 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/TrustUtils.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/TrustUtils.java @@ -1,14 +1,22 @@ + package eu.dnetlib.dhp.broker.oa.util; public class TrustUtils { public static float rescale(final double score, final double threshold) { - if (score >= BrokerConstants.MAX_TRUST) { return BrokerConstants.MAX_TRUST; } + if (score >= BrokerConstants.MAX_TRUST) { + return BrokerConstants.MAX_TRUST; + } - final double val = (score - threshold) * (BrokerConstants.MAX_TRUST - BrokerConstants.MIN_TRUST) / (BrokerConstants.MAX_TRUST - threshold); + final double val = (score - threshold) * (BrokerConstants.MAX_TRUST - BrokerConstants.MIN_TRUST) + / (BrokerConstants.MAX_TRUST - threshold); - if (val < BrokerConstants.MIN_TRUST) { return BrokerConstants.MIN_TRUST; } - if (val > BrokerConstants.MAX_TRUST) { return BrokerConstants.MAX_TRUST; } + if (val < BrokerConstants.MIN_TRUST) { + return BrokerConstants.MIN_TRUST; + } + if (val > BrokerConstants.MAX_TRUST) { + return BrokerConstants.MAX_TRUST; + } return (float) val; } diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/UpdateInfo.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/UpdateInfo.java index de6a713974..893aa2827d 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/UpdateInfo.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/UpdateInfo.java @@ -68,8 +68,10 @@ public final class UpdateInfo { private float calculateTrust(final DedupConfig dedupConfig, final Result r1, final Result r2) { try { final ObjectMapper objectMapper = new ObjectMapper(); - final MapDocument doc1 = MapDocumentUtil.asMapDocumentWithJPath(dedupConfig, objectMapper.writeValueAsString(r1)); - final MapDocument doc2 = MapDocumentUtil.asMapDocumentWithJPath(dedupConfig, objectMapper.writeValueAsString(r2)); + final MapDocument doc1 = MapDocumentUtil + .asMapDocumentWithJPath(dedupConfig, objectMapper.writeValueAsString(r1)); + final MapDocument doc2 = MapDocumentUtil + .asMapDocumentWithJPath(dedupConfig, objectMapper.writeValueAsString(r2)); final double score = new TreeProcessor(dedupConfig).computeScore(doc1, doc2); final double threshold = dedupConfig.getWf().getThreshold(); @@ -118,7 +120,8 @@ public final class UpdateInfo { .map(Instance::getUrl) .flatMap(List::stream) .findFirst() - .orElse(null);; + .orElse(null); + ; final Provenance provenance = new Provenance().setId(provId).setRepositoryName(provRepo).setUrl(provUrl); diff --git a/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/util/TrustUtilsTest.java b/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/util/TrustUtilsTest.java index 58f391c24b..bb23d6085e 100644 --- a/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/util/TrustUtilsTest.java +++ b/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/util/TrustUtilsTest.java @@ -1,3 +1,4 @@ + package eu.dnetlib.dhp.broker.oa.util; import static org.junit.jupiter.api.Assertions.assertTrue; diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid/oozie_app/config-default.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid/oozie_app/config-default.xml index 5621415d97..fe14bb8cb5 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid/oozie_app/config-default.xml +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid/oozie_app/config-default.xml @@ -1,14 +1,18 @@ jobTracker - yarnRM + hadoop-rm3.garr-pa1.d4science.org:8032 nameNode - hdfs://nameservice1 + hdfs://hadoop-rm1.garr-pa1.d4science.org:8020 - oozie.action.sharelib.for.java + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark spark2 @@ -16,7 +20,23 @@ true - oozie.launcher.mapreduce.map.java.opts - -Xmx4g + hive_metastore_uris + thrift://hadoop-edge2.garr-pa1.d4science.org:9083 + + + spark2YarnHistoryServerAddress + http://hadoop-edge1.garr-pa1.d4science.org:18089/ + + + spark2EventLogDir + /user/spark/spark2ApplicationHistory + + + spark2ExtraListeners + "com.cloudera.spark.lineage.NavigatorAppListener" + + + spark2SqlQueryExecutionListeners + "com.cloudera.spark.lineage.NavigatorQueryListener" \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/DatasetScholexplorerParser.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/DatasetScholexplorerParser.java index f49163c87a..afba57bb8a 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/DatasetScholexplorerParser.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/DatasetScholexplorerParser.java @@ -159,7 +159,7 @@ public class DatasetScholexplorerParser extends AbstractScholexplorerParser { .setDescription( descs .stream() - .map(it -> it.length() < 10000 ? it : it.substring(0, 10000)) +// .map(it -> it.length() < 10000 ? it : it.substring(0, 10000)) .map( it -> { final Field d = new Field<>(); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/PublicationScholexplorerParser.