diff --git a/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/PromoteActionSetFromHDFSFunctionsTest.java b/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/PromoteActionSetFromHDFSFunctionsTest.java index f5db613475..a4db01f7ad 100644 --- a/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/PromoteActionSetFromHDFSFunctionsTest.java +++ b/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/PromoteActionSetFromHDFSFunctionsTest.java @@ -2,9 +2,8 @@ package eu.dnetlib.dhp.actionmanager; import com.fasterxml.jackson.databind.JsonNode; import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.schema.oaf.OafEntity; +import eu.dnetlib.dhp.schema.oaf.Oaf; import org.apache.spark.SparkConf; -import org.apache.spark.sql.Column; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SparkSession; @@ -13,13 +12,11 @@ import org.junit.BeforeClass; import org.junit.Test; import java.io.IOException; -import java.io.Serializable; import java.util.Arrays; import java.util.List; import java.util.function.BiFunction; -import java.util.stream.Collectors; +import java.util.function.Function; -import static org.apache.spark.sql.functions.get_json_object; import static org.junit.Assert.assertEquals; public class PromoteActionSetFromHDFSFunctionsTest { @@ -32,6 +29,7 @@ public class PromoteActionSetFromHDFSFunctionsTest { conf.setMaster("local"); conf.setAppName(PromoteActionSetFromHDFSFunctionsTest.class.getSimpleName()); conf.set("spark.driver.host", "localhost"); + spark = SparkSession.builder().config(conf).getOrCreate(); } @@ -40,24 +38,93 @@ public class PromoteActionSetFromHDFSFunctionsTest { spark.stop(); } + @Test + public void shouldJoinWithActionPayloadUsingIdAndMerge() { + // given + String id1 = "id1"; + String id2 = "id2"; + String id3 = "id3"; + String id4 = "id4"; + List oafData = Arrays.asList( + createOafImpl(id1), createOafImpl(id2), createOafImpl(id3), createOafImpl(id4) + ); + Dataset oafDS = spark.createDataset(oafData, Encoders.bean(OafImpl.class)); + + List actionPayloadData = Arrays.asList( + createActionPayload(id1), + createActionPayload(id2), createActionPayload(id2), + createActionPayload(id3), createActionPayload(id3), createActionPayload(id3) + ); + Dataset actionPayloadDS = spark.createDataset(actionPayloadData, Encoders.STRING()); + + SerializableSupplier> oafIdFn = () -> OafImpl::getId; + SerializableSupplier, OafImpl>> actionPayloadToOafFn = () -> (s, clazz) -> { + try { + JsonNode jsonNode = new ObjectMapper().readTree(s); + String id = jsonNode.at("/id").asText(); + return createOafImpl(id); + } catch (IOException e) { + throw new RuntimeException(e); + } + }; + SerializableSupplier> mergeAndGetFn = () -> (x, y) -> { + x.mergeFrom(y); + return x; + }; + + // when + List results = PromoteActionSetFromHDFSFunctions + .joinOafEntityWithActionPayloadAndMerge(oafDS, + actionPayloadDS, + oafIdFn, + actionPayloadToOafFn, + mergeAndGetFn, + OafImpl.class) + .collectAsList(); +// System.out.println(results.stream().map(x -> String.format("%s:%d", x.getId(), x.merged)).collect(Collectors.joining(","))); + + // then + assertEquals(7, results.size()); + results.forEach(result -> { + switch (result.getId()) { + case "id1": + case "id2": + case "id3": + assertEquals(2, result.merged); + break; + case "id4": + assertEquals(1, result.merged); + break; + } + }); + } + @Test public void shouldGroupOafEntitiesByIdAndMergeWithinGroup() { // given String id1 = "id1"; String id2 = "id2"; String id3 = "id3"; - List entityData = Arrays.asList( - createOafEntityImpl(id1), - createOafEntityImpl(id2), createOafEntityImpl(id2), - createOafEntityImpl(id3), createOafEntityImpl(id3), createOafEntityImpl(id3) + List oafData = Arrays.asList( + createOafImpl(id1), + createOafImpl(id2), createOafImpl(id2), + createOafImpl(id3), createOafImpl(id3), createOafImpl(id3) ); - Dataset entityDS = spark.createDataset(entityData, Encoders.bean(OafEntityImpl.class)); + Dataset oafDS = spark.createDataset(oafData, Encoders.bean(OafImpl.class)); + SerializableSupplier> idFn = () -> OafImpl::getId; + SerializableSupplier> mergeAndGetFn = () -> (x, y) -> { + x.mergeFrom(y); + return x; + }; // when - List results = PromoteActionSetFromHDFSFunctions - .groupEntitiesByIdAndMerge(entityDS, OafEntityImpl.class) + List results = PromoteActionSetFromHDFSFunctions + .groupOafByIdAndMerge(oafDS, + idFn, + mergeAndGetFn, + OafImpl.class) .collectAsList(); - System.out.println(results.stream().map(x -> String.format("%s:%d", x.getId(), x.merged)).collect(Collectors.joining(","))); +// System.out.println(results.stream().map(x -> String.format("%s:%d", x.getId(), x.merged)).collect(Collectors.joining(","))); // then assertEquals(3, results.size()); @@ -76,76 +143,20 @@ public class PromoteActionSetFromHDFSFunctionsTest { }); } - @Test - public void shouldJoinWithActionPayloadUsingIdAndMerge() { - // given - String id1 = "id1"; - String id2 = "id2"; - String id3 = "id3"; - String id4 = "id4"; - List entityData = Arrays.asList( - createOafEntityImpl(id1), createOafEntityImpl(id2), createOafEntityImpl(id3), createOafEntityImpl(id4) - ); - Dataset entityDS = spark.createDataset(entityData, Encoders.bean(OafEntityImpl.class)); - - List actionPayloadData = Arrays.asList( - actionPayload(id1), - actionPayload(id2), actionPayload(id2), - actionPayload(id3), actionPayload(id3), actionPayload(id3) - ); - Dataset actionPayloadDS = spark.createDataset(actionPayloadData, Encoders.STRING()); - - BiFunction, Dataset, Column> entityToActionPayloadJoinExpr = (left, right) -> - left.col("id").equalTo(get_json_object(right.col("value"), "$.id")); - BiFunction, OafEntityImpl> actionPayloadToEntityFn = - (BiFunction, OafEntityImpl> & Serializable) (s, clazz) -> { - try { - JsonNode jsonNode = new ObjectMapper().readTree(s); - String id = jsonNode.at("/id").asText(); - OafEntityImpl x = new OafEntityImpl(); - x.setId(id); - return x; - } catch (IOException e) { - throw new RuntimeException(e); - } - }; - - // when - List results = PromoteActionSetFromHDFSFunctions - .joinEntitiesWithActionPayloadAndMerge(entityDS, - actionPayloadDS, - entityToActionPayloadJoinExpr, - actionPayloadToEntityFn, - OafEntityImpl.class) - .collectAsList(); - System.out.println(results.stream().map(x -> String.format("%s:%d", x.getId(), x.merged)).collect(Collectors.joining(","))); - - // then - assertEquals(7, results.size()); - results.forEach(result -> { - switch (result.getId()) { - case "id1": - assertEquals(2, result.merged); - break; - case "id2": - assertEquals(2, result.merged); - break; - case "id3": - assertEquals(2, result.merged); - break; - case "id4": - assertEquals(1, result.merged); - break; - } - }); - } - - public static class OafEntityImpl extends OafEntity { + public static class OafImpl extends Oaf { + private String id; private int merged = 1; - @Override - public void mergeFrom(OafEntity e) { - merged += ((OafEntityImpl) e).merged; + public void mergeFrom(Oaf e) { + merged += ((OafImpl) e).merged; + } + + public String getId() { + return id; + } + + public void