fixed pom definitions, bumped dependency version for the dhp-schema module, removed unnecessary dependencies

dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/support/TreeNodeStats.java

@@ -25,10 +25,10 @@ public class TreeNodeStats implements Serializable {
 	}
 
 	public int fieldsCount() {
-		if(ignoreUndefined)
+		if (ignoreUndefined)
 			return this.results.size();
 		else
-			return this.results.size() - undefinedCount();	//do not count undefined
+			return this.results.size() - undefinedCount(); // do not count undefined
 	}
 
 	public int undefinedCount() {
@@ -87,20 +87,17 @@ public class TreeNodeStats implements Serializable {
 				if (fs.getResult() == -1) {
 					if (fs.isCountIfUndefined()) {
 						min = 0.0;
-					}
+					} else {
-					else {
 						min = -1;
 					}
-				}
+				} else {
-				else {
 					min = fs.getResult();
 				}
 			}
 		}
 		if (ignoreUndefined) {
-			return min==-1.0? 0.0 : min;
+			return min == -1.0 ? 0.0 : min;
-		}
+		} else {
-		else {
 			return min;
 		}
 	}
@@ -111,7 +108,7 @@ public class TreeNodeStats implements Serializable {
 			if (fieldStats.getResult() >= fieldStats.getThreshold())
 				return 1.0;
 		}
-		if (!ignoreUndefined && undefinedCount()>0){
+		if (!ignoreUndefined && undefinedCount() > 0) {
 			return -1.0;
 		} else {
 			return 0.0;
@@ -124,7 +121,7 @@ public class TreeNodeStats implements Serializable {
 
 			if (fieldStats.getResult() == -1) {
 				if (fieldStats.isCountIfUndefined())
-					return ignoreUndefined? 0.0 : -1.0;
+					return ignoreUndefined ? 0.0 : -1.0;
 			} else {
 				if (fieldStats.getResult() < fieldStats.getThreshold())
 					return 0.0;

dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/support/TreeProcessor.java

@@ -45,7 +45,7 @@ public class TreeProcessor {
 			treeStats.addNodeStats(nextNodeName, stats);
 
 			double finalScore = stats.getFinalScore(currentNode.getAggregation());
-			if(finalScore == -1.0)
+			if (finalScore == -1.0)
 				nextNodeName = currentNode.getUndefined();
 			else if (finalScore >= currentNode.getThreshold()) {
 				nextNodeName = currentNode.getPositive();
@@ -53,7 +53,6 @@ public class TreeProcessor {
 				nextNodeName = currentNode.getNegative();
 			}
 
-
 		} while (MatchType.parse(nextNodeName) == MatchType.UNDEFINED);
 
 		treeStats.setResult(MatchType.parse(nextNodeName));

dhp-pace-core/src/test/java/eu/dnetlib/pace/clustering/ClusteringFunctionTest.java

@@ -3,12 +3,12 @@ package eu.dnetlib.pace.clustering;
 
 import java.util.Map;
 
-import com.mongodb.connection.Cluster;
 import org.junit.jupiter.api.BeforeAll;
 import org.junit.jupiter.api.Test;
 
 import com.google.common.collect.Lists;
 import com.google.common.collect.Maps;
+import com.mongodb.connection.Cluster;
 
 import eu.dnetlib.pace.AbstractPaceTest;
 import eu.dnetlib.pace.common.AbstractPaceFunctions;

dhp-pace-core/src/test/java/eu/dnetlib/pace/comparators/ComparatorTest.java

@@ -61,7 +61,7 @@ public class ComparatorTest extends AbstractPaceTest {
 		assertEquals(0.0, codeMatch.distance("testing1 key::1", "testing2 key::2", conf));
 
 		// both names with codes (1 same, 1 different)
-		assertEquals(0.5,codeMatch.distance("key::1 key::2 testing1", "key::1 testing", conf));
+		assertEquals(0.5, codeMatch.distance("key::1 key::2 testing1", "key::1 testing", conf));
 
 	}
 

dhp-workflows/dhp-actionmanager/pom.xml

@@ -51,48 +51,5 @@
             <artifactId>hadoop-distcp</artifactId>
         </dependency>
 