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/PublicationScholexplorerParser.java index edbb444db7..bf59a6f0ef 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/PublicationScholexplorerParser.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/PublicationScholexplorerParser.java @@ -213,10 +213,10 @@ public class PublicationScholexplorerParser extends AbstractScholexplorerParser .setValue( VtdUtilityParser.getSingleValue(ap, vn, "//*[local-name()='description']")); - if (StringUtils.isNotBlank(description.getValue()) - && description.getValue().length() > 10000) { - description.setValue(description.getValue().substring(0, 10000)); - } +// if (StringUtils.isNotBlank(description.getValue()) +// && description.getValue().length() > 10000) { +// description.setValue(description.getValue().substring(0, 10000)); +// } parsedObject.setDescription(Collections.singletonList(description)); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/step1/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/step1/oozie_app/workflow.xml index ce00eff7b3..d74d68663f 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/step1/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/step1/oozie_app/workflow.xml @@ -47,8 +47,8 @@ - ${wf:conf('reuseContent') eq false} - ${wf:conf('reuseContent') eq true} + ${wf:conf('reuseContent') eq false} + ${wf:conf('reuseContent') eq true} diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/export/DLIToOAF.scala b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/export/DLIToOAF.scala new file mode 100644 index 0000000000..5d7c444b2c --- /dev/null +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/export/DLIToOAF.scala @@ -0,0 +1,376 @@ +package eu.dnetlib.dhp.export + +import java.time.LocalDateTime +import java.time.format.DateTimeFormatter + +import eu.dnetlib.dhp.common.PacePerson +import eu.dnetlib.dhp.schema.oaf.{Author, DataInfo, Dataset, Field, Instance, KeyValue, Publication, Qualifier, Relation, StructuredProperty} +import eu.dnetlib.dhp.schema.scholexplorer.{DLIDataset, DLIPublication, DLIRelation} +import org.apache.commons.lang3.StringUtils + +import scala.collection.JavaConverters._ + + +case class DLIExternalReference(id: String, url: String, sitename: String, label: String, pid: String, classId: String) {} + +object DLIToOAF { + + + val collectedFromMap: Map[String, KeyValue] = Map( + "dli_________::r3d100010527" -> generateKeyValue("10|re3data_____::c2a591f440598b63d854556beaf01591", "European Nucleotide Archive"), + "dli_________::r3d100010255" -> generateKeyValue("10|re3data_____::480d275ed6f9666ee76d6a1215eabf26", "Inter-university Consortium for Political and Social Research"), + "dli_________::r3d100011868" -> generateKeyValue("10|re3data_____::db814dc656a911b556dba42a331cebe9", "Mendeley Data"), + "dli_________::elsevier" -> generateKeyValue("10|openaire____::8f87e10869299a5fe80b315695296b88", "Elsevier"), + "dli_________::openaire" -> generateKeyValue("10|infrastruct_::f66f1bd369679b5b077dcdf006089556", "OpenAIRE"), + "dli_________::thomsonreuters" -> generateKeyValue("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2", "Crossref"), + "dli_________::r3d100010216" -> generateKeyValue("10|re3data_____::0fd79429de04343dbbec705d9b5f429f", "4TU.Centre for Research Data"), + "dli_________::r3d100010134" -> generateKeyValue("10|re3data_____::9633d1e8c4309c833c2c442abeb0cfeb", "PANGAEA"), + "dli_________::ieee" -> generateKeyValue("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2", "Crossref"), + "dli_________::r3d100010197" -> generateKeyValue("10|re3data_____::9fd1d79973f7fda60cbe1d82e3819a68", "The Cambridge Structural Database"), + "dli_________::nature" -> generateKeyValue("10|openaire____::6e380d9cf51138baec8480f5a0ce3a2e", "Springer Nature"), + "dli_________::datacite" -> generateKeyValue("10|openaire____::9e3be59865b2c1c335d32dae2fe7b254", "Datacite"), + "dli_________::r3d100010578" -> generateKeyValue("10|re3data_____::c4d751f29a7568011a4c80136b30b444", "IEDA"), + "dli_________::r3d100010464" -> generateKeyValue("10|re3data_____::23e2a81591099828f6b83a1c83150666", "Research Data Australia"), + "dli_________::r3d100010327" -> generateKeyValue("10|re3data_____::a644620b81135243dc9acc15d2362246", "Worldwide Protein Data Bank"), + "dli_________::pubmed" -> generateKeyValue("10|opendoar____::eda80a3d5b344bc40f3bc04f65b7a357", "PubMed