From 391aa1373bbc948a447ce2bdc026d5aacb9eb7ab Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Wed, 19 Jan 2022 17:13:21 +0100 Subject: [PATCH] added unit test --- .../oa/merge/DispatchEntitiesSparkJob.java | 2 +- .../dhp/oa/merge/GroupEntitiesSparkJob.java | 2 +- .../merge}/dispatch_entities_parameters.json | 0 .../group_graph_entities_parameters.json | 0 .../group/dispatch_entities_parameters.json | 26 ------ .../group_graph_entities_parameters.json | 20 ---- .../group/GroupEntitiesSparkJobTest.java | 91 +++++++++++++++++++ .../dhp/oa/graph/group/dataset/dataset.json | 3 + .../graph/group/publication/publication.json | 3 + 9 files changed, 99 insertions(+), 48 deletions(-) rename {dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup => dhp-common/src/main/resources/eu/dnetlib/dhp/oa/merge}/dispatch_entities_parameters.json (100%) rename {dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup => dhp-common/src/main/resources/eu/dnetlib/dhp/oa/merge}/group_graph_entities_parameters.json (100%) delete mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/group/dispatch_entities_parameters.json delete mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/group/group_graph_entities_parameters.json create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/group/GroupEntitiesSparkJobTest.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/group/dataset/dataset.json create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/group/publication/publication.json diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/DispatchEntitiesSparkJob.java b/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/DispatchEntitiesSparkJob.java index d2bc8f45d..3f65d754f 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/DispatchEntitiesSparkJob.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/DispatchEntitiesSparkJob.java @@ -38,7 +38,7 @@ public class DispatchEntitiesSparkJob { .requireNonNull( DispatchEntitiesSparkJob.class .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/group/dispatch_entities_parameters.json"))); + "/eu/dnetlib/dhp/oa/merge/dispatch_entities_parameters.json"))); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); parser.parseArgument(args); diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/GroupEntitiesSparkJob.java b/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/GroupEntitiesSparkJob.java index 91cb543ab..e652bd5b6 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/GroupEntitiesSparkJob.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/GroupEntitiesSparkJob.java @@ -53,7 +53,7 @@ public class GroupEntitiesSparkJob { .toString( GroupEntitiesSparkJob.class .getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/group/group_graph_entities_parameters.json")); + "/eu/dnetlib/dhp/oa/merge/group_graph_entities_parameters.json")); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); parser.parseArgument(args); diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/dispatch_entities_parameters.json b/dhp-common/src/main/resources/eu/dnetlib/dhp/oa/merge/dispatch_entities_parameters.json similarity index 100% rename from dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/dispatch_entities_parameters.json rename to dhp-common/src/main/resources/eu/dnetlib/dhp/oa/merge/dispatch_entities_parameters.json diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/group_graph_entities_parameters.json b/dhp-common/src/main/resources/eu/dnetlib/dhp/oa/merge/group_graph_entities_parameters.json similarity index 100% rename from dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/group_graph_entities_parameters.json rename to dhp-common/src/main/resources/eu/dnetlib/dhp/oa/merge/group_graph_entities_parameters.json diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/group/dispatch_entities_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/group/dispatch_entities_parameters.json deleted file mode 100644 index aa8d2a7c2..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/group/dispatch_entities_parameters.json +++ /dev/null @@ -1,26 +0,0 @@ -[ - { - "paramName": "issm", - "paramLongName": "isSparkSessionManaged", - "paramDescription": "when true will stop SparkSession after job execution", - "paramRequired": false - }, - { - "paramName": "i", - "paramLongName": "inputPath", - "paramDescription": "the source path", - "paramRequired": true - }, - { - "paramName": "o", - "paramLongName": "outputPath", - "paramDescription": "path of the output graph", - "paramRequired": true - }, - { - "paramName": "c", - "paramLongName": "graphTableClassName", - "paramDescription": "the graph entity class name", - "paramRequired": true - } -] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/group/group_graph_entities_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/group/group_graph_entities_parameters.json deleted file mode 100644 index e65acb3c4..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/group/group_graph_entities_parameters.json +++ /dev/null @@ -1,20 +0,0 @@ -[ - { - "paramName": "issm", - "paramLongName": "isSparkSessionManaged", - "paramDescription": "when true will stop SparkSession after job execution", - "paramRequired": false - }, - { - "paramName": "gin", - "paramLongName": "graphInputPath", - "paramDescription": "the graph root path", - "paramRequired": true - }, - { - "paramName": "out", - "paramLongName": "outputPath", - "paramDescription": "the output merged graph root path", - "paramRequired": true - } -] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/group/GroupEntitiesSparkJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/group/GroupEntitiesSparkJobTest.java new file mode 100644 index 000000000..5214c1783 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/group/GroupEntitiesSparkJobTest.java @@ -0,0 +1,91 @@ + +package eu.dnetlib.dhp.oa.graph.group; + +import com.fasterxml.jackson.databind.DeserializationFeature; +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.oa.merge.GroupEntitiesSparkJob; +import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.oaf.Result; +import org.apache.commons.io.FileUtils; +import org.apache.commons.lang3.StringUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.FilterFunction; +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.jupiter.api.*; + +import java.io.IOException; +import java.net.URISyntaxException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.nio.file.Paths; + +public class GroupEntitiesSparkJobTest { + + private static SparkSession spark; + + private Path workingDir; + //private Path inputDir; + private Path graphInputPath; + + private Path outputPath; + + @BeforeAll + public static void beforeAll() { + SparkConf conf = new SparkConf(); + conf.setAppName(GroupEntitiesSparkJob.class.getSimpleName()); + conf.setMaster("local"); + conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); + conf.registerKryoClasses(ModelSupport.getOafModelClasses()); + spark = SparkSession.builder().config(conf).getOrCreate(); + } + + @BeforeEach + public void beforeEach() throws IOException, URISyntaxException { + workingDir = Files.createTempDirectory(GroupEntitiesSparkJob.class.getSimpleName()); + //inputDir = workingDir.resolve("input"); + graphInputPath = Paths.get(ClassLoader.getSystemResource("eu/dnetlib/dhp/oa/graph/group").toURI()); + outputPath = workingDir.resolve("output"); + } + + @AfterEach + public void afterEach() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + } + + @AfterAll + public static void afterAll() { + spark.stop(); + } + + @Test + void testGroupEntities() throws Exception { + GroupEntitiesSparkJob.main(new String[] { + "-isSparkSessionManaged", + Boolean.FALSE.toString(), + "-graphInputPath", + graphInputPath.toString(), + "-outputPath", + outputPath.toString() + }); + + ObjectMapper mapper = new ObjectMapper().configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); + Dataset output = spark + .read() + .textFile(outputPath.toString()) + .map((MapFunction) s -> StringUtils.substringAfter(s, "|"), Encoders.STRING()) + .map((MapFunction) s -> mapper.readValue(s, Result.class), Encoders.bean(Result.class)); + + Assertions.assertEquals( + 1, + output + .filter((FilterFunction) r -> + "50|doi_________::09821844208a5cd6300b2bfb13bca1b9".equals(r.getId()) && + r.getCollectedfrom().stream().anyMatch(kv -> kv.getValue().equalsIgnoreCase("zenodo")) ) + .count()); + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/group/dataset/dataset.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/group/dataset/dataset.json new file mode 100644 index 000000000..e30be47e9 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/group/dataset/dataset.json @@ -0,0 +1,3 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