Merge branch 'eosc_dimitris' of https://code-repo.d4science.org/D-Net/dnet-hadoop into eosc_dimitris

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextSparkJob.java

@@ -0,0 +1,113 @@
+package eu.dnetlib.dhp.oa.graph.clean;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.common.HdfsSupport;
+import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
+import eu.dnetlib.dhp.schema.common.ModelConstants;
+import eu.dnetlib.dhp.schema.oaf.Context;
+import eu.dnetlib.dhp.schema.oaf.Oaf;
+import eu.dnetlib.dhp.schema.oaf.OafEntity;
+import eu.dnetlib.dhp.schema.oaf.Result;
+import eu.dnetlib.dhp.utils.ISLookupClientFactory;
+import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
+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 java.io.Serializable;
+import java.util.List;
+import java.util.Optional;
+import java.util.stream.Collectors;
+
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
+
+public class CleanContextSparkJob implements Serializable {
+    private static final Logger log = LoggerFactory.getLogger(CleanContextSparkJob.class);
+
+    private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+    public static void main(String[] args) throws Exception {
+
+        String jsonConfiguration = IOUtils
+                .toString(
+                        CleanContextSparkJob.class
+                                .getResourceAsStream(
+                                        "/eu/dnetlib/dhp/oa/graph/input_clean_context_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 inputPath = parser.get("inputPath");
+        log.info("inputPath: {}", inputPath);
+
+        String workingPath = parser.get("workingPath");
+        log.info("workingPath: {}", workingPath);
+
+        String contextId = parser.get("contextId");
+        log.info("contextId: {}", contextId);
+
+        String verifyParam = parser.get("verifyParam");
+        log.info("verifyParam: {}", verifyParam);
+
+
+        String graphTableClassName = parser.get("graphTableClassName");
+        log.info("graphTableClassName: {}", graphTableClassName);
+
+        Class<? extends Result> entityClazz = (Class<? extends Result>) Class.forName(graphTableClassName);
+
+
+        SparkConf conf = new SparkConf();
+        runWithSparkSession(
+                conf,
+                isSparkSessionManaged,
+                spark -> {
+
+                    cleanContext(spark, contextId, verifyParam, inputPath, entityClazz, workingPath);
+                });
+    }
+
+    private static <T extends Result> void  cleanContext(SparkSession spark, String contextId, String verifyParam, String inputPath, Class<T> entityClazz, String workingPath) {
+        Dataset<T> res = spark
+                .read()
+                .textFile(inputPath)
+                .map(
+                        (MapFunction<String, T>) value -> OBJECT_MAPPER.readValue(value, entityClazz),
+                        Encoders.bean(entityClazz));
+
+        res.map((MapFunction<T, T>) r -> {
+            if(!r.getTitle()
+                    .stream()
+                    .filter(t -> t.getQualifier().getClassid()
+                            .equalsIgnoreCase(ModelConstants.MAIN_TITLE_QUALIFIER.getClassid()))
+                    .anyMatch(t -> t.getValue().toLowerCase().startsWith(verifyParam.toLowerCase()))){
+                return r;
+            }
+            r.setContext(r.getContext().stream().filter(c -> !c.getId().split("::")[0]
+                    .equalsIgnoreCase(contextId)).collect(Collectors.toList()));
+            return r;
+        } ,Encoders.bean(entityClazz))
+                .write()
+                .mode(SaveMode.Overwrite)
+                .option("compression","gzip")
+                .json(workingPath);
+
+        spark.read().textFile(workingPath).map((MapFunction<String, T>) value -> OBJECT_MAPPER.readValue(value, entityClazz),
+                Encoders.bean(entityClazz))
+                .write()
+                .mode(SaveMode.Overwrite)
+                .option("compression","gzip")
+                .json(inputPath);
+    }
+}

dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_context_parameters.json

@@ -0,0 +1,37 @@
+[
+  {
+    "paramName": "issm",
+    "paramLongName": "isSparkSessionManaged",
+    "paramDescription": "when true will stop SparkSession after job execution",
+    "paramRequired": false
+  },
+  {
+    "paramName": "in",
+    "paramLongName": "inputPath",
+    "paramDescription": "the path to the graph data dump to read",
+    "paramRequired": true
+  },
+  {
+    "paramName": "wp",
+    "paramLongName": "workingPath",
+    "paramDescription": "the path to store the output graph",
+    "paramRequired": true
+  },
+  {
+    "paramName": "ci",
+    "paramLongName": "contextId",
+    "paramDescription": "the id of the context to be removed",
+    "paramRequired": true
+  },
+  {
+    "paramName": "class",
+    "paramLongName": "graphTableClassName",
+    "paramDescription": "class name moelling the graph table",
+    "paramRequired": true
+  },{
+  "paramName": "vf",
+  "paramLongName": "verifyParam",
+  "paramDescription": "the parameter to be verified to remove the context",
+  "paramRequired": true
+}
+]

dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextTest.java

@@ -0,0 +1,159 @@
+package eu.dnetlib.dhp.oa.graph.clean;
+
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import eu.dnetlib.dhp.oa.graph.dump.Constants;
+import eu.dnetlib.dhp.oa.graph.dump.DumpJobTest;
+import eu.dnetlib.dhp.oa.graph.dump.DumpProducts;
+import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
+import eu.dnetlib.dhp.schema.common.ModelConstants;
+import eu.dnetlib.dhp.schema.dump.oaf.Instance;
+import eu.dnetlib.dhp.schema.dump.oaf.OpenAccessRoute;
+import eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult;
+import eu.dnetlib.dhp.schema.oaf.Publication;
+import eu.dnetlib.dhp.schema.oaf.Software;
+import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
+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.api.java.function.MapFunction;
+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;
+import java.util.List;
+import java.util.Locale;
+
+public class CleanContextTest {
+
+    private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+    private static SparkSession spark;
+
+    private static Path workingDir;
+
+    private static final Logger log = LoggerFactory.getLogger(CleanContextTest.class);
+
+    @BeforeAll
+    public static void beforeAll() throws IOException {
+        workingDir = Files.createTempDirectory(DumpJobTest.class.getSimpleName());
+        log.info("using work dir {}", workingDir);
+
+        SparkConf conf = new SparkConf();
+        conf.setAppName(DumpJobTest.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(DumpJobTest.class.getSimpleName())
+                .config(conf)
+                .getOrCreate();
+    }
+
+    @AfterAll
+    public static void afterAll() throws IOException {
+        FileUtils.deleteDirectory(workingDir.toFile());
+        spark.stop();
+    }
+
+    @Test
+    public void testResultClean() throws Exception {
+        final String sourcePath = getClass()
+                .getResource("/eu/dnetlib/dhp/oa/graph/clean/publication_clean_context.json")
+                .getPath();
+        final String prefix = "gcube ";
+
+
+        spark.read().textFile(sourcePath).map((MapFunction<String, Publication>)  r -> OBJECT_MAPPER.readValue(r, Publication.class), Encoders.bean(Publication.class))
+                        .write().json(workingDir.toString() + "/publication");
+
+
+        CleanContextSparkJob.main(new String[] {
+                        "--isSparkSessionManaged", Boolean.FALSE.toString(),
+                        "--inputPath", workingDir.toString() + "/publication",
+                        "-graphTableClassName", Publication.class.getCanonicalName(),
+                        "-workingPath", workingDir.toString() + "/working",
+                "-contextId","sobigdata",
+                "-verifyParam","gCube "
+                });
+
+        final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
+        JavaRDD<Publication> tmp = sc
+                .textFile(workingDir.toString() + "/publication")
+                .map(item -> OBJECT_MAPPER.readValue(item, Publication.class));
+
+        Assertions.assertEquals(7, tmp.count());
+
+        //original result with sobigdata context and gcube as starting string in the main title for the publication
+        Assertions.assertEquals(0,
+                tmp.filter(p->p.getId().equals("50|DansKnawCris::0224aae28af558f21768dbc6439c7a95")).collect().get(0).getContext().size());