-        <dependency>
-            <groupId>eu.dnetlib</groupId>
-            <artifactId>dnet-actionmanager-api</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>eu.dnetlib</groupId>
-            <artifactId>dnet-actionmanager-common</artifactId>
-            <exclusions>
-                <exclusion>
-                    <groupId>eu.dnetlib</groupId>
-                    <artifactId>dnet-openaireplus-mapping-utils</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>saxonica</groupId>
-                    <artifactId>saxon</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>saxonica</groupId>
-                    <artifactId>saxon-dom</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>jgrapht</groupId>
-                    <artifactId>jgrapht</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>net.sf.ehcache</groupId>
-                    <artifactId>ehcache</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>org.springframework</groupId>
-                    <artifactId>spring-test</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>org.apache.*</groupId>
-                    <artifactId>*</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>apache</groupId>
-                    <artifactId>*</artifactId>
-                </exclusion>
-            </exclusions>
-        </dependency>
-
     </dependencies>
 </project>

dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/ISClient.java

@@ -4,7 +4,6 @@ package eu.dnetlib.dhp.actionmanager;
 import java.io.Serializable;
 import java.io.StringReader;
 import java.util.List;
-import java.util.NoSuchElementException;
 import java.util.Optional;
 import java.util.Set;
 import java.util.stream.Collectors;
@@ -22,7 +21,6 @@ import com.google.common.base.Splitter;
 import com.google.common.collect.Iterables;
 import com.google.common.collect.Sets;
 
-import eu.dnetlib.actionmanager.rmi.ActionManagerException;
 import eu.dnetlib.dhp.utils.ISLookupClientFactory;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
@@ -65,7 +63,7 @@ public class ISClient implements Serializable {
 						.map(t -> buildDirectory(basePath, t))
 						.collect(Collectors.toList()))
 				.orElseThrow(() -> new IllegalStateException("empty set list"));
-		} catch (ActionManagerException | ISLookUpException e) {
+		} catch (ISLookUpException e) {
 			throw new IllegalStateException("unable to query ActionSets info from the IS");
 		}
 	}
@@ -89,31 +87,18 @@ public class ISClient implements Serializable {
 		return Joiner.on("/").join(basePath, t.getMiddle(), t.getRight());
 	}
 
-	private String getBasePathHDFS(ISLookUpService isLookup) throws ActionManagerException {
+	private String getBasePathHDFS(ISLookUpService isLookup) throws ISLookUpException {
 		return queryServiceProperty(isLookup, "basePath");
 	}
 
 	private String queryServiceProperty(ISLookUpService isLookup, final String propertyName)
-		throws ActionManagerException {
+		throws ISLookUpException {
 		final String q = "for $x in /RESOURCE_PROFILE[.//RESOURCE_TYPE/@value='ActionManagerServiceResourceType'] return $x//SERVICE_PROPERTIES/PROPERTY[./@ key='"
 			+ propertyName
 			+ "']/@value/string()";
 		log.debug("quering for service property: {}", q);
-		try {
+
-			final List<String> value = isLookup.quickSearchProfile(q);
+		final List<String> value = isLookup.quickSearchProfile(q);
-			return Iterables.getOnlyElement(value);
+		return Iterables.getOnlyElement(value);
-		} catch (ISLookUpException e) {
-			String msg = "Error accessing service profile, using query: " + q;
-			log.error(msg, e);
-			throw new ActionManagerException(msg, e);
-		} catch (NoSuchElementException e) {
-			String msg = "missing service property: " + propertyName;
-			log.error(msg, e);
-			throw new ActionManagerException(msg, e);
-		} catch (IllegalArgumentException e) {
-			String msg = "found more than one service property: " + propertyName;
-			log.error(msg, e);
-			throw new ActionManagerException(msg, e);
-		}
 	}
 }

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateActionSetFromWebEntries.java

@@ -106,7 +106,6 @@ public class CreateActionSetFromWebEntries implements Serializable {
 					+ IdentifierFactory.md5(PidCleaner.normalizePidValue("ROR", row.getAs("ror")));
 				ret.addAll(createAffiliationRelationPairDOI(row.getAs("doi"), ror));
 
-
 				return ret
 					.iterator();
 			}, Encoders.bean(Relation.class))

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/researchfi/ResearchFiCollectorPlugin.java