Central"), + "dli_________::europe_pmc__" -> generateKeyValue("10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c", "Europe PubMed Central"), + "dli_________::crossref" -> generateKeyValue("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2", "Crossref") + ) + + + val relationTypeMapping: Map[String, (String, String)] = Map( + "IsReferencedBy" -> ("isRelatedTo", "relationship"), + "References" -> ("isRelatedTo", "relationship"), + "IsRelatedTo" -> ("isRelatedTo", "relationship"), + "IsSupplementedBy" -> ("IsSupplementedBy", "supplement"), + "Cites" -> ("cites", "citation"), + "Unknown" -> ("isRelatedTo", "relationship"), + "IsSourceOf" -> ("isRelatedTo", "relationship"), + "IsCitedBy" -> ("IsCitedBy", "citation"), + "Reviews" -> ("reviews", "review"), + "Describes" -> ("isRelatedTo", "relationship"), + "HasAssociationWith" -> ("isRelatedTo", "relationship") + ) + + val expectecdPidType = List("uniprot", "ena", "chembl", "ncbi-n", "ncbi-p", "genbank", "pdb", "url") + + + val filteredURL = List( + "www.ebi.ac.uk", + "www.uniprot.org", + "f1000.com", + "en.wikipedia.org", + "flybase.org", + "www.yeastgenome.org", + "research.bioinformatics.udel.edu", + "cancer.sanger.ac.uk", + "www.iedb.org", + "www.crd.york.ac.uk", + "www.wormbase.org", + "web.expasy.org", + "www.hal.inserm.fr", + "sabiork.h-its.org", + "zfin.org", + "www.pombase.org", + "www.guidetopharmacology.org", + "reactome.org" + ) + + + def filterPid(p: StructuredProperty): Boolean = { + if (expectecdPidType.contains(p.getQualifier.getClassname) && p.getQualifier.getClassname.equalsIgnoreCase("url")) + if (filteredURL.exists(u => p.getValue.contains(u))) + return true + else + return false + expectecdPidType.contains(p.getQualifier.getClassname) + } + + + def extractTitle(titles: java.util.List[StructuredProperty]): String = { + + if (titles == null) + return null + + val label = titles.asScala.map(p => p.getValue).find(p => p.nonEmpty) + label.orNull + } + + def convertDLIDatasetToExternalReference(dataset: DLIDataset): DLIExternalReference = { + val currentId = generateId(dataset.getId) + val pids = dataset.getPid.asScala.filter(filterPid) + + if (pids == null || pids.isEmpty) + return null + + val pid: StructuredProperty = pids.head + + + pid.getQualifier.getClassname match { + case "uniprot" => DLIExternalReference(generateId(dataset.getId), s"https://www.uniprot.org/uniprot/${pid.getValue}", "UniProt", extractTitle(dataset.getTitle), pid.getValue, "accessionNumber") + case "ena" => + if(pid.getValue!= null && pid.getValue.nonEmpty && pid.getValue.length>7) + DLIExternalReference(generateId(dataset.getId), s"https://www.ebi.ac.uk/ena/data/view/${pid.getValue.substring(0, 8)}", "European Nucleotide Archive", extractTitle(dataset.getTitle), pid.getValue, "accessionNumber") + else + null + case "chembl" => DLIExternalReference(generateId(dataset.getId), s"https://www.ebi.ac.uk/chembl/compound_report_card/${pid.getValue}", "ChEMBL", extractTitle(dataset.getTitle), pid.getValue, "accessionNumber") + case "ncbi-n" => DLIExternalReference(generateId(dataset.getId), s"https://www.ncbi.nlm.nih.gov/nuccore/${pid.getValue}", "Nucleotide Database", extractTitle(dataset.getTitle), pid.getValue, "accessionNumber") + case "ncbi-p" => DLIExternalReference(generateId(dataset.getId), s"https://www.ncbi.nlm.nih.gov/nuccore/${pid.getValue}", "Nucleotide Database", extractTitle(dataset.getTitle), pid.getValue, "accessionNumber") + case "genbank" => DLIExternalReference(generateId(dataset.getId), s"https://www.ncbi.nlm.nih.gov/nuccore/${pid.getValue}", "GenBank", extractTitle(dataset.getTitle), pid.getValue, "accessionNumber") + case "pdb" => DLIExternalReference(generateId(dataset.getId), s"https://www.ncbi.nlm.nih.gov/nuccore/${pid.getValue}", "Protein Data Bank", extractTitle(dataset.getTitle), pid.getValue, "accessionNumber") + case "url" => DLIExternalReference(generateId(dataset.getId), pid.getValue, "", extractTitle(dataset.getTitle), pid.getValue, "url") + + } + + + } + + + def convertDLIPublicationToOAF(p: DLIPublication): Publication = { + + val result = new Publication + result.setId(generateId(p.getId)) + result.setDataInfo(generateDataInfo(invisibile = true)) + if (p.getCollectedfrom == null || p.getCollectedfrom.size() == 0 || (p.getCollectedfrom.size() == 1 && p.getCollectedfrom.get(0) == null)) + return null + + result.setCollectedfrom(p.getCollectedfrom.asScala.map(c => collectedFromMap.getOrElse(c.getKey, null)).asJava) + result.setPid(p.getPid) + result.setDateofcollection(p.getDateofcollection) + result.setOriginalId(p.getPid.asScala.map(p => p.getValue).asJava) + result.setDateoftransformation(LocalDateTime.now().format(DateTimeFormatter.ofPattern("yyyy-MM-dd'T'HH:mm:ss'Z'"))) + if (p.getAuthor == null || p.getAuthor.isEmpty) + return null + result.setAuthor(p.getAuthor.asScala.map(convertAuthor).asJava) + result.setResulttype(createQualifier(p.getResulttype.getClassid, p.getResulttype.getClassname, "dnet:result_typologies", "dnet:result_typologies")) + + if (p.getSubject != null) + result.setSubject(p.getSubject.asScala.map(convertSubject).asJava) + + if (p.getTitle == null || p.getTitle.isEmpty) + return null + + result.setTitle(List(patchTitle(p.getTitle.get(0))).asJava) + + if (p.getRelevantdate == null || p.getRelevantdate.size() == 0) + return null + + result.setRelevantdate(p.getRelevantdate.asScala.map(patchRelevantDate).asJava) + + + result.setDescription(p.getDescription) + + result.setDateofacceptance(asField(p.getRelevantdate.get(0).getValue)) + result.setPublisher(p.getPublisher) + result.setSource(p.getSource) + result.setBestaccessright(createQualifier("UNKNOWN", "not available", "dnet:access_modes", "dnet:access_modes")) + + val dois = result.getPid.asScala.filter(p => "doi".equalsIgnoreCase(p.getQualifier.getClassname)).map(p => p.getValue) + if (dois.isEmpty) + return null + + + val i: Instance = createInstance(s"https://dx.doi.org/${dois.head}", firstInstanceOrNull(p.getInstance()), result.getDateofacceptance) + + if (i != null) + result.setInstance(List(i).asJava) + + result + } + + + def convertDLIRelation(r: DLIRelation): Relation = { + + val result = new Relation + if (!relationTypeMapping.contains(r.getRelType)) + return null + + if (r.getCollectedFrom == null || r.getCollectedFrom.size() == 0 || (r.getCollectedFrom.size() == 1 && r.getCollectedFrom.get(0) == null)) + return null + val t = relationTypeMapping.get(r.getRelType) + + result.setRelType("resultResult") + result.setRelClass(t.get._1) + result.setSubRelType(t.get._2) + result.setCollectedfrom(r.getCollectedFrom.asScala.map(c => collectedFromMap.getOrElse(c.getKey, null)).filter(p => p != null).asJava) + result.setSource(generateId(r.getSource)) + result.setTarget(generateId(r.getTarget)) + + if (result.getSource.equals(result.getTarget)) + return null + result.setDataInfo(generateDataInfo()) + + result + } + + + def convertDLIDatasetTOOAF(d: DLIDataset): Dataset = { + + if (d.getCollectedfrom == null || d.getCollectedfrom.size() == 0 || (d.getCollectedfrom.size() == 1 && d.getCollectedfrom.get(0) == null)) + return null + val result: Dataset = new Dataset + result.setId(generateId(d.getId)) + result.setDataInfo(generateDataInfo()) + result.setCollectedfrom(d.getCollectedfrom.asScala.map(c => collectedFromMap.getOrElse(c.getKey, null)).asJava) + + + result.setPid(d.getPid) + + val fpids = result.getPid.asScala.filter(p => "doi".equalsIgnoreCase(p.getQualifier.getClassname) || + "pdb".equalsIgnoreCase(p.getQualifier.getClassname) + ).map(p => p.getValue) + + if (fpids == null || fpids.isEmpty) + return null + + + result.setDateofcollection(d.getDateofcollection) + result.setOriginalId(d.getPid.asScala.map(d => d.getValue).asJava) + result.setDateoftransformation(LocalDateTime.now().format(DateTimeFormatter.ofPattern("yyyy-MM-dd'T'HH:mm:ss'Z'"))) + if (d.getAuthor == null || d.getAuthor.isEmpty) + return null + result.setAuthor(d.getAuthor.asScala.map(convertAuthor).asJava) + result.setResulttype(createQualifier(d.getResulttype.getClassid, d.getResulttype.getClassname, "dnet:result_typologies", "dnet:result_typologies")) + + if (d.getSubject != null) + result.setSubject(d.getSubject.asScala.map(convertSubject).asJava) + + if (d.getTitle == null || d.getTitle.isEmpty) + return null + + result.setTitle(List(patchTitle(d.getTitle.get(0))).asJava) + + if (d.getRelevantdate == null || d.getRelevantdate.size() == 0) + return null + + result.setRelevantdate(d.getRelevantdate.asScala.map(patchRelevantDate).asJava) + + + result.setDescription(d.getDescription) + + result.setDateofacceptance(asField(d.getRelevantdate.get(0).getValue)) + result.setPublisher(d.getPublisher) + result.setSource(d.getSource) + result.setBestaccessright(createQualifier("UNKNOWN", "not available", "dnet:access_modes", "dnet:access_modes")) + + + val instance_urls = if (fpids.head.length < 5) s"https://www.rcsb.org/structure/${fpids.head}" else s"https://dx.doi.org/${fpids.head}" + + val i: Instance = createInstance(instance_urls, firstInstanceOrNull(d.getInstance()), result.getDateofacceptance, true) + if (i != null) + result.setInstance(List(i).asJava) + + result + } + + + def firstInstanceOrNull(instances: java.util.List[Instance]): Instance = { + + if (instances == null || instances.size() == 0) + return null + instances.get(0) + + } + + + def createInstance(url: String, originalInstance: Instance, doa: Field[String], dataset: Boolean = false): Instance = { + + val i = new Instance + i.setUrl(List(url).asJava) + if (dataset) + i.setInstancetype(createQualifier("0021", "Dataset", "dnet:publication_resource", "dnet:publication_resource")) + else + i.setInstancetype(createQualifier("0000", "UNKNOWN", "dnet:publication_resource", "dnet:publication_resource")) + if (originalInstance != null && originalInstance.getHostedby != null) + i.setHostedby(originalInstance.getHostedby) + + i.setAccessright(createQualifier("UNKNOWN", "not available", "dnet:access_modes", "dnet:access_modes")) + i.setDateofacceptance(doa) + + i + + + } + + + def patchRelevantDate(d: StructuredProperty): StructuredProperty = { + d.setQualifier(createQualifier("UNKNOWN", "dnet:dataCite_date")) + d + + } + + def patchTitle(t: StructuredProperty): StructuredProperty = { + t.setQualifier(createQualifier("main title", "dnet:dataCite_title")) + t + } + + + def convertSubject(s: StructuredProperty): StructuredProperty = { + s.setQualifier(createQualifier("keyword", "dnet:subject_classification_typologies")) + s + + + } + + + def convertAuthor(a: Author): Author = { + if (a == null) + return a + val p = new PacePerson(a.getFullname, false) + if (p.isAccurate) { + a.setName(p.getNameString) + a.setSurname(p.getSurnameString) + } + a + } + + + def generateId(id: String): String = { + val md5 = if (id.contains("::")) StringUtils.substringAfter(id, "::") else StringUtils.substringAfter(id, "|") + s"50|scholix_____::$md5" + } + + + def generateKeyValue(key: String, value: String): KeyValue = { + val kv: KeyValue = new KeyValue() + kv.setKey(key) + kv.setValue(value) + kv.setDataInfo(generateDataInfo("0.9")) + kv + } + + + def generateDataInfo(trust: String = "0.9", invisibile: Boolean = false): DataInfo = { + val di = new DataInfo + di.setDeletedbyinference(false) + di.setInferred(false) + di.setInvisible(false) + di.setTrust(trust) + di.setProvenanceaction(createQualifier("sysimport:actionset", "dnet:provenanceActions")) + di + } + + def createQualifier(cls: String, sch: String): Qualifier = { + createQualifier(cls, cls, sch, sch) + } + + + def createQualifier(classId: String, className: String, schemeId: String, schemeName: String): Qualifier = { + val q: Qualifier = new Qualifier + q.setClassid(classId) + q.setClassname(className) + q.setSchemeid(schemeId) + q.setSchemename(schemeName) + q + } + + + def asField[T](value: T): Field[T] = { + val tmp = new Field[T] + tmp.setValue(value) + tmp + + + } + +} diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/export/SparkExportContentForOpenAire.scala b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/export/SparkExportContentForOpenAire.scala new file mode 100644 index 0000000000..f3aa35549c --- /dev/null +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/export/SparkExportContentForOpenAire.scala @@ -0,0 +1,118 @@ +package eu.dnetlib.dhp.`export` + +import eu.dnetlib.dhp.application.ArgumentApplicationParser +import eu.dnetlib.dhp.schema.oaf.{Publication, Relation, Dataset => OafDataset} +import eu.dnetlib.dhp.schema.scholexplorer.{DLIDataset, DLIPublication, DLIRelation} +import org.apache.commons.io.IOUtils +import org.apache.spark.rdd.RDD +import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession} +import org.apache.spark.{SparkConf, SparkContext} +import org.codehaus.jackson.map.ObjectMapper +import scala.collection.mutable.ArrayBuffer + + +object SparkExportContentForOpenAire { + + + def main(args: Array[String]): Unit = { + val conf: SparkConf = new SparkConf() + val parser = new ArgumentApplicationParser(IOUtils.toString(SparkExportContentForOpenAire.getClass.getResourceAsStream("input_export_content_parameters.json"))) + parser.parseArgument(args) + val spark: SparkSession = + SparkSession + .builder() + .config(conf) + .appName(SparkExportContentForOpenAire.getClass.getSimpleName) + .master(parser.get("master")).getOrCreate() + + + val sc:SparkContext = spark.sparkContext + + val workingPath = parser.get("workingDirPath") + + implicit val pubEncoder: Encoder[Publication] = Encoders.bean(classOf[Publication]) + implicit val datEncoder: Encoder[OafDataset] = Encoders.bean(classOf[OafDataset]) + implicit val relEncoder: Encoder[Relation] = Encoders.bean(classOf[Relation]) + implicit val dliRelEncoder: Encoder[DLIRelation] = Encoders.bean(classOf[DLIRelation]) + import spark.implicits._ + +// +// val relRDD:RDD[Relation] = sc.textFile(s"$workingPath/relation_j") +// .map(s => new ObjectMapper().readValue(s, classOf[DLIRelation])) +// .filter(p => p.getDataInfo.getDeletedbyinference == false) +// .map(DLIToOAF.convertDLIRelation).filter(p=>p!