[Tagging Projects and Datasource] changed the way the pathMap parameter is passed. It was too long and was truncated

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java

@@ -4,10 +4,23 @@ package eu.dnetlib.dhp.bulktag;
 import static eu.dnetlib.dhp.PropagationConstant.removeOutputDir;
 import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
 
+import java.io.BufferedOutputStream;
+import java.io.IOException;
+import java.nio.charset.StandardCharsets;
 import java.util.*;
 import java.util.stream.Collectors;
+import java.util.zip.GZIPOutputStream;
 
+import org.apache.avro.TestAnnotation;
+import org.apache.commons.compress.archivers.tar.TarArchiveEntry;
+import org.apache.commons.compress.archivers.tar.TarArchiveInputStream;
+import org.apache.commons.compress.compressors.gzip.GzipCompressorInputStream;
 import org.apache.commons.io.IOUtils;
+import org.apache.hadoop.conf.Configuration;
+import org.apache.hadoop.fs.FSDataInputStream;
+import org.apache.hadoop.fs.FSDataOutputStream;
+import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.fs.Path;
 import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.function.FilterFunction;
 import org.apache.spark.api.java.function.MapFunction;
@@ -18,8 +31,10 @@ import org.apache.spark.sql.SparkSession;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import com.google.gson.Gson;
+import com.sun.media.sound.ModelInstrumentComparator;
 
 import eu.dnetlib.dhp.api.Utils;
 import eu.dnetlib.dhp.api.model.CommunityEntityMap;
@@ -73,8 +88,20 @@ public class SparkBulkTagJob {
 		log.info("baseURL: {}", baseURL);
 
 		log.info("pathMap: {}", parser.get("pathMap"));
-		ProtoMap protoMappingParams = new Gson().fromJson(parser.get("pathMap") + "}}", ProtoMap.class);
+		String protoMappingPath = parser.get("pathMap");
-		log.info("pathMap: {}", new Gson().toJson(protoMappingParams));
+		// log.info("pathMap: {}", new Gson().toJson(protoMappingParams));
+
+		final String hdfsNameNode = parser.get("nameNode");
+		log.info("nameNode: {}", hdfsNameNode);
+
+		Configuration configuration = new Configuration();
+		configuration.set("fs.defaultFS", hdfsNameNode);
+		FileSystem fs = FileSystem.get(configuration);
+
+		String temp = IOUtils.toString(fs.open(new Path(protoMappingPath)), StandardCharsets.UTF_8);
+		log.info("protoMap: {}", temp);
+		ProtoMap protoMap = new Gson().fromJson(temp, ProtoMap.class);
+		log.info("pathMap: {}", new Gson().toJson(protoMap));
 
 		SparkConf conf = new SparkConf();
 		CommunityConfiguration cc;
@@ -96,7 +123,8 @@ public class SparkBulkTagJob {
 			isSparkSessionManaged,
 			spark -> {
 				extendCommunityConfigurationForEOSC(spark, inputPath, cc);
-				execBulkTag(spark, inputPath, outputPath, protoMappingParams, cc);
+				execBulkTag(
+					spark, inputPath, outputPath, protoMap, cc);
 				execDatasourceTag(spark, inputPath, outputPath, Utils.getDatasourceCommunities(baseURL));
 				execProjectTag(spark, inputPath, outputPath, Utils.getCommunityProjects(baseURL));
 			});
@@ -256,6 +284,11 @@ public class SparkBulkTagJob {
 		ProtoMap protoMappingParams,
 		CommunityConfiguration communityConfiguration) {
 
+		try {
+			System.out.println(new ObjectMapper().writeValueAsString(protoMappingParams));
+		} catch (JsonProcessingException e) {
+			throw new RuntimeException(e);
+		}
 		ModelSupport.entityTypes
 			.keySet()
 			.parallelStream()

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ProtoMap.java

@@ -7,8 +7,8 @@ import java.util.HashMap;
 import eu.dnetlib.dhp.bulktag.actions.MapModel;
 
 public class ProtoMap extends HashMap<String, MapModel> implements Serializable {
-
 	public ProtoMap() {
 		super();
 	}
+
 }

dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/main/job.properties

@@ -1,4 +1,4 @@
-sourcePath=/tmp/beta_provision/graph/10_graph_orcid_enriched
+sourcePath=/tmp/beta_provision/graph/09_graph_orcid_enriched
 resumeFrom=ResultProject
 allowedsemrelsorcidprop=isSupplementedBy;isSupplementTo
 allowedsemrelsresultproject=isSupplementedBy;isSupplementTo

dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflows/bulktag/input_bulkTag_parameters.json

@@ -34,5 +34,10 @@
     "paramLongName": "baseURL",
     "paramDescription": "this parameter is to specify the api to be queried (beta or production)",
     "paramRequired": true
-  }
+  },{
+  "paramName": "nn",
+  "paramLongName": "nameNode",
+  "paramDescription": "this parameter is to specify the api to be queried (beta or production)",
+  "paramRequired": true
+}
 ]

dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflows/bulktag/oozie_app/config-default.xml