+
+        //original result with sobigdata context without gcube as starting string in the main title for the publication
+        Assertions.assertEquals(1,
+                tmp.filter(p->p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9")).collect().get(0).getContext().size());
+        Assertions.assertEquals("sobigdata::projects::2",tmp.filter(p->p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9")).collect().get(0).getContext().get(0).getId() );
+
+        //original result with sobigdata context with gcube as starting string in the subtitle
+        Assertions.assertEquals(1,
+                tmp.filter(p->p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")).collect().get(0).getContext().size());
+        Assertions.assertEquals("sobigdata::projects::2",tmp.filter(p->p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")).collect().get(0).getContext().get(0).getId() );
+        List<StructuredProperty> titles = tmp.filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")).collect().get(0).getTitle();
+        Assertions.assertEquals(1, titles.size());
+        Assertions.assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix) );
+        Assertions.assertEquals("subtitle", titles.get(0).getQualifier().getClassid());
+
+        //original result with sobigdata context with gcube not as starting string in the main title
+        Assertions.assertEquals(1,
+                tmp.filter(p->p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f")).collect().get(0).getContext().size());
+        Assertions.assertEquals("sobigdata::projects::1",tmp.filter(p->p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f")).collect().get(0).getContext().get(0).getId() );
+        titles = tmp.filter(p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f")).collect().get(0).getTitle();
+        Assertions.assertEquals(1, titles.size());
+        Assertions.assertFalse(titles.get(0).getValue().toLowerCase().startsWith(prefix) );
+        Assertions.assertTrue(titles.get(0).getValue().toLowerCase().contains(prefix.trim()) );
+        Assertions.assertEquals("main title", titles.get(0).getQualifier().getClassid());
+
+        //original result with sobigdata in context and also other contexts with gcube as starting string for the main title
+        Assertions.assertEquals(1,
+                tmp.filter(p->p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53")).collect().get(0).getContext().size());
+        Assertions.assertEquals("dh-ch",tmp.filter(p->p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53")).collect().get(0).getContext().get(0).getId() );
+        titles = tmp.filter(p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53")).collect().get(0).getTitle();
+        Assertions.assertEquals(1, titles.size());
+        Assertions.assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix) );
+        Assertions.assertEquals("main title", titles.get(0).getQualifier().getClassid());
+
+        //original result with multiple main title one of which whith gcube as starting string and with 2 contextes
+        Assertions.assertEquals(1,
+                tmp.filter(p->p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff")).collect().get(0).getContext().size());
+        Assertions.assertEquals("dh-ch",tmp.filter(p->p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff")).collect().get(0).getContext().get(0).getId() );
+        titles = tmp.filter(p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff")).collect().get(0).getTitle();
+        Assertions.assertEquals(2, titles.size());
+        Assertions.assertTrue(titles.stream().anyMatch(t -> t.getQualifier().getClassid().equals("main title") && t.getValue().toLowerCase().startsWith(prefix)) );
+
+
+        //original result without sobigdata in context with gcube as starting string for the main title
+        Assertions.assertEquals(1,
+                tmp.filter(p->p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")).collect().get(0).getContext().size());
+        Assertions.assertEquals("dh-ch",tmp.filter(p->p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")).collect().get(0).getContext().get(0).getId() );
+        titles = tmp.filter(p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")).collect().get(0).getTitle();
+        Assertions.assertEquals(2, titles.size());
+
+        Assertions.assertTrue(titles.stream().anyMatch(t -> t.getQualifier().getClassid().equals("main title") && t.getValue().toLowerCase().startsWith(prefix)));
+
+
+    }
+}