= null) +// spark.createDataset(relRDD).write.mode(SaveMode.Overwrite).save(s"$workingPath/relationDS") +// +// val datRDD:RDD[OafDataset] = sc.textFile(s"$workingPath/dataset") +// .map(s => new ObjectMapper().readValue(s, classOf[DLIDataset])) +// .filter(p => p.getDataInfo.getDeletedbyinference == false) +// .map(DLIToOAF.convertDLIDatasetTOOAF).filter(p=>p!= null) +// spark.createDataset(datRDD).write.mode(SaveMode.Overwrite).save(s"$workingPath/datasetDS") +// +// +// val pubRDD:RDD[Publication] = sc.textFile(s"$workingPath/publication") +// .map(s => new ObjectMapper().readValue(s, classOf[DLIPublication])) +// .filter(p => p.getDataInfo.getDeletedbyinference == false) +// .map(DLIToOAF.convertDLIPublicationToOAF).filter(p=>p!= null) +// spark.createDataset(pubRDD).write.mode(SaveMode.Overwrite).save(s"$workingPath/publicationDS") +// +// +// +// val pubs:Dataset[Publication] = spark.read.load(s"$workingPath/publicationDS").as[Publication] +// val dats :Dataset[OafDataset] = spark.read.load(s"$workingPath/datasetDS").as[OafDataset] + var relDS :Dataset[Relation] = spark.read.load(s"$workingPath/relationDS").as[Relation] +// +// +// pubs.joinWith(relDS, pubs("id").equalTo(relDS("source"))).map(k => k._2).write.mode(SaveMode.Overwrite).save(s"$workingPath/relationDS_f1") +// +// relDS= spark.read.load(s"$workingPath/relationDS_f1").as[Relation] +// +// relDS.joinWith(dats, relDS("target").equalTo(dats("id"))).map(k => k._1).write.mode(SaveMode.Overwrite).save(s"$workingPath/relationDS_filtered") +// +// +// val r_source = relDS.select(relDS("source")).distinct() +// val r_target = relDS.select(relDS("source")).distinct() +// +// +// pubs.joinWith(r_source, pubs("id").equalTo(r_source("source")), "inner").map(k => k._1).write.mode(SaveMode.Overwrite).save(s"$workingPath/publicationDS_filtered") +// +// dats.joinWith(r_target, dats("id").equalTo(r_target("target")), "inner").map(k => k._1).write.mode(SaveMode.Overwrite).save(s"$workingPath/datasetDS_filtered") +// +// spark.createDataset(sc.textFile(s"$workingPath/dataset") +// .map(s => new ObjectMapper().readValue(s, classOf[DLIDataset])) +// .map(DLIToOAF.convertDLIDatasetToExternalReference) +// .filter(p => p != null)).as[DLIExternalReference].write.mode(SaveMode.Overwrite).save(s"$workingPath/externalReference") +// + + val pf = spark.read.load(s"$workingPath/publicationDS_filtered").select("id") + relDS = spark.read.load(s"$workingPath/relationDS").as[Relation] + val relationTo = pf.joinWith(relDS, pf("id").equalTo(relDS("source")),"inner").map(t =>t._2) + + val extRef = spark.read.load(s"$workingPath/externalReference").as[DLIExternalReference] + + spark.createDataset(relationTo.joinWith(extRef, relationTo("target").equalTo(extRef("id")), "inner").map(d => { + val r = d._1 + val ext = d._2 + (r.getSource, ext) + }).rdd.groupByKey.map(f => { + var dli_ext = ArrayBuffer[DLIExternalReference]() + f._2.foreach(d => if (dli_ext.size < 100) dli_ext += d ) + (f._1, dli_ext) + })).write.mode(SaveMode.Overwrite).save(s"$workingPath/externalReference_grouped") + + + + + + + + + + + + + + + } + +} diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/export/input_export_content_parameters.json b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/export/input_export_content_parameters.json new file mode 100644 index 0000000000..b92f87e084 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/export/input_export_content_parameters.json @@ -0,0 +1,14 @@ +[ + { + "paramName": "mt", + "paramLongName": "master", + "paramDescription": "should be local or yarn", + "paramRequired": true + }, + { + "paramName": "w", + "paramLongName": "workingDirPath", + "paramDescription": "the working path where generated files", + "paramRequired": true + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/export/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/export/oozie_app/config-default.xml new file mode 100644 index 0000000000..59e5c059fc --- /dev/null +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/export/oozie_app/config-default.xml @@ -0,0 +1,42 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + + oozie.wf.rerun.failnodes + false + + + hive_metastore_uris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + spark2YarnHistoryServerAddress + http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089 + + + spark2EventLogDir + /user/spark/spark2ApplicationHistory + + + spark2ExtraListeners + "com.cloudera.spark.lineage.NavigatorAppListener" + + + spark2SqlQueryExecutionListeners + "com.cloudera.spark.lineage.NavigatorQueryListener" + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/export/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/export/oozie_app/workflow.xml new file mode 100644 index 0000000000..181ab80bf6 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/export/oozie_app/workflow.xml @@ -0,0 +1,49 @@ + + + + workingDirPath + the source path + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + memory for individual executor + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + yarn-cluster + cluster + ExtractOAF + eu.dnetlib.dhp.export.SparkExportContentForOpenAire + dhp-graph-provision-scholexplorer-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.sql.shuffle.partitions=3840 + ${sparkExtraOPT} + + --workingDirPath${workingDirPath} + --masteryarn-cluster + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/test/java/eu/dnetlib/dhp/export/ExportDLITOOAFTest.scala b/dhp-workflows/dhp-graph-provision-scholexplorer/src/test/java/eu/dnetlib/dhp/export/ExportDLITOOAFTest.scala new file mode 100644 index 0000000000..c9d33dbe47 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/test/java/eu/dnetlib/dhp/export/ExportDLITOOAFTest.scala @@ -0,0 +1,75 @@ +package eu.dnetlib.dhp.export + +import java.time.LocalDateTime +import java.time.format.DateTimeFormatter + +import eu.dnetlib.dhp.schema.oaf.Relation +import eu.dnetlib.dhp.schema.scholexplorer.{DLIDataset, DLIPublication, DLIRelation} +import org.apache.spark.SparkConf +import org.apache.spark.rdd.RDD +import org.apache.spark.sql.SparkSession +import org.codehaus.jackson.map.{ObjectMapper, SerializationConfig} +import org.junit.jupiter.api.Test + +import scala.io.Source + +class ExportDLITOOAFTest { + + val mapper = new ObjectMapper() + + @Test + def testDate():Unit = { + println(LocalDateTime.now().format(DateTimeFormatter.ofPattern("yyyy-MM-dd'T'HH:mm:ss'Z'"))) + + } + + @Test + def testPublicationMapping():Unit = { + + mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT) + val json = Source.fromInputStream(getClass.getResourceAsStream("publication.json")).mkString + + + val oaf =DLIToOAF.convertDLIPublicationToOAF(mapper.readValue(json, classOf[DLIPublication])) + + println(mapper.writeValueAsString(oaf)) + + + } + + + @Test + def testExternalReferenceMapping():Unit = { + + mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT) + val json = Source.fromInputStream(getClass.getResourceAsStream("dataset.json")).mkString + + + val oaf =DLIToOAF.convertDLIDatasetToExternalReference(mapper.readValue(json, classOf[DLIDataset])) + + println(oaf) + + + } + + + + + + + + @Test + def testRelationMapping():Unit = { + + mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT) + val json = Source.fromInputStream(getClass.getResourceAsStream("relation.json")).mkString + + + val oaf =DLIToOAF.convertDLIRelation(mapper.readValue(json, classOf[DLIRelation])) + + println(mapper.writeValueAsString(oaf)) + + + } + +} diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/test/resources/eu/dnetlib/dhp/export/dataset.json b/dhp-workflows/dhp-graph-provision-scholexplorer/src/test/resources/eu/dnetlib/dhp/export/dataset.json new file mode 100644 index 0000000000..dae6357305 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/test/resources/eu/dnetlib/dhp/export/dataset.json @@ -0,0 +1,101 @@ +{ + "dataInfo": { + "invisible": false, + "inferred": null, + "deletedbyinference": false, + "trust": "0.9", + "inferenceprovenance": null, + "provenanceaction": null + }, + "lastupdatetimestamp": null, + "id": "60|719f19e5a996de1b87cddf93871bf2d4", + "originalId": [ + "a0a3p2gws9::uniprot" + ], + "collectedfrom": [ + { + "key": "dli_________::europe_pmc__", + "value": "Europe PMC", + "dataInfo": null + } + ], + "pid": [ + { + "value": "acc63471", + "qualifier": { + "classid": "ena", + "classname": "ena", + "schemeid": "dnet:pid_types", + "schemename": "dnet:pid_types" + }, + "dataInfo": null + } + ], + "dateofcollection": "2019-07-05T12:47:11.545+02:00", + "dateoftransformation": null, + "extraInfo": null, + "oaiprovenance": null, + "author": null, + "resulttype": { + "classid": "dataset", + "classname": "dataset", + "schemeid": "dataset", + "schemename": "dataset" + }, + "language": null, + "country": null, + "subject": [], + "title": [ + { + "value": "CMD domain-containing protein", + "qualifier": null, + "dataInfo": null + } + ], + "relevantdate": [ + { + "value": "2019-07-15T16:14:28.636", + "qualifier": { + "classid": "resolvedDate", + "classname": "resolvedDate", + "schemeid": "dnet::date", + "schemename": "dnet::date" + }, + "dataInfo": null + } + ], + "description": null, + "dateofacceptance": null, + "publisher": { + "value": "UniProt", + "dataInfo": null + }, + "embargoenddate": null, + "source": null, + "fulltext": null, + "format": null, + "contributor": null, + "resourcetype": null, + "coverage": null, + "bestaccessright": null, + "context": null, + "externalReference": null, + "instance": [], + "storagedate": null, + "device": null, + "size": null, + "version": null, + "lastmetadataupdate": null, + "metadataversionnumber": null, + "geolocation": null, + "originalObjIdentifier": "europe_pmc__::719f19e5a996de1b87cddf93871bf2d4", + "dlicollectedfrom": [ + { + "id": "dli_________::europe_pmc__", + "name": "Europe PMC", + "completionStatus": "complete", + "collectionMode": null + } + ], + "completionStatus": "complete" +} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/test/resources/eu/dnetlib/dhp/export/publication.json b/dhp-workflows/dhp-graph-provision-scholexplorer/src/test/resources/eu/dnetlib/dhp/export/publication.json new file mode 100644 index 0000000000..4ab3de2da0 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/test/resources/eu/dnetlib/dhp/export/publication.json @@ -0,0 +1,128 @@ +{ + "dataInfo": { + "invisible": false, + "inferred": null, + "deletedbyinference": false, + "trust": "0.9", + "inferenceprovenance": null, + "provenanceaction": null + }, + "lastupdatetimestamp": null, + "id": "50|9e117414be07bf03cbce8889d22d661a", + "originalId": [ + "9e117414be07bf03cbce8889d22d661a" + ], + "collectedfrom": [ + { + "key": "dli_________::crossref", + "value": "Crossref", + "dataInfo": null + } + ], + "pid": [ + { + "value": "10.1007/978-94-017-3490-5_15", + "qualifier": { + "classid": "doi", + "classname": "doi", + "schemeid": "dnet:pid_types", + "schemename": "dnet:pid_types" + }, + "dataInfo": null + } + ], + "dateofcollection": "2020-06-08T07:28:55.731Z", + "dateoftransformation": null, + "extraInfo": null, + "oaiprovenance": null, + "author": [ + { + "fullname": "Calcaterra Domenico", + "name": null, + "surname": null, + "rank": null, + "pid": null, + "affiliation": null + }, + { + "fullname": "Parise Mario", + "name": null, + "surname": null, + "rank": null, + "pid": null, + "affiliation": null + } + ], + "resulttype": { + "classid": "publication", + "classname": "publication", + "schemeid": "publication", + "schemename": "publication" + }, + "language": null, + "country": null, + "subject":[ + { + "value":"Strain-linked information about bacterial and archaeal biodiversity", + "qualifier":{ + "classid":"dnet:subject", + "classname":"dnet:subject", + "schemeid":"", + "schemename":"" + }, + "dataInfo":null + } + ], + "title": [ + { + "value": "The Contribution of Historical Information in the Assessment of Landslide Hazard", + "qualifier": null, + "dataInfo": null + } + ], + "relevantdate": [ + { + "value": "2013-01-29T16:50:44Z", + "qualifier": { + "classid": "date", + "classname": "date", + "schemeid": "dnet::date", + "schemename": "dnet::date" + }, + "dataInfo": null + } + ], + "description": [ + { + "value": null, + "dataInfo": null + } + ], + "dateofacceptance": null, + "publisher": { + "value": "Springer Netherlands", + "dataInfo": null + }, + "embargoenddate": null, + "source": null, + "fulltext": null, + "format": null, + "contributor": null, + "resourcetype": null, + "coverage": null, + "bestaccessright": null, + "context": null, + "externalReference": null, + "instance": [], + "journal": null, + "originalObjIdentifier": "dli_resolver::9e117414be07bf03cbce8889d22d661a", + "dlicollectedfrom": [ + { + "id": "dli_________::crossref", + "name": "Crossref", + "completionStatus": "complete", + "collectionMode": "resolved" + } + ], + "completionStatus": "complete" +} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/test/resources/eu/dnetlib/dhp/export/relation.json b/dhp-workflows/dhp-graph-provision-scholexplorer/src/test/resources/eu/dnetlib/dhp/export/relation.json new file mode 100644 index 0000000000..cdb0cfa1d5 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/test/resources/eu/dnetlib/dhp/export/relation.json @@ -0,0 +1,23 @@ +{ + "subRelType": null, + "relClass": "datacite", + "dataInfo": { + "deletedbyinference": false, + "provenanceaction": null, + "inferred": null, + "inferenceprovenance": null, + "invisible": false, + "trust": "0.9" + }, + "target": "50|00062410e2a15322480277d063c181bb", + "lastupdatetimestamp": null, + "relType": "IsReferencedBy", + "source": "60|4ee78ab329b49416b45c3774c132f244", + "collectedFrom": [ + { + "dataInfo": null, + "value": "Europe PMC", + "key": "dli_________::europe_pmc__" + } + ] +}