@@ -53,10 +53,10 @@
     </property>
     <property>
         <name>memoryOverhead</name>
-        <value>3G</value>
+        <value>4G</value>
     </property>
     <property>
         <name>partitions</name>
-        <value>3284</value>
+        <value>15000</value>
     </property>
 </configuration>

dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflows/bulktag/oozie_app/workflow.xml

@@ -76,6 +76,7 @@
             <arg>--outputPath</arg><arg>${workingDir}/bulktag/</arg>
             <arg>--pathMap</arg><arg>${pathMap}</arg>
             <arg>--baseURL</arg><arg>${baseURL}</arg>
+            <arg>--nameNode</arg><arg>${nameNode}</arg>
         </spark>
         <ok to="End"/>
         <error to="Kill"/>

dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java

@@ -6,14 +6,19 @@ import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.ZENODO_COMMUNITY
 import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.Path;
+import java.util.Arrays;
 import java.util.List;
 
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.IOUtils;
+import org.apache.hadoop.conf.Configuration;
+import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.fs.LocalFileSystem;
 import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.JavaRDD;
 import org.apache.spark.api.java.JavaSparkContext;
 import org.apache.spark.api.java.function.FilterFunction;
+import org.apache.spark.api.java.function.MapFunction;
 import org.apache.spark.sql.Encoders;
 import org.apache.spark.sql.Row;
 import org.apache.spark.sql.SparkSession;
@@ -25,14 +30,16 @@ import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
+import com.google.gson.Gson;
 
+import eu.dnetlib.dhp.bulktag.community.ProtoMap;
 import eu.dnetlib.dhp.schema.oaf.*;
 
 public class BulkTagJobTest {
 
 	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
 
-	public static final String pathMap = "{\"author\":{\"path\":\"$['author'][*]['fullname']\"}," +
+	public static final String pathMap = "{\"protoMap\":{\"author\":{\"path\":\"$['author'][*]['fullname']\"}," +
 		" \"title\":{\"path\":\"$['title'][*]['value']\"}, " +
 		" \"orcid\":{\"path\":\"$['author'][*]['pid'][*][?(@['qualifier']['classid']=='orcid')]['value']\"} , " +
 		" \"orcid_pending\":{\"path\":\"$['author'][*]['pid'][*][?(@['qualifier']['classid']=='orcid_pending')]['value']\"} ,"
@@ -51,7 +58,7 @@ public class BulkTagJobTest {
 		"\"method\":\"execSubstring\"," +
 		"\"params\":[" +
 		"{\"paramName\":\"From\",  \"paramValue\":0}, " +
-		"{\"paramName\":\"To\",\"paramValue\":4}]}}}";
+		"{\"paramName\":\"To\",\"paramValue\":4}]}}}}";
 
 	private static SparkSession spark;
 
@@ -231,6 +238,14 @@ public class BulkTagJobTest {
 
 	@Test
 	void bulktagBySubjectPreviousContextNoProvenanceTest() throws Exception {
+		LocalFileSystem fs = FileSystem.getLocal(new Configuration());
+		fs
+			.copyFromLocalFile(
+				false, new org.apache.hadoop.fs.Path(getClass()
+					.getResource("/eu/dnetlib/dhp/bulktag/pathMap/")
+					.getPath()),
+				new org.apache.hadoop.fs.Path(workingDir.toString() + "/data/bulktagging/protoMap"));
+
 		final String sourcePath = getClass()
 			.getResource(
 				"/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject/contextnoprovenance/")
@@ -246,7 +261,8 @@ public class BulkTagJobTest {
 
 					"-outputPath", workingDir.toString() + "/",
 
-					"-pathMap", pathMap
+					"-pathMap", workingDir.toString() + "/data/bulktagging/protoMap",
+					"-nameNode", "local"
 				});
 
 		final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
@@ -316,6 +332,7 @@ public class BulkTagJobTest {
 		final String sourcePath = getClass()
 			.getResource("/eu/dnetlib/dhp/bulktag/sample/publication/update_datasource/")
 			.getPath();
+
 		SparkBulkTagJob
 			.main(
 				new String[] {
@@ -390,6 +407,13 @@ public class BulkTagJobTest {
 		final String sourcePath = getClass()
 			.getResource("/eu/dnetlib/dhp/bulktag/sample/publication/update_datasource/")
 			.getPath();
+		LocalFileSystem fs = FileSystem.getLocal(new Configuration());
+		fs
+			.copyFromLocalFile(
+				false, new org.apache.hadoop.fs.Path(getClass()
+					.getResource("/eu/dnetlib/dhp/bulktag/pathMap/")
+					.getPath()),
+				new org.apache.hadoop.fs.Path(workingDir.toString() + "/data/bulktagging/protoMap"));
 		SparkBulkTagJob
 			.main(
 				new String[] {
@@ -400,7 +424,9 @@ public class BulkTagJobTest {
 