setId(String id) { + this.id = id; } public int getMerged() { @@ -157,13 +168,13 @@ public class PromoteActionSetFromHDFSFunctionsTest { } } - private static OafEntityImpl createOafEntityImpl(String id) { - OafEntityImpl x = new OafEntityImpl(); + private static OafImpl createOafImpl(String id) { + OafImpl x = new OafImpl(); x.setId(id); return x; } - private static String actionPayload(String id) { + private static String createActionPayload(String id) { return String.format("{\"id\":\"%s\"}", id); } } diff --git a/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/PromoteActionSetFromHDFSJobTest.java b/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/PromoteActionSetFromHDFSJobTest.java index 50b191ee25..465102b96f 100644 --- a/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/PromoteActionSetFromHDFSJobTest.java +++ b/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/PromoteActionSetFromHDFSJobTest.java @@ -1,79 +1,269 @@ package eu.dnetlib.dhp.actionmanager; -import org.junit.Before; -import org.junit.Test; +import com.fasterxml.jackson.databind.DeserializationFeature; +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.schema.oaf.*; +import org.apache.commons.io.FileUtils; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.io.Text; +import org.apache.hadoop.mapreduce.Job; +import org.apache.hadoop.mapreduce.lib.output.SequenceFileOutputFormat; +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.SparkSession; +import org.junit.*; +import scala.Tuple2; import java.io.IOException; import java.nio.file.Files; import java.nio.file.Path; import java.nio.file.Paths; +import java.util.Comparator; +import java.util.List; import java.util.Objects; +import java.util.stream.Collectors; + +import static org.apache.spark.sql.functions.base64; +import static org.apache.spark.sql.functions.col; +import static org.junit.Assert.*; public class PromoteActionSetFromHDFSJobTest { - private ClassLoader cl = getClass().getClassLoader(); + private static SparkSession spark; + private static Configuration configuration; + private Path workingDir; private Path inputDir; + private Path inputGraphDir; + private Path inputActionSetsDir; private Path outputDir; + private ClassLoader cl = getClass().getClassLoader(); + + @BeforeClass + public static void beforeClass() throws IOException { + SparkConf conf = new SparkConf(); + conf.setAppName(PromoteActionSetFromHDFSJobTest.class.getSimpleName()); + conf.setMaster("local"); + conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); + conf.registerKryoClasses(new Class[]{ + Author.class, + Context.class, + Country.class, + DataInfo.class, + eu.dnetlib.dhp.schema.oaf.Dataset.class, + Datasource.class, + ExternalReference.class, + ExtraInfo.class, + Field.class, + GeoLocation.class, + Instance.class, + Journal.class, + KeyValue.class, + Oaf.class, + OafEntity.class, + OAIProvenance.class, + Organization.class, + OriginDescription.class, + OtherResearchProduct.class, + Project.class, + Publication.class, + Qualifier.class, + Relation.class, + Result.class, + Software.class, + StructuredProperty.class + }); + + spark = SparkSession.builder().config(conf).getOrCreate(); + + configuration = Job.getInstance().getConfiguration(); + } + @Before public void before() throws IOException { workingDir = Files.createTempDirectory("promote_action_set"); inputDir = workingDir.resolve("input"); + inputGraphDir = inputDir.resolve("graph"); + + inputActionSetsDir = inputDir.resolve("action_sets"); + outputDir = workingDir.resolve("output"); } -// @After -// public void after() throws IOException { -// FileUtils.deleteDirectory(workingDir.toFile()); -// } + @After + public void after() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + } + + @AfterClass + public static void afterAll() { + spark.stop(); + } @Test - public void shouldReadAtomicActionsFromHDFSAndWritePartitionedAsParquetFiles() throws Exception { + public void shouldThrowWhenGraphTableIsInvalid() { + fail("not yet implemented"); + } + + @Test + public void shouldReadActionsFromHDFSAndPromoteThemForDatasetsUsingMergeFromStrategy() throws Exception { + readActionsFromHDFSAndPromoteThemFor("dataset", + OafMergeAndGet.Strategy.MERGE_FROM_AND_GET, + eu.dnetlib.dhp.schema.oaf.Dataset.class); + } + + @Test + public void shouldReadActionsFromHDFSAndPromoteThemForDatasourcesUsingMergeFromStrategy() throws Exception { + readActionsFromHDFSAndPromoteThemFor("datasource", + OafMergeAndGet.Strategy.MERGE_FROM_AND_GET, + Datasource.class); + } + + @Test + public void shouldReadActionsFromHDFSAndPromoteThemForOrganizationUsingMergeFromStrategy() throws Exception { + readActionsFromHDFSAndPromoteThemFor("organization", + OafMergeAndGet.Strategy.MERGE_FROM_AND_GET, + Organization.class); + } + + @Test + public void shouldReadActionsFromHDFSAndPromoteThemForOtherResearchProductUsingMergeFromStrategy() throws Exception { + readActionsFromHDFSAndPromoteThemFor("otherresearchproduct", + OafMergeAndGet.Strategy.MERGE_FROM_AND_GET, + OtherResearchProduct.class); + } + + @Test + public void shouldReadActionsFromHDFSAndPromoteThemForProjectUsingMergeFromStrategy() throws Exception { + readActionsFromHDFSAndPromoteThemFor("project", + OafMergeAndGet.Strategy.MERGE_FROM_AND_GET, + Project.class); + } + + @Test + public void shouldReadActionsFromHDFSAndPromoteThemForPublicationUsingMergeFromStrategy() throws Exception { + readActionsFromHDFSAndPromoteThemFor("publication", + OafMergeAndGet.Strategy.MERGE_FROM_AND_GET, + Publication.class); + } + + @Test + public void shouldReadActionsFromHDFSAndPromoteThemForRelationUsingMergeFromStrategy() throws Exception { + readActionsFromHDFSAndPromoteThemFor("relation", + OafMergeAndGet.Strategy.MERGE_FROM_AND_GET, + Relation.class); + } + + @Test + public void shouldReadActionsFromHDFSAndPromoteThemForSoftwareUsingMergeFromStrategy() throws Exception { + readActionsFromHDFSAndPromoteThemFor("software", + OafMergeAndGet.Strategy.MERGE_FROM_AND_GET, + Software.class); + } + + private void readActionsFromHDFSAndPromoteThemFor(String graphTableName, + OafMergeAndGet.Strategy strategy, + Class clazz) throws Exception { // given - // NOTE: test resource should contain atomic actions in a human readable form, probably as json files; here the - // files should be converted to a serialized format and written out to workingDir/input - // for current testing: actions from iis export, given as sequence file are copied to workingDir/input/ - - //graph - Path inputGraphDir = inputDir.resolve("graph"); - Files.createDirectories(inputGraphDir); - copyFiles(Paths.get(Objects.requireNonNull(cl.getResource("graph")).getFile()), inputGraphDir); - - //actions - Path inputActionsDir = inputDir.resolve("actions"); - Files.createDirectories(inputActionsDir); - - Path inputEntitiesPatentDir = inputActionsDir.resolve("entities_patent"); - Files.createDirectories(inputEntitiesPatentDir); - copyFiles(Paths.get(Objects.requireNonNull(cl.getResource("actions/entities_patent")).getFile()), inputEntitiesPatentDir); - - Path