@@ -1,3 +1,4 @@
+
 package eu.dnetlib.dhp.collection.plugin.researchfi;
 
 import java.util.ArrayList;
@@ -32,7 +33,7 @@ public class ResearchFiCollectorPlugin implements CollectorPlugin {
 
 	@Override
 	public Stream<String> collect(final ApiDescriptor api, final AggregatorReport report)
-			throws CollectorException {
+		throws CollectorException {
 
 		final String authUrl = api.getParams().get("auth_url");
 		final String clientId = api.getParams().get("auth_client_id");
@@ -45,7 +46,8 @@ public class ResearchFiCollectorPlugin implements CollectorPlugin {
 		return StreamSupport.stream(Spliterators.spliteratorUnknownSize(iter, Spliterator.ORDERED), false);
 	}
 
-	private String authenticate(final String authUrl, final String clientId, final String clientSecret) throws CollectorException {
+	private String authenticate(final String authUrl, final String clientId, final String clientSecret)
+		throws CollectorException {
 		try (final CloseableHttpClient client = HttpClients.createDefault()) {
 			final HttpPost req = new HttpPost(authUrl);
 			final List<NameValuePair> params = new ArrayList<>();
@@ -59,7 +61,9 @@ public class ResearchFiCollectorPlugin implements CollectorPlugin {
 				final String content = IOUtils.toString(response.getEntity().getContent());
 				final JSONObject obj = new JSONObject(content);
 				final String token = obj.getString("access_token");
-				if (StringUtils.isNotBlank(token)) { return token; }
+				if (StringUtils.isNotBlank(token)) {
+					return token;
+				}
 			}
 		} catch (final Throwable e) {
 			log.warn("Error obtaining access token", e);

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/researchfi/ResearchFiIterator.java

@@ -1,3 +1,4 @@
+
 package eu.dnetlib.dhp.collection.plugin.researchfi;
 
 import java.util.Iterator;

dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/researchfi/ResearchFiCollectorPluginTest.java

@@ -1,3 +1,4 @@
+
 package eu.dnetlib.dhp.collection.plugin.researchfi;
 
 import java.util.HashSet;
@@ -23,7 +24,9 @@ public class ResearchFiCollectorPluginTest {
 		final ApiDescriptor api = new ApiDescriptor();
 		api.setBaseUrl("https://research.fi/api/rest/v1/funding-decisions?FunderName=AKA&FundingStartYearFrom=2022");
 		api.setProtocol("research_fi");
-		api.getParams().put("auth_url", "https://researchfi-auth.2.rahtiapp.fi/realms/publicapi/protocol/openid-connect/token");
+		api
+			.getParams()
+			.put("auth_url", "https://researchfi-auth.2.rahtiapp.fi/realms/publicapi/protocol/openid-connect/token");
 		api.getParams().put("auth_client_id", "");
 		api.getParams().put("auth_client_secret", "");
 

dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/jpath/JsonPathTest.java

@@ -3,13 +3,13 @@ package eu.dnetlib.dhp.oa.dedup.jpath;
 
 import java.io.IOException;
 
-import eu.dnetlib.dhp.oa.dedup.SparkOpenorgsDedupTest;
 import org.apache.commons.io.IOUtils;
 import org.apache.spark.sql.Row;
 import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.Test;
 import org.junit.platform.commons.util.StringUtils;
 
+import eu.dnetlib.dhp.oa.dedup.SparkOpenorgsDedupTest;
 import eu.dnetlib.pace.config.DedupConfig;
 import eu.dnetlib.pace.model.SparkModel;
 
@@ -33,13 +33,14 @@ class JsonPathTest {
 	}
 
 	@Test
-	void jsonToModelTest() throws IOException{
+	void jsonToModelTest() throws IOException {
 		DedupConfig conf = DedupConfig
-				.load(IOUtils
+			.load(
-						.toString(
+				IOUtils
-								SparkOpenorgsDedupTest.class
+					.toString(
-										.getResourceAsStream(
+						SparkOpenorgsDedupTest.class
-												"/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json")));
+							.getResourceAsStream(
+								"/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json")));
 
 		final String org = IOUtils.toString(getClass().getResourceAsStream("organization_example1.json"));
 

