diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/bioschema/oozie_app/config-default.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/bioschema/oozie_app/config-default.xml
index d3fad7dfe..2ba83ba73 100644
--- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/bioschema/oozie_app/config-default.xml
+++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/bioschema/oozie_app/config-default.xml
@@ -2,64 +2,13 @@
-
- jobTracker
- yarnRM
-
-
- nameNode
- hdfs://nameservice1
-
-
- oozie.use.system.libpath
- true
-
-
- oozie.action.sharelib.for.spark
- spark2
-
-
- oozie.launcher.mapreduce.user.classpath.first
- true
-
-
- spark2YarnHistoryServerAddress
- http://hadoop-rm2.garr-pa1.d4science.org:19888
-
-
- spark2EventLogDir
- /user/spark/spark2ApplicationHistory
-
-
- spark2ExtraListeners
- "com.cloudera.spark.lineage.NavigatorAppListener"
-
-
- spark2SqlQueryExecutionListeners
- "com.cloudera.spark.lineage.NavigatorQueryListener"
-
-
-
-
-
+
-
-
-
-
-
-
-
-
-
-
-
-
-
+
@@ -70,6 +19,14 @@
+
+
+
+
+
+
+
+
@@ -81,4 +38,47 @@
+
+
+
+
+ jobTracker
+ hadoop-rm3.garr-pa1.d4science.org:8032
+
+
+ nameNode
+ hdfs://hadoop-rm1.garr-pa1.d4science.org:8020
+
+
+ hive_metastore_uris
+ thrift://hadoop-edge3.garr-pa1.d4science.org:9083
+
+
+ spark2YarnHistoryServerAddress
+ http://hadoop-rm2.garr-pa1.d4science.org:19888
+
+
+ oozie.launcher.mapreduce.user.classpath.first
+ true
+
+
+ oozie.use.system.libpath
+ true
+
+
+ oozie.action.sharelib.for.spark
+ spark2
+
+
+ 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-aggregation/src/main/resources/eu/dnetlib/dhp/bioschema/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/bioschema/oozie_app/workflow.xml
index 92205ed96..92af9a8ef 100644
--- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/bioschema/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/bioschema/oozie_app/workflow.xml
@@ -17,12 +17,20 @@
-
+
Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]
+
+
+
+
+
+
+
+
diff --git a/dhp-workflows/dhp-rdfconverter/src/main/java/eu/dnetlib/dhp/rdfconverter/bioschema/model/BioSchemaProtein.java b/dhp-workflows/dhp-rdfconverter/src/main/java/eu/dnetlib/dhp/rdfconverter/bioschema/model/BioSchemaProtein.java
index ececaf413..8b71520b9 100644
--- a/dhp-workflows/dhp-rdfconverter/src/main/java/eu/dnetlib/dhp/rdfconverter/bioschema/model/BioSchemaProtein.java
+++ b/dhp-workflows/dhp-rdfconverter/src/main/java/eu/dnetlib/dhp/rdfconverter/bioschema/model/BioSchemaProtein.java
@@ -5,6 +5,9 @@ import java.util.List;
import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
import com.fasterxml.jackson.annotation.JsonProperty;
+import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
+
+import eu.dnetlib.dhp.rdfconverter.utils.CustomPropertyValueDeserializer;
@JsonIgnoreProperties(ignoreUnknown = true)
public class BioSchemaProtein {
@@ -58,6 +61,7 @@ public class BioSchemaProtein {
@JsonProperty("https://schema.org/additionalProperty")
private List sequenceAnnotation;
@JsonProperty("https://schema.org/value")
+ @JsonDeserialize(using = CustomPropertyValueDeserializer.class)
private Link propertyValue;
@JsonProperty("https://schema.org/termCode")
private String termCode;
diff --git a/dhp-workflows/dhp-rdfconverter/src/main/java/eu/dnetlib/dhp/rdfconverter/utils/CustomPropertyValueDeserializer.java b/dhp-workflows/dhp-rdfconverter/src/main/java/eu/dnetlib/dhp/rdfconverter/utils/CustomPropertyValueDeserializer.java
new file mode 100644
index 000000000..44b582ad3
--- /dev/null
+++ b/dhp-workflows/dhp-rdfconverter/src/main/java/eu/dnetlib/dhp/rdfconverter/utils/CustomPropertyValueDeserializer.java
@@ -0,0 +1,43 @@
+
+package eu.dnetlib.dhp.rdfconverter.utils;
+
+import java.io.IOException;
+
+import com.fasterxml.jackson.core.JsonParser;
+import com.fasterxml.jackson.core.ObjectCodec;
+import com.fasterxml.jackson.databind.DeserializationContext;