inputEntitiesSoftwareDir = inputActionsDir.resolve("entities_software"); - Files.createDirectories(inputEntitiesSoftwareDir); - copyFiles(Paths.get(Objects.requireNonNull(cl.getResource("actions/entities_software")).getFile()), inputEntitiesSoftwareDir); - - String inputActionSetPaths = String.join(",", inputEntitiesSoftwareDir.toString()); //inputEntitiesPatentDir.toString(), + String inputGraphTableJsonDumpPath = + String.format("%s/%s.json", "eu/dnetlib/dhp/actionmanager/input/graph", graphTableName); + createGraphTableFor(inputGraphTableJsonDumpPath, graphTableName, clazz); + String inputActionSetPaths = createActionSets(); + Path outputGraphDir = outputDir.resolve("graph"); + // when PromoteActionSetFromHDFSJob.main(new String[]{ - "-master", "local[*]", + "-isSparkSessionManaged", Boolean.FALSE.toString(), "-inputGraphPath", inputGraphDir.toString(), "-inputActionSetPaths", inputActionSetPaths, - "-outputGraphPath", outputDir.toString() + "-graphTableName", graphTableName, + "-outputGraphPath", outputGraphDir.toString(), + "mergeAndGetStrategy", strategy.name() }); + + // then + Path outputGraphTableDir = outputGraphDir.resolve(graphTableName); + assertTrue(Files.exists(outputGraphDir)); + + List outputGraphTableRows = readGraphTableFromParquet(outputGraphTableDir.toString(), clazz).collectAsList(); + outputGraphTableRows.sort(Comparator.comparingInt(Object::hashCode)); + + assertEquals(10, outputGraphTableRows.size()); + + String expectedOutputGraphTableJsonDumpPath = + String.format("%s/%s/%s.json", "eu/dnetlib/dhp/actionmanager/output/graph", strategy.name().toLowerCase(), graphTableName); + Path expectedOutputGraphTableJsonDumpFile = Paths + .get(Objects.requireNonNull(cl.getResource(expectedOutputGraphTableJsonDumpPath)).getFile()); + List expectedOutputGraphTableRows = readGraphTableFromJSON( + expectedOutputGraphTableJsonDumpFile, clazz) + .collectAsList(); + expectedOutputGraphTableRows.sort(Comparator.comparingInt(Object::hashCode)); + + assertArrayEquals(expectedOutputGraphTableRows.toArray(), outputGraphTableRows.toArray()); } - private static void copyFiles(Path source, Path target) throws IOException { - Files.list(source).forEach(f -> { - try { - if (Files.isDirectory(f)) { - Path subTarget = Files.createDirectories(target.resolve(f.getFileName())); - copyFiles(f, subTarget); - } else { - Files.copy(f, target.resolve(f.getFileName())); - } - } catch (IOException e) { - e.printStackTrace(); - throw new RuntimeException(e); - } - }); + private void createGraphTableFor(String inputGraphTableJsonDumpPath, + String inputGraphTableDirRelativePath, + Class clazz) { + Path inputGraphTableJsonDumpFile = Paths + .get(Objects.requireNonNull(cl.getResource(inputGraphTableJsonDumpPath)).getFile()); + Dataset inputGraphTableDS = readGraphTableFromJSON(inputGraphTableJsonDumpFile, clazz); + Path inputGraphTableDir = inputGraphDir.resolve(inputGraphTableDirRelativePath); + inputGraphTableDS + .toJSON() + .javaRDD() + .mapToPair(json -> new Tuple2<>(new Text(clazz.getCanonicalName()), new Text(json))) + .saveAsNewAPIHadoopFile(inputGraphTableDir.toString(), + Text.class, + Text.class, + SequenceFileOutputFormat.class, + configuration); + } + + private String createActionSets() throws IOException { + Path inputActionPayloadJsonDumpsDir = Paths + .get(Objects.requireNonNull(cl.getResource("eu/dnetlib/dhp/actionmanager/input/action_sets/")) + .getFile()); + Files + .list(inputActionPayloadJsonDumpsDir) + .forEach(inputActionPayloadJsonDump -> { + String