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java

@@ -37,6 +37,7 @@ import eu.dnetlib.dhp.schema.solr.Measure;
 import eu.dnetlib.dhp.schema.solr.OpenAccessColor;
 import eu.dnetlib.dhp.schema.solr.OpenAccessRoute;
 import eu.dnetlib.dhp.schema.solr.Organization;
+import eu.dnetlib.dhp.schema.solr.Pid;
 import eu.dnetlib.dhp.schema.solr.Project;
 import eu.dnetlib.dhp.schema.solr.Result;
 import eu.dnetlib.dhp.schema.solr.Subject;

dhp-workflows/dhp-swh/pom.xml

@@ -51,49 +51,6 @@
             <artifactId>hadoop-distcp</artifactId>
         </dependency>
 
-        <dependency>
-            <groupId>eu.dnetlib</groupId>
-            <artifactId>dnet-actionmanager-api</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>eu.dnetlib</groupId>
-            <artifactId>dnet-actionmanager-common</artifactId>
-            <exclusions>
-                <exclusion>
-                    <groupId>eu.dnetlib</groupId>
-                    <artifactId>dnet-openaireplus-mapping-utils</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>saxonica</groupId>
-                    <artifactId>saxon</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>saxonica</groupId>
-                    <artifactId>saxon-dom</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>jgrapht</groupId>
-                    <artifactId>jgrapht</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>net.sf.ehcache</groupId>
-                    <artifactId>ehcache</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>org.springframework</groupId>
-                    <artifactId>spring-test</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>org.apache.*</groupId>
-                    <artifactId>*</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>apache</groupId>
-                    <artifactId>*</artifactId>
-                </exclusion>
-            </exclusions>
-        </dependency>
-
         <dependency>
             <groupId>org.apache.httpcomponents</groupId>
             <artifactId>httpclient</artifactId>

pom.xml

@@ -440,29 +440,6 @@
                 <scope>provided</scope>
             </dependency>
 
-            <dependency>
-                <groupId>eu.dnetlib</groupId>
-                <artifactId>dnet-actionmanager-common</artifactId>
-                <version>${dnet-actionmanager-common.version}</version>
-                <exclusions>
-                    <exclusion>
-                        <groupId>org.apache.hadoop</groupId>
-                        <artifactId>hadoop-common</artifactId>
-                    </exclusion>
-                </exclusions>
-            </dependency>
-            <dependency>
-                <groupId>eu.dnetlib</groupId>
-                <artifactId>dnet-actionmanager-api</artifactId>
-                <version>${dnet-actionmanager-api.version}</version>
-                <exclusions>
-                    <exclusion>
-                        <groupId>eu.dnetlib</groupId>
-                        <artifactId>cnr-misc-utils</artifactId>
-                    </exclusion>
-                </exclusions>
-            </dependency>
-
             <dependency>
                 <groupId>eu.dnetlib</groupId>
                 <artifactId>cnr-rmi-api</artifactId>
@@ -960,7 +937,7 @@
         <commons.logging.version>1.1.3</commons.logging.version>
         <commons-validator.version>1.7</commons-validator.version>
         <dateparser.version>1.0.7</dateparser.version>
-        <dhp-schemas.version>[6.1.4-SNAPSHOT]</dhp-schemas.version>
+        <dhp-schemas.version>[7.0.0]</dhp-schemas.version>
         <dhp.cdh.version>cdh5.9.2</dhp.cdh.version>
         <dhp.commons.lang.version>3.5</dhp.commons.lang.version>
         <dhp.guava.version>11.0.2</dhp.guava.version>
@@ -969,8 +946,6 @@
         <dhp.oozie.version>4.1.0-${dhp.cdh.version}</dhp.oozie.version>
         <dhp.site.skip>true</dhp.site.skip>
         <dhp.spark.version>2.4.0.cloudera2</dhp.spark.version>
-        <dnet-actionmanager-api.version>[4.0.3]</dnet-actionmanager-api.version>
-        <dnet-actionmanager-common.version>[6.0.5]</dnet-actionmanager-common.version>
         <dnet-openaire-broker-common.version>[3.1.6]</dnet-openaire-broker-common.version>
         <google.gson.version>2.2.2</google.gson.version>
         <log4j.version>1.2.17</log4j.version>