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.deser.std.StdDeserializer;
+
+import eu.dnetlib.dhp.rdfconverter.bioschema.model.BioSchemaProtein;
+
+public class CustomPropertyValueDeserializer
+ extends StdDeserializer {
+
+ public CustomPropertyValueDeserializer() {
+ this(null);
+ }
+
+ public CustomPropertyValueDeserializer(Class vc) {
+ super(vc);
+ }
+
+ @Override
+ public BioSchemaProtein.Link deserialize(
+ JsonParser jsonparser, DeserializationContext context)
+ throws IOException {
+ ObjectCodec oc = jsonparser.getCodec();
+ JsonNode node = oc.readTree(jsonparser);
+ JsonNode id = node.get("@id");
+ if (id != null) {
+ BioSchemaProtein.Link link = new BioSchemaProtein.Link();
+ link.setId(id.asText());
+ return link;
+ } else {
+ String txt = node.asText();
+ BioSchemaProtein.Link link = new BioSchemaProtein.Link();
+ link.setId(txt);
+ return link;
+ }
+ }
+}
diff --git a/dhp-workflows/dhp-rdfconverter/src/main/java/eu/dnetlib/dhp/rdfconverter/utils/RDFConverter.java b/dhp-workflows/dhp-rdfconverter/src/main/java/eu/dnetlib/dhp/rdfconverter/utils/RDFConverter.java
index 9172ff087..f284d49df 100644
--- a/dhp-workflows/dhp-rdfconverter/src/main/java/eu/dnetlib/dhp/rdfconverter/utils/RDFConverter.java
+++ b/dhp-workflows/dhp-rdfconverter/src/main/java/eu/dnetlib/dhp/rdfconverter/utils/RDFConverter.java
@@ -16,6 +16,7 @@ import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.DeserializationFeature;
import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.module.SimpleModule;
import com.github.jsonldjava.core.JsonLdOptions;
import com.github.jsonldjava.core.JsonLdProcessor;
import com.github.jsonldjava.utils.JsonUtils;
@@ -50,6 +51,8 @@ public class RDFConverter {
objectMapper.enable(DeserializationFeature.ACCEPT_SINGLE_VALUE_AS_ARRAY);
objectMapper.enable(DeserializationFeature.ACCEPT_EMPTY_STRING_AS_NULL_OBJECT);
objectMapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
+ objectMapper.configure(DeserializationFeature.FAIL_ON_INVALID_SUBTYPE, false);
+ objectMapper.configure(DeserializationFeature.FAIL_ON_MISSING_CREATOR_PROPERTIES, false);
BioSchemaProtein bioSchemaProtein = objectMapper.readValue(compactContent, BioSchemaProtein.class);
BioSchemaProtein.DateTimeType retrievedOnType = bioSchemaProtein.getRetrievedOn();
diff --git a/dhp-workflows/dhp-rdfconverter/src/test/java/eu/dnetlib/dhp/rdfconverter/bioschema/ConverterTest.java b/dhp-workflows/dhp-rdfconverter/src/test/java/eu/dnetlib/dhp/rdfconverter/bioschema/ConverterTest.java
index a203dcd40..15cda0118 100644
--- a/dhp-workflows/dhp-rdfconverter/src/test/java/eu/dnetlib/dhp/rdfconverter/bioschema/ConverterTest.java
+++ b/dhp-workflows/dhp-rdfconverter/src/test/java/eu/dnetlib/dhp/rdfconverter/bioschema/ConverterTest.java
@@ -15,17 +15,16 @@ public class ConverterTest {
static Logger logger = LoggerFactory.getLogger(ConverterTest.class);
-// @Test
-// private void nqToDataciteTest() throws Exception {
-// InputStream is = ConverterTest.class.getResourceAsStream("/eu/dnetlib/dhp/rdfconverter/bioschema/disprot.nq");
-// String nq = IOUtils.toString(is);
-// logger.debug("NQ: " + nq);
-// RDFConverter converter = new RDFConverter();
-// ArrayList results = converter.nQuadsFile2DataciteJson(nq, "Protein");
-// if (results != null && !results.isEmpty()) {
-// logger.info("JSON DATACITE: " + results.get(0));
-// }
-// }
+ @Test
+ public void disprotToDataciteTest() throws Exception {
+ InputStream is = ConverterTest.class.getResourceAsStream("/eu/dnetlib/dhp/rdfconverter/bioschema/disprot.nq");
+ String nq = IOUtils.toString(is);
+ RDFConverter converter = new RDFConverter();
+ ArrayList results = converter.nQuadsFile2DataciteJson(nq, "Protein");
+ results.stream().forEach(r -> {
+ logger.info("JSON DATACITE >> " + r);
+ });
+ }
@Test
public void pedCitationTest() throws Exception {