inputActionSetId = inputActionPayloadJsonDump.getFileName().toString(); + Path inputActionSetDir = inputActionSetsDir.resolve(inputActionPayloadJsonDump.getFileName()); + spark.read() + .textFile(inputActionPayloadJsonDump.toString()) + .withColumn("TargetValue", base64(col("value"))) + .select("TargetValue") + .toJSON() + .javaRDD() + .mapToPair(json -> new Tuple2<>(new Text(inputActionSetId), new Text(json))) + .saveAsNewAPIHadoopFile(inputActionSetDir.toString(), + Text.class, + Text.class, + SequenceFileOutputFormat.class, + configuration); + }); + return Files.list(inputActionSetsDir).map(Path::toString).collect(Collectors.joining(",")); + } + + private static Dataset readGraphTableFromJSON(Path path, Class clazz) { + return spark.read() + .format("json") + .load(path.toString()) + .toJSON() + .map((MapFunction) json -> newObjectMapper().readValue(json, clazz), Encoders.bean(clazz)); + } + + //TODO: enable strict deserialization later + private static ObjectMapper newObjectMapper() { + return new ObjectMapper().disable(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES); + } + + private static Dataset readGraphTableFromParquet(String outputGraphTablePath, Class clazz) { + return spark.read() + .format("parquet") + .load(outputGraphTablePath) + .as(Encoders.bean(clazz)); } } \ No newline at end of file diff --git a/dhp-workflows/dhp-actionmanager/src/test/resources/entities/entities_software/_SUCCESS b/dhp-workflows/dhp-actionmanager/src/test/resources/entities/entities_software/_SUCCESS deleted file mode 100644 index e69de29bb2..0000000000 diff --git a/dhp-workflows/dhp-actionmanager/src/test/resources/entities/entities_software/part-r-00000 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a/dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/input/action_sets/payload_dataset.json b/dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/input/action_sets/payload_dataset.json new file mode 100644 index 0000000000..4f9afa4c17 --- /dev/null +++ b/dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/input/action_sets/payload_dataset.json @@ -0,0 +1,20 @@ +{"author":[{"affiliation":[],"fullname":"Boža, Pal","name":"Pal","pid":[],"rank":1,"surname":"Boža"},{"affiliation":[],"fullname":"Anačkov, Goran","name":"Goran","pid":[],"rank":2,"surname":"Anačkov"},{"affiliation":[],"fullname":"Karaman, Ivo","name":"Ivo","pid":[],"rank":3,"surname":"Karaman"},{"affiliation":[],"fullname":"Bjelić-Čabrilo, Olivera","name":"Olivera","pid":[],"rank":4,"surname":"Bjelić-Čabrilo"},{"affiliation":[],"fullname":"Karaman, Maja","name":"Maja","pid":[{"qualifier":{"classid":"ORCID","classname":"ORCID"},"value":"https://orcid.org/0000-0002-8788-9206"}],"rank":5,"surname":"Karaman"},{"affiliation":[],"fullname":"Radenković, Snežana","name":"Snežana","pid":[{"qualifier":{"classid":"ORCID","classname":"ORCID"},"value":"https://orcid.org/0000-0002-7805-9614"}],"rank":6,"surname":"Radenković"},{"affiliation":[],"fullname":"Radulović, Snežana","name":"Snežana","pid":[],"rank":7,"surname":"Radulović"},{"affiliation":[],"fullname":"Vukov, Dragana","name":"Dragana","pid":[{"qualifier":{"classid":"ORCID","classname":"ORCID"},"value":"https://orcid.org/0000-0001-9737-6538"}],"rank":8,"surname":"Vukov"},{"affiliation":[],"fullname":"Igić, Ružica","name":"Ružica","pid":[],"rank":9,"surname":"Igić"},{"affiliation":[],"fullname":"Šimić, Smiljka","name":"Smiljka","pid":[],"rank":10,"surname":"Šimić"},{"affiliation":[],"fullname":"Vujić, 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