[FoS] added check for null on level1 subject

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

@@ -62,7 +62,7 @@ public class Constants {
 
 	public static Subject getSubject(String sbj, String classid, String classname,
 		String diqualifierclassid) {
-		if (sbj.equals(NULL))
+		if (sbj == null || sbj.equals(NULL))
 			return null;
 		Subject s = new Subject();
 		s.setValue(sbj);

dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/GetFosTest.java

@@ -0,0 +1,96 @@
+package eu.dnetlib.dhp.actionmanager.createunresolvedentities;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.FOSDataModel;
+import org.apache.commons.io.FileUtils;
+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.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;
+
+/**
+ * @author miriam.baglioni
+ * @Date 13/02/23
+ */
+public class GetFosTest {
+
+    private static final Logger log = LoggerFactory.getLogger(ProduceTest.class);
+
+    private static Path workingDir;
+    private static SparkSession spark;
+    private static LocalFileSystem fs;
+    private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+    @BeforeAll
+    public static void beforeAll() throws IOException {
+        workingDir = Files.createTempDirectory(PrepareTest.class.getSimpleName());
+
+        fs = FileSystem.getLocal(new Configuration());
+        log.info("using work dir {}", workingDir);
+
+        SparkConf conf = new SparkConf();
+        conf.setAppName(ProduceTest.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(PrepareTest.class.getSimpleName())
+                .config(conf)
+                .getOrCreate();
+    }
+
+    @AfterAll
+    public static void afterAll() throws IOException {
+        FileUtils.deleteDirectory(workingDir.toFile());
+        spark.stop();
+    }
+    	@Test
+	void test3() throws Exception {
+            final String sourcePath = getClass()
+                    .getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/fos/fos_sbs.tsv")
+                    .getPath();
+
+
+		final String outputPath = workingDir.toString() + "/fos.json";
+		GetFOSSparkJob
+			.main(
+				new String[] {
+					"--isSparkSessionManaged", Boolean.FALSE.toString(),
+					"--sourcePath", sourcePath,
+
+					"-outputPath", outputPath
+
+				});
+
+		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
+
+		JavaRDD<FOSDataModel> tmp = sc
+			.textFile(outputPath)
+			.map(item -> OBJECT_MAPPER.readValue(item, FOSDataModel.class));
+
+		tmp.foreach(t -> Assertions.assertTrue(t.getDoi() != null));
+		tmp.foreach(t -> Assertions.assertTrue(t.getLevel1() != null));
+		tmp.foreach(t -> Assertions.assertTrue(t.getLevel2() != null));
+		tmp.foreach(t -> Assertions.assertTrue(t.getLevel3() != null));
+
+	}
+}

dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/fos/fos_sbs.tsv

@@ -0,0 +1,40 @@
+doi	level1	level2	level3
+10.1080/09638237.2018.1466033	03 medical and health sciences	0302 clinical medicine	030212 general & internal medicine
+10.1016/j.dsi.2015.10.003	03 medical and health sciences	0301 basic medicine	030105 genetics & heredity
+10.1007/s10072-017-2914-9	03 medical and health sciences	0302 clinical medicine	030217 neurology & neurosurgery
+10.1016/j.bspc.2021.102726	02 engineering and technology	0206 medical engineering	020601 biomedical engineering
+10.1177/0306312706069439	06 humanities and the arts	0601 history and archaeology	060101 anthropology
+10.1016/j.jacep.2016.05.010	03 medical and health sciences	0302 clinical medicine	030212 general & internal medicine
+10.1111/anae.13418	03 medical and health sciences	0302 clinical medicine	030212 general & internal medicine
+10.1142/s1793744210000168	01 natural sciences	0103 physical sciences	010306 general physics
+10.1016/j.jadohealth.2019.04.029	03 medical and health sciences	0302 clinical medicine	030212 general & internal medicine
+10.1109/icais50930.2021.9395847	02 engineering and technology	0202 electrical engineering, electronic engineering, information engineering	020201 artificial intelligence & image processing
+10.1145/3154837	01 natural sciences	0101 mathematics	010102 general mathematics
+10.1038/srep38130	03 medical and health sciences	0301 basic medicine	030106 microbiology
+10.1007/s13369-017-2871-x	02 engineering and technology	0202 electrical engineering, electronic engineering, information engineering	020201 artificial intelligence & image processing
+10.1063/1.4964718	03 medical and health sciences	0301 basic medicine	030104 developmental biology
+10.1007/s12603-019-1276-9	03 medical and health sciences	0302 clinical medicine	030212 general & internal medicine
+10.1002/cam4.1463	03 medical and health sciences	0301 basic medicine	030104 developmental biology
+10.1164/rccm.201611-2290ed	03 medical and health sciences	0302 clinical medicine	030212 general & internal medicine
+10.1088/1757-899x/225/1/012132	01 natural sciences	0105 earth and related environmental sciences	010504 meteorology & atmospheric sciences
+10.1117/1.jmm.15.1.015501	02 engineering and technology	0210 nano-technology	021001 nanoscience & nanotechnology
+10.1088/1361-6587/ab569d	01 natural sciences	0103 physical sciences	010303 astronomy & astrophysics
+10.1016/j.rser.2015.11.092	02 engineering and technology	0202 electrical engineering, electronic engineering, information engineering	020209 energy
+10.1016/j.jhydrol.2013.06.035	01 natural sciences	0105 earth and related environmental sciences	010504 meteorology & atmospheric sciences
+10.1111/php.12892	03 medical and health sciences	0301 basic medicine	030104 developmental biology
+10.1088/0264-9381/27/10/105001	01 natural sciences	0103 physical sciences	010308 nuclear & particles physics
+10.1016/j.matchemphys.2018.02.039	02 engineering and technology	0210 nano-technology	021001 nanoscience & nanotechnology
+10.1098/rsos.160993	03 medical and health sciences	0301 basic medicine	030104 developmental biology
+10.1016/j.rinp.2017.07.054	02 engineering and technology	0209 industrial biotechnology	020901 industrial engineering & automation
+10.1111/eip.12348	03 medical and health sciences	0302 clinical medicine	030227 psychiatry
+10.20965/jrm.2016.p0371	02 engineering and technology	0201 civil engineering	020101 civil engineering
+10.2337/dci19-0036	03 medical and health sciences	0302 clinical medicine	030212 general & internal medicine
+10.1155/2018/7692913	01 natural sciences	0104 chemical sciences	010404 medicinal & biomolecular chemistry
+10.1117/12.2262306	02 engineering and technology	0202 electrical engineering, electronic engineering, information engineering	020206 networking & telecommunications
+10.1021/acs.jpcb.7b01885	01 natural sciences	0104 chemical sciences	010405 organic chemistry
+10.1177/0033294117711131	05 social sciences	0502 economics and business	050203 business & management
+10.1016/j.jrurstud.2017.08.019	05 social sciences	0502 economics and business	050203 business & management
+10.1111/febs.15296	03 medical and health sciences	0301 basic medicine	030104 developmental biology
+10.3923/jeasci.2017.6922.6927	05 social sciences	0505 law	050501 criminology
+10.1007/s10854-017-6376-x	02 engineering and technology	0202 electrical engineering, electronic engineering, information engineering	020208 electrical & electronic engineering
+10.3390/app10176095	02 engineering and technology	0202 electrical engineering, electronic engineering, information engineering	020209 energy