 					"-outputPath", workingDir.toString() + "/",
 					"-baseURL", "https://services.openaire.eu/openaire/community/",
-					"-pathMap", pathMap
+
+					"-pathMap", workingDir.toString() + "/data/bulktagging/protoMap/pathMap",
+					"-nameNode", "local"
 				});
 
 		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
@@ -1757,4 +1783,40 @@ public class BulkTagJobTest {
 
 	}
 
+	@Test
+	public void prova() throws Exception {
+		LocalFileSystem fs = FileSystem.getLocal(new Configuration());
+		fs
+			.copyFromLocalFile(
+				false, new org.apache.hadoop.fs.Path(getClass()
+					.getResource("/eu/dnetlib/dhp/bulktag/pathMap/")
+					.getPath()),
+				new org.apache.hadoop.fs.Path(workingDir.toString() + "/data/bulktagging/protoMap"));
+
+		final String sourcePath = getClass()
+			.getResource(
+				"/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject/contextnoprovenance/")
+			.getPath();
+
+		ProtoMap prova = new Gson()
+			.fromJson(
+				"{\"author\":{\"path\":\"$['author'][]['fullname']\"},\"title\":{\"path\":\"$['title'][]['value']\"},\"orcid\":{\"path\":\"$['author'][]['pid'][][?(@['qualifier']['classid']=='orcid')]['value']\"},\"orcid_pending\":{\"path\":\"$['author'][]['pid'][][?(@['qualifier']['classid']=='orcid_pending')]['value']\"},\"contributor\":{\"path\":\"$['contributor'][]['value']\"},\"description\":{\"path\":\"$['description'][]['value']\"},\"subject\":{\"path\":\"$['subject'][]['value']\"},\"fos\":{\"path\":\"$['subject'][?(@['qualifier']['classid']=='FOS')].value\"},\"sdg\":{\"path\":\"$['subject'][?(@['qualifier']['classid']=='SDG')].value\"},\"journal\":{\"path\":\"$['journal'].name\"},\"hostedby\":{\"path\":\"$['instance'][]['hostedby']['key']\"},\"collectedfrom\":{\"path\":\"$['instance'][*]['collectedfrom']['key']\"},\"publisher\":{\"path\":\"$['publisher'].value\"},\"publicationyear\":{\"path\":\"$['dateofacceptance'].value\",\"action\":{\"clazz\":\"eu.dnetlib.dhp.bulktag.actions.ExecSubstringAction\",\"method\":\"execSubstring\",\"params\":[{\"paramName\":\"From\",\"paramValue\":0},{\"paramName\":\"To\",\"paramValue\":4}]}}}",
+				ProtoMap.class);
+		SparkBulkTagJob
+			.main(
+				new String[] {
+
+					"-isSparkSessionManaged", Boolean.FALSE.toString(),
+					"-sourcePath", sourcePath,
+					"-taggingConf", taggingConf,
+
+					"-outputPath", workingDir.toString() + "/",
+
+					"-pathMap", workingDir.toString() + "/data/bulktagging/protoMap/pathMap",
+					"-baseURL", "none",
+					"-nameNode", "local"
+				});
+
+	}
+
 }

dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/pathMap/pathMap

@@ -0,0 +1,58 @@
+{
+  "author":{
+     "path":"$['author'][*]['fullname']"
+  },
+  "title":{
+     "path":"$['title'][*]['value']"
+  },
+  "orcid":{
+     "path":"$['author'][*]['pid'][*][?(@['qualifier']['classid']=='orcid')]['value']"
+  },
+  "orcid_pending":{
+     "path":"$['author'][*]['pid'][*][?(@['qualifier']['classid']=='orcid_pending')]['value']"
+  },
+  "contributor":{
+     "path":"$['contributor'][*]['value']"
+  },
+  "description":{
+     "path":"$['description'][*]['value']"
+  },
+  "subject":{
+     "path":"$['subject'][*]['value']"
+  },
+   "fos":{
+      "path":"$['subject'][?(@['qualifier']['classid']=='FOS')].value"
+   },
+   "sdg":{
+      "path":"$['subject'][?(@['qualifier']['classid']=='SDG')].value"
+   },
+   "journal":{
+      "path":"$['journal'].name"
+   },
+   "hostedby":{
+      "path":"$['instance'][*]['hostedby']['key']"
+   },
+   "collectedfrom":{
+      "path":"$['instance'][*]['collectedfrom']['key']"
+   },
+   "publisher":{
+      "path":"$['publisher'].value"
+   },
+   "publicationyear":{
+      "path":"$['dateofacceptance'].value",
+      "action":{
+         "clazz":"eu.dnetlib.dhp.bulktag.actions.ExecSubstringAction",
+         "method":"execSubstring",
+         "params":[
+            {
+               "paramName":"From",
+               "paramValue":0
+            },
+            {
+               "paramName":"To",
+               "paramValue":4
+            }
+         ]
+      }